Part 5. Protein structure annotation settings
Index
These options include some of the most complex types of queries
and structural analysis provided by POLYVIEW-3D. For
example, they enable performing various structural and
functional analyses, using both in house software, such as
SPPIDER
for the recognition of protein interaction interfaces, as
well as several external servers, including
CASTp
for structural pockets identification, and
ConSurf
for assessment of evolutionary conservation. The results
of these external resources are processed further (to a
different degree) and combined with additional analysis
performed by POLYVIEW-3D. One example is the ability to
combine identification, prediction, and mapping of protein
interaction interfaces performed by SPPIDER with the
analysis of structural pockets identified by CASTp (and
other topological features). See sections below for
details.
There are two groups of settings within this options set. The
first group invokes automatic requests to other
web-servers and databases to obtain additional structural
annotations. The second group uses precomputed results
that were previously received (and possibly processed)
from the other resources. In both cases, the resulting data is
further processed by the POLYVIEW-3D server in order to
yield 3D images of the macromolecular structures overlaid
with the requested annotations, as described below.
Finding pockets using CASTp
This option sends an automated request to the
CASTp
server in order to perform a search for structural pockets
within a given query protein. Identified pockets can
be filtered by their area or volume. They
are also automatically colored according to the
CASTp color convention. Both atoms and residues
constituting the corresponding cavities are listed as well.
Pockets can also be optionally overlaid with the prediction of
interacting sites automatically performed using the
SPPIDER
server. Pockets overlapping with predicted interfaces may
represent potential targets for drug design and docking
simulations.
Below is an example of a request to find pockets using CASTp, with
pocket area cutoff of 100Å2. The
structure of purine nucleoside phosphorylase in transition
state was taken as a query structure (PDB id 1b8o).
Pockets with surface area larger or equal to 100Å2 |
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Click on respective image to see options used for its rendering.
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Generated image is accompanied with the annotation table listing the
residues located at each pocket.
Pockets determined using CASTp
(Show full version)
|
Pocket |
Area, Å2 |
Volume Å3 |
Color |
Atoms (Residue name:Residue number:Atom:Chain)
Residues (Chain:Residue numbers)
|
37 |
460.6 |
543.9 |
green |
Atoms: ALA:116:C:A ALA:116:CB:A ALA:116:N:A ALA:116:O:A ALA:117:C:A ALA:117:CA:A ALA:255:CB:A ...
Residues: A:32 33 61 64 84 86 88 115 116 117 118 192 ...
|
36 |
103.3 |
167.3 |
blue |
Atoms: ARG:148:CA:A ARG:148:CB:A ARG:148:CG:A ARG:148:N:A ARG:158:NE:A ARG:158:NH1:A ...
Residues: A:140 143 145 147 148 149 158 159 160
|
35 |
136.5 |
124.8 |
cyan |
Atoms: ARG:101:NH1:A ARG:101:NH2:A ARG:148:O:A ARG:158:NH2:A ASN:151:CA:A ASN:151:OD1:A ASN:3:CB:A ASN:3:N:A ASN:3:OD1:A ...
Residues: A:3 101 146 147 148 149 150 151 152 158 230
|
34 |
115.9 |
109.7 |
yellow |
Atoms: ARG:210:CG:A ASN:121:C:A ASN:121:O:A GLY:119:C:A GLY:119:CA:A GLY:119:O:A LEU:120:C:A ...
Residues: A:119 120 121 122 124 210 244 245 247
|
33 |
111.8 |
85.6 |
magenta |
Atoms: GLN:273:CA:A GLU:272:C:A GLU:272:CA:A GLU:272:CB:A GLU:272:CG:A GLU:272:O:A ...
Residues: A:38 41 73 272 273 275 276
|
31 |
103.8 |
80.5 |
orange |
Atoms: ARG:101:CD:A ARG:101:CZ:A ARG:101:NE:A ARG:101:NH1:A ARG:101:NH2:A ASN:3:OD1:A ...
Residues: A:3 10 94 97 98 101 146 227
|
29 |
101.5 |
44.2 |
brown |
Atoms: GLU:224:OE2:A HIS:86:CA:A MET:194:CE:A MET:219:O:A MET:87:N:A PHE:85:O:A ...
Residues: A:85 86 87 93 96 194 219 220 221 223 224
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Pockets determined using CASTp
(Show brief version)
|
Pocket |
Area, Å2 |
Volume Å3 |
Color |
Atoms (Residue name:Residue number:Atom:Chain)
Residues (Chain:Residue numbers)
|
37 |
460.6 |
543.9 |
green |
Atoms: ALA:116:C:A ALA:116:CB:A ALA:116:N:A ALA:116:O:A ALA:117:C:A ALA:117:CA:A ALA:255:CB:A ALA:255:N:A ALA:255:O:A ARG:84:NH1:A ASN:115:CA:A ASN:115:CB:A ASN:243:ND2:A ASN:243:OD1:A CYS:206:CB:A GLU:201:CB:A GLU:201:N:A GLU:201:O:A GLU:201:OE1:A GLU:201:OE2:A GLY:118:CA:A GLY:118:N:A GLY:218:CA:A GLY:32:CA:A HIS:257:CE1:A HIS:257:ND1:A HIS:64:NE2:A HIS:86:CD2:A HIS:86:NE2:A ILE:246:CB:A ILE:246:CG1:A ILE:246:N:A ILE:246:O:A LEU:195:CD1:A LYS:254:CG:A MET:219:C:A MET:219:CA:A MET:219:CB:A MET:219:CE:A MET:219:CG:A MET:219:N:A MET:219:SD:A PHE:200:CB:A PHE:200:CD1:A PHE:200:CE1:A PHE:200:CZ:A SER:220:CB:A SER:220:OG:A SER:33:CB:A SER:33:N:A SER:33:OG:A THR:202:C:A THR:202:O:A THR:242:OG1:A TYR:192:OH:A TYR:88:CE2:A TYR:88:OH:A VAL:203:CG2:A VAL:203:N:A VAL:217:CG1:A VAL:217:CG2:A VAL:217:O:A VAL:245:CA:A VAL:245:CB:A VAL:245:CG1:A VAL:260:CG1:A VAL:260:CG2:A VAL:61:CG1:A
Residues: A:32 33 61 64 84 86 88 115 116 117 118 192 195 200 201 202 203 206 217 218 219 220 242 243 245 246 254 255 257 260
|
36 |
103.3 |
167.3 |
blue |
Atoms: ARG:148:CA:A ARG:148:CB:A ARG:148:CG:A ARG:148:N:A ARG:158:NE:A ARG:158:NH1:A ARG:158:NH2:A ARG:158:O:A ASN:145:CB:A ASN:145:CG:A ASN:145:ND2:A GLY:140:O:A GLY:143:CA:A GLY:143:O:A GLY:149:N:A LEU:147:C:A LEU:147:CB:A LEU:147:CD1:A LEU:147:O:A PHE:159:CA:A PHE:159:CD1:A PHE:159:CE1:A PRO:160:CD:A
Residues: A:140 143 145 147 148 149 158 159 160
|
35 |
136.5 |
124.8 |
cyan |
Atoms: ARG:101:NH1:A ARG:101:NH2:A ARG:148:O:A ARG:158:NH2:A ASN:151:CA:A ASN:151:OD1:A ASN:3:CB:A ASN:3:N:A ASN:3:OD1:A GLU:152:CB:A GLU:152:N:A GLY:149:CA:A HIS:230:CE1:A LEU:147:C:A LEU:147:CA:A LEU:147:CB:A LEU:147:CD2:A LEU:147:O:A PRO:146:O:A PRO:150:CD:A PRO:150:O:A
Residues: A:3 101 146 147 148 149 150 151 152 158 230
|
34 |
115.9 |
109.7 |
yellow |
Atoms: ARG:210:CG:A ASN:121:C:A ASN:121:O:A GLY:119:C:A GLY:119:CA:A GLY:119:O:A LEU:120:C:A LEU:120:CA:A LEU:120:O:A LYS:244:CB:A LYS:244:CG:A LYS:244:NZ:A MET:247:CE:A MET:247:CG:A MET:247:SD:A PHE:124:CB:A PRO:122:CA:A PRO:122:CB:A PRO:122:CD:A PRO:122:CG:A VAL:245:CG2:A VAL:245:O:A
Residues: A:119 120 121 122 124 210 244 245 247
|
33 |
111.8 |
85.6 |
magenta |
Atoms: GLN:273:CA:A GLU:272:C:A GLU:272:CA:A GLU:272:CB:A GLU:272:CG:A GLU:272:O:A LEU:38:CD2:A LEU:38:O:A LEU:73:CD1:A LEU:73:CD2:A LYS:41:CB:A LYS:41:CG:A LYS:41:NZ:A SER:276:CB:A VAL:275:CB:A VAL:275:CG1:A
Residues: A:38 41 73 272 273 275 276
|
31 |
103.8 |
80.5 |
orange |
Atoms: ARG:101:CD:A ARG:101:CZ:A ARG:101:NE:A ARG:101:NH1:A ARG:101:NH2:A ASN:3:OD1:A PHE:98:CA:A PRO:146:CB:A PRO:146:O:A THR:97:C:A THR:97:O:A THR:97:OG1:A TRP:94:CA:A TRP:94:CB:A TRP:94:O:A TYR:10:CE1:A TYR:10:OH:A VAL:227:CG2:A
Residues: A:3 10 94 97 98 101 146 227
|
29 |
101.5 |
44.2 |
brown |
Atoms: GLU:224:OE2:A HIS:86:CA:A MET:194:CE:A MET:219:O:A MET:87:N:A PHE:85:O:A PHE:93:CE1:A PRO:223:CG:A SER:220:CA:A SER:220:CB:A THR:221:N:A VAL:96:CG1:A
Residues: A:85 86 87 93 96 194 219 220 221 223 224
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Mapping domains using Pfam
When this option is selected, POLYVIEW-3D performs a sequence homology
search using
BLAST
against the local version of
Pfam database.
Amino acid sequence used for query is derived from the
ATOM section of a PDB
file. If significant sequence homology
(E-value ≤ 0.001 AND
sequence identity ≥ 70%) is found to one or
more domains, they are mapped to the query structure
using distinct colors for each domain. Below is the
example of the annotated structure of ZAP-70
tyrosine kinase (PDB id 2ozo).
Domains from Pfam |
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Click on respective image to see options used for its rendering.
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Generated image is accompanied with the annotation table listing the
identified domains.
Protein families found using Pfam
(Show full version)
|
Chain |
Entry |
Description |
E-value |
Color |
Residues |
A |
Domain Pkinase_Tyr |
Protein tyrosine kinase |
1e-140 |
pink |
PDB numbering 338 339 340 341 342 343 344 345 346... Amino acid sequence LIADIELGCG NFGSVRQGVY... |
A |
Domain SH2 |
SH2 domain | 3e-39 |
gold |
PDB numbering 10 11 12 13 14 15 16 17 18 19 20 21 22... Amino acid sequence FFYGSISRAE AEEHLKLAGM... |
A |
Domain SH2 |
SH2 domain |
6e-38 |
purple |
PDB numbering 163 164 165 166 167 168 169 170 171... Amino acid sequence WYHSSLTREE AERKLYSGAQ... |
Protein families found using Pfam
(Show brief version)
|
Chain |
Entry |
Description |
E-value |
Color |
Residues |
A |
Domain Pkinase_Tyr |
Protein tyrosine kinase |
1e-140 |
pink |
PDB numbering 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 Amino acid sequence LIADIELGCG NFGSVRQGVY RMRKKQIDVA IKVLKQGTEK ADTEEMMREA QIMHQLDNPY IVRLIGVCQA EALMLVMEMA GGGPLHKFLV GKREEIPVSN VAELLHQVSM GMKYLEEKNF VHRNLAARNV LLVNRHYAKI SDFGLSKALG XXXXXXXXXX XXXXPLKWYA PECINFRKFS SRSDVWSYGV TMWEALSYGQ KPYKKMKGPE VMAFIEQGKR MECPPECPPE LYALMSDCWI YKWEDRPDFL TVEQRM |
A |
Domain SH2 |
SH2 domain | 3e-39 |
gold |
PDB numbering 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 Amino acid sequence FFYGSISRAE AEEHLKLAGM ADGLFLLRQC LRSLGGYVLS LVHDVRFHHF PIERQLNGTY AIAGGKAHCG PAELCEFY |
A |
Domain SH2 |
SH2 domain |
6e-38 |
purple |
PDB numbering 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 Amino acid sequence WYHSSLTREE AERKLYSGAQ TDGKFLLRPR KEQGTYALSL IYGKTVYHYL ISQDKAGKYC IPEGTKFDTL WQLVEYL |
Mapping putative TM segments using PDBTM
Upon request of this option, POLYVIEW-3D makes search in the local copy of the
PDBTM
database of putative trans-membrane segments. Specifically,
it performs a sequence homology search using
BLAST.
Amino acid sequence used for query is
derived from the ATOM section
of a PDB file. If significant sequence homology
(E-value ≤ 0.001 AND
sequence identity ≥ 70%) is found to one or
more proteins, the best matching homolog is taken. Images
below demonstrate the annotation on membrane spanning segments
as determined in PDBTM using the TMDET
automated algorithm (for details, please refer to the
original papers).
The structure of Catalytic Core (Subunits I and II) of
Cytochrome c oxidase from Rhodobacter sphaeroides
serves as an example of alpha-helical TM protein (PDB id
2gsm), whereas the structure of the
sucrose-specific porin ScrY (PDB id 1a0s) from
Salmonella typhimurium represents beta-barrel TM
proteins.
TM segments from PDBTM Alpha helical |
TM segments from PDBTM Beta barrel |
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Click on respective image to see options used for its rendering.
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Generated image is accompanied with the annotation table listing the
TM spanning regions (if any found).
Trans-membrane domains found using PDBTM
(Show full version)
|
Chain |
PDBTM (Type) |
E-value |
Residues in the membrane spanning regions |
A |
1m56 (Alpha) |
0.0 |
PDB numbering 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53= 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124= ... Amino acid sequence YLFTGGLVGLISVAFTVYMRM= ILMMFFVVIPALFGGFGNYFM= ... |
B |
2gsm (Alpha) |
0.0 | PDB numbering 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80= 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117=
Amino acid sequence ILVIIAAITIFVTLLILYAV= LEIAWTIVPIVILVAIGA=
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Trans-membrane domains found using PDBTM
(Show brief version)
|
Chain |
PDBTM (Type) |
E-value |
Residues in the membrane spanning regions |
A |
1m56 (Alpha) |
0.0 |
PDB numbering 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53= 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124= 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162= 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212= 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255= 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305= 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334= 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375= 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402= 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441= 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472= 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521=
Amino acid sequence YLFTGGLVGLISVAFTVYMRM= ILMMFFVVIPALFGGFGNYFM= SYWLYVAGTSLAVASLFAPGG= FAVHLSGASSILGAINMITTF= SIFVTAWLILLALPVLAGAITMLLT= FFGHPEVYIIVLPAFGIVSHVIATF= LPMVYAMVAIGVLGFVVWAHH= VIAVPTGIKIFSWIATMWGGSI= TPMLWALGFLFLFTVGGVTGIVLS= YVMSLGAVFGIFAGIYFWIG= AGKLHFWMMFVGANLTFFPQH= LSFASFLFFLGVIFYTLTR=
|
B |
2gsm (Alpha) |
0.0 | PDB numbering 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80= 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117=
Amino acid sequence ILVIIAAITIFVTLLILYAV= LEIAWTIVPIVILVAIGA=
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Trans-membrane domains found using PDBTM
(Show full version)
|
Chain |
PDBTM (Type) |
E-value |
Residues in the membrane spanning regions |
P |
1a0s (Beta) |
0 |
PDB numbering 77 78 79 80 81 82 83 84 85= 117 118 119 120 121 122 123= 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153= ... Amino acid sequence GYARSGVIM= TYVEMNL= KVMVADGQTSYNDWTA= ...
|
Q |
1a0s (Beta) |
0 | PDB numbering 77 78 79 80 81 82 83 84 85= 117 118 119 120 121 122 123= 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153= ... Amino acid sequence GYARSGVIM= TYVEMNL= KVMVADGQTSYNDWTA= ...
|
R |
1a0s (Beta) |
0 |
PDB numbering 77 78 79 80 81 82 83 84 85= 117 118 119 120 121 122 123= 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153= ... Amino acid sequence GYARSGVIM= TYVEMNL= KVMVADGQTSYNDWTA= ...
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Trans-membrane domains found using PDBTM
(Show brief version)
|
Chain |
PDBTM (Type) |
E-value |
Residues in the membrane spanning regions |
P |
1a0s (Beta) |
0 |
PDB numbering 77 78 79 80 81 82 83 84 85= 117 118 119 120 121 122 123= 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153= 156 157 158 159 160 161 162 163 164 165= 183 184 185 186 187 188= 204 205 206 207 208 209 210 211 212= 224 225 226 227 228 229 230= 245 246 247 248 249 250 251= 257 258 259 260 261 262 263= 288 289 290 291 292 293 294= 308 309 310 311 312 313 314= 337 338 339 340 341 342 343= 353 354 355 356 357 358 359 360= 375 376 377 378 379 380 381= 391 392 393 394 395 396 397 398= 418 419 420 421 422 423 424 425= 440 441 442 443 444 445 446= 473 474 475 476 477 478 479 480 481 482=
Amino acid sequence GYARSGVIM= TYVEMNL= KVMVADGQTSYNDWTA= SDLNVRQAFV= WAGKRF= FLAGTGGGI= NFSLYGR= YILTMNH= QMMVSGL= VHALLGL= KTALLYG= WRIASYG= VAPAMLAQ= ATFNLRL= LAYEGSYQ= YKLTFAPT= IRFYTSW= WSFGVQMETW=
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Q |
1a0s (Beta) |
0 |
PDB numbering 77 78 79 80 81 82 83 84 85= 117 118 119 120 121 122 123= 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153= 156 157 158 159 160 161 162 163 164 165= 183 184 185 186 187 188= 204 205 206 207 208 209 210 211 212= 224 225 226 227 228 229 230= 245 246 247 248 249 250 251= 257 258 259 260 261 262 263= 288 289 290 291 292 293 294= 308 309 310 311 312 313 314= 337 338 339 340 341 342 343= 353 354 355 356 357 358 359 360= 375 376 377 378 379 380 381= 391 392 393 394 395 396 397 398= 418 419 420 421 422 423 424 425= 440 441 442 443 444 445 446= 473 474 475 476 477 478 479 480 481 482=
Amino acid sequence GYARSGVIM= TYVEMNL= KVMVADGQTSYNDWTA= SDLNVRQAFV= WAGKRF= FLAGTGGGI= NFSLYGR= YILTMNH= QMMVSGL= VHALLGL= KTALLYG= WRIASYG= VAPAMLAQ= ATFNLRL= LAYEGSYQ= YKLTFAPT= IRFYTSW= WSFGVQMETW=
|
R |
1a0s (Beta) |
0 |
PDB numbering 77 78 79 80 81 82 83 84 85= 117 118 119 120 121 122 123= 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153= 156 157 158 159 160 161 162 163 164 165= 183 184 185 186 187 188= 204 205 206 207 208 209 210 211 212= 224 225 226 227 228 229 230= 245 246 247 248 249 250 251= 257 258 259 260 261 262 263= 288 289 290 291 292 293 294= 308 309 310 311 312 313 314= 337 338 339 340 341 342 343= 353 354 355 356 357 358 359 360= 375 376 377 378 379 380 381= 391 392 393 394 395 396 397 398= 418 419 420 421 422 423 424 425= 440 441 442 443 444 445 446= 473 474 475 476 477 478 479 480 481 482=
Amino acid sequence GYARSGVIM= TYVEMNL= KVMVADGQTSYNDWTA= SDLNVRQAFV= WAGKRF= FLAGTGGGI= NFSLYGR= YILTMNH= QMMVSGL= VHALLGL= KTALLYG= WRIASYG= VAPAMLAQ= ATFNLRL= LAYEGSYQ= YKLTFAPT= IRFYTSW= WSFGVQMETW=
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Mapping interaction sites from PDB complexes using SCORPPION
With this option, one can retrieve information about all interaction
sites found among close sequence homologs deposited in
PDB.
Search is automatically performed using the
SCORPPION
server. Interaction sites are the residues in contact with
other protein chains, DNA or RNA, or ligands. Different
types of interactions, as well as their combinations are
colored distinctly. Interaction sites can be optionally
contrasted with protein interfaces predicted by
SPPIDER.
Below is example of mapping different types of interactions from the
close sequence homologs to the structure of
transcription factor CSL (PDB id 1ttu, chain A).
Interfaces by SCORPPION |
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Click on respective image to see options used for its rendering.
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Generated image is accompanied with the annotation table listing
residues involved in intermolecular interactions.
Interacting sites mapped from homologs
(Show full version)
|
Chain |
Type of contact |
Residues |
A |
P−DNA |
226 227 229 230 231 232 233 234 235 236 237 334 366 367 368 369 370 371... |
A |
P−Protein |
223 281 282 285 287 289 294 298 299 301 319 338 339 340 342 346 348 350... |
A |
P− Protein/DNA |
337 |
Interacting sites mapped from homologs
(Show brief version)
|
Chain |
Type of contact |
Residues |
A |
P−DNA |
226 227 229 230 231 232 233 234 235 236 237 334 366 367 368 369 370 371 372 373 374 395 397 398 399 400 401 402 403 405 475 476 495 537 |
A |
P−Protein |
223 281 282 285 287 289 294 298 299 301 319 338 339 340 342 346 348 350 352 354 356 357 362 381 382 383 387 388 389 390 391 414 415 428 431 440 441 442 443 444 445 446 447 448 458 463 464 465 466 467 500 508 515 516 517 542 556 557 558 560 561 566 567 568 569 570 571 572 573 574 575 576 578 580 582 584 585 587 588 589 591 600 601 602 603 604 605 606 607 608 610 633 635 637 645 646 657 659 660 |
A |
P− Protein/DNA |
337 |
Mapping linear immune epitopes from IEDB
This option allows the user to map all linear Ab- and
MHC-targeted epitopes currently known
for a submitted protein or its close sequence homologs.
Immune Epitope Database
(IEDB)
is employed to retrieve information about epitopes. Mapping is performed based on
sequence homology. Peptides with at least 70% sequence
identity are considered as putative
matches. Multiple matches are clustered by their location
in the target sequence extending the boundaries of each
cluster to the longest match. In addition,
average relative solvent accessibility (RSA) is computed for a
given match that allows to evaluate burial state of identified peptides
within the structure. Based on observations in PDB,
peptides with the average RSA below 40% most likely represent MHC
epitopes, as they become accessible upon protein
degradation.
Epitope mapping can be overlaid with other annotations
available at POLYVIEW-3D, e.g., with protein-protein or
protein-ligand binding sites. Such a combined annotation
facilitates the inference of functional implications for a
given antibody-antigen binding.
Below is an example of the mapping of different types of epitopes (linear and
conformational) based on sequence data from IEDB and
automated structure analysis performed by POLYVIEW-3D
for ribonuclease A (RNase A). In this case, the peptide
colored pink is a MHC epitope; yellow is an Ab epitope;
red is a conformational Ab epitope identified using the 3D
structure (biological unit) PDB ID 1bzq.
Immune epitopes by IEDB |
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Click on respective image to see options used for its rendering.
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Generated image is accompanied with the annotation table listing the
identified epitopes.
Peptidic epitopes found using IEDB |
Chain |
Epitope IDs, Epitope match (Sequence identity, %) |
Color |
Residues* |
A |
108593
PVNTFVHESLADVQA (100)
124828
VNTFVHESLADVQA (100)
108594
PVNTFVHESLKDVQA (93)
108591
PVNTFVHEALADVQA (93)
108592
PVNTFVHESAADVQA (93)
108586
PVNAFVHESLADVQA (93)
108587
PVNTAVHESLADVQA (93)
108584
PVATFVHESLADVQA (93)
108590
PVNTFVHASLADVQA (93)
108588
PVNTFAHESLADVQA (93)
108589
PVNTFVAESLADVQA (93)
|
pink |
Matching peptide
PVNTFVHESLADVQA
PDB numbering 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56
Average RSA 27%
|
A |
130980
NCAYKTTQANK (100)
|
gold |
Matching peptide
NCAYKTTQANK
PDB numbering 94 95 96 97 98 99 100 101 102 103 104
Average RSA 38%
|
* RSA -- relative solvent accessibility. In case of complexes,
RSA values refer to an 'unbound' state of the protein
chain. Average RSA below 40% indicates that the
peptide is more likely to be a MHC-targeted
epitope. RSA above 40% may represent both Ab and
MHC epitopes.
Interface analysis |
Chain |
Interface SA*, Å2 |
HP index** |
Residues |
A |
568 |
0.59±0.74 |
59 60 61 62 64 68 69 70 71 73 76 111 112 115 |
L |
557 |
0.91±0.85 |
1027 1028 1029 1031 1032 1099 1100 1101 1104 1106 1107 1109 1110 |
* SA -- Surface area ** HP -- hydrophobicity
Predicting protein interface using SPPIDER
This setting belongs to the second group of options that utilize
pre-computed results, which were received prior to
submitting a query to POLYVIEW-3D. The SPPIDER server
optionally generates a PDB file with temperature factor
fields modified according to the probability of that
residue to be involved in protein-protein
interactions. These files can be submitted to the
POLYVIEW-3D server as custom PDB files with
chain of interest to be colored using the
By B-factors color
scheme (see
Chains rendering settings).
Two examples below illustrate the use of POLYVIEW-3D to visualize
predictions by SPPIDER of interaction sites within the CSL
transcription factor (PDB id 1ttu, chain A). The
predictions are encoded using either classification or
regression approach (with a binary class assignment in the
first case, and a probability of being within an
interaction interface in the latter case, respectively),
and incorporated in the corresponding B-factor
fields. Color scheme applied is
By B-factor and described
in Chains rendering settings
section. Modified PDB files, used here for the images, are
also available for download
(classification-based and
regression-based
prediction).
Interfaces by SPPIDER as classification |
Interfaces by SPPIDER as regression |
|
|
Click on respective image to see options used for its rendering.
|
Generated images are accompanied with lists of residues that are grouped
either by class assignment or in probability bins (see the
corresponding tables below).
Interface prediction using SPPIDER as classification
(Show full version)
|
Chain |
Class |
Residues |
A |
Positive |
230 399 400 401 402 403 412 413 415 416 419 426 428 429 430 431 432 433 435 436 ... |
A |
Negative |
195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 ... |
Interface prediction using SPPIDER as classification
(Show brief version)
|
Chain |
Class |
Residues |
A |
Positive |
230 399 400 401 402 403 412 413 415 416 419 426 428 429 430 431 432 433 435 436 437 439 440 441 442 458 462 463 464 465 466 467 512 516 519 556 557 569 570 571 572 573 574 575 576 577 578 622 626 631 632 654 655 659 660 |
A |
Negative |
195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 404 405 406 407 408 409 410 411 414 417 418 420 421 422 423 424 425 427 434 438 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 459 460 461 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 513 514 515 517 518 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 558 559 560 561 562 563 564 565 566 567 568 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 623 624 625 627 628 629 630 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 656 657 658 |
Interface prediction using SPPIDER as regression
(Show full version)
|
Chain |
Probability, % |
Residues |
A |
90-100 |
403 467 572 573 574 |
A |
80-89 |
402 413 431 433 463 464 570 575 576 578 622 |
A |
70-79 |
400 401 412 416 436 440 458 516 519 557 571 577 626 655 |
A |
60-69 |
230 415 429 430 437 439 556 660 |
A |
50-59 |
399 419 426 428 432 435 441 442 462 466 512 569 631 632 654 659 |
A |
40-49 |
231 233 391 398 406 407 411 414 443 465 502 515 517 567 568 612 617 623 ... |
A |
30-39 |
195 229 234 319 328 354 389 397 404 405 409 410 434 438 445 447 456 460 ... |
A |
20-29 |
232 235 243 245 259 262 280 281 285 297 320 329 377 378 388 390 418 420 ... |
A |
10-19 |
196 197 199 205 207 208 211 212 220 226 227 237 247 250 252 254 255 258 ... |
A |
0-9 |
198 200 201 202 203 204 206 209 210 213 214 215 216 217 218 219 221 222 ... |
Interface prediction using SPPIDER as regression
(Show brief version)
|
Chain |
Probability, % |
Residues |
A |
90-100 |
403 467 572 573 574 |
A |
80-89 |
402 413 431 433 463 464 570 575 576 578 622 |
A |
70-79 |
400 401 412 416 436 440 458 516 519 557 571 577 626 655 |
A |
60-69 |
230 415 429 430 437 439 556 660 |
A |
50-59 |
399 419 426 428 432 435 441 442 462 466 512 569 631 632 654 659 |
A |
40-49 |
231 233 391 398 406 407 411 414 443 465 502 515 517 567 568 612 617 623 657 |
A |
30-39 |
195 229 234 319 328 354 389 397 404 405 409 410 434 438 445 447 456 460 461 468 500 501 521 560 613 616 618 621 625 629 633 634 639 653 656 |
A |
20-29 |
232 235 243 245 259 262 280 281 285 297 320 329 377 378 388 390 418 420 444 446 454 505 508 511 514 518 523 524 525 531 545 565 566 582 605 627 630 637 645 658 |
A |
10-19 |
196 197 199 205 207 208 211 212 220 226 227 237 247 250 252 254 255 258 260 261 282 286 287 289 294 296 299 301 303 304 321 323 327 333 334 335 337 339 348 350 351 352 353 357 367 368 376 382 387 421 423 448 453 470 476 477 478 481 483 484 486 487 489 493 503 504 510 513 522 526 527 532 533 535 537 547 552 553 554 555 558 561 564 580 583 584 587 588 589 591 599 600 601 602 603 604 606 607 615 620 635 636 646 652 |
A |
0-9 |
198 200 201 202 203 204 206 209 210 213 214 215 216 217 218 219 221 222 223 224 225 228 236 238 239 240 241 242 244 246 248 249 251 253 256 257 283 284 288 290 291 292 293 295 298 300 302 322 324 325 326 330 331 332 336 338 340 341 342 343 344 345 346 347 349 355 356 358 359 360 361 362 363 364 365 366 369 370 371 372 373 374 375 379 380 381 383 384 385 386 392 393 394 395 396 408 417 422 424 425 427 449 450 451 452 455 457 459 469 471 472 473 474 475 479 480 482 485 488 490 491 492 494 495 496 497 498 499 506 507 509 520 528 529 530 534 536 538 539 540 541 542 543 544 546 548 549 550 551 559 562 563 579 581 585 586 590 592 593 594 595 596 597 598 608 609 610 611 614 619 624 628 638 640 641 642 643 644 647 648 649 650 651 |
Finding functional regions using ConSurf
The ConSurf
server ranks residues according to their relative
conservation scores that can be used for the
identification of putative functional regions within a
given structure. The server also modifies the original PDB
file to encode conservation scores by replacing B-factor
fields. Such a file can be submitted to POLYVIEW-3D.
Then, by specifying the chain of interest to be colored
by B-factors, one can obtain high-quality images of
ConSurf results using its original color scheme.
Below is example of the ConSurf output, with conservation scores
encoded as B-factors and residues colored using the
ConSurf color scheme. The same protein was used as in the
previous section (PDB id 1ttu, chain A). Color
scheme applied is
By B-factor and described
in Chains rendering settings
section. PDB file modified by the ConSurf server and used
for the image is also available for
download.
Functional regions by ConSurf |
|
Click on the image to see options used for its rendering.
|
Generated image is accompanied with the annotation table listing the
residues binned by the ConSurf conservation scores.
Relative amino acid conservation using ConSurf
(Show full version)
|
Chain |
Color |
Residues |
A |
9 |
199 203 221 222 223 224 225 226 227 228 231 232 233 234 238 239 240 300 327 328... |
A |
8 |
198 229 230 235 237 241 243 244 248 291 302 319 330 341 343 356 358 384 385 389... |
A |
7 |
219 249 288 290 295 340 387 390 393 419 422 460 465 479 483 490 511 515 516 517... |
A |
6 |
208 209 252 257 258 259 260 261 262 280 281 282 283 284 292 298 301 362 371 379... |
A |
5 |
214 220 236 246 293 294 304 320 331 335 348 350 352 376 413 416 423 440 444 448... |
A |
4 |
202 206 207 289 325 424 435 449 450 461 482 499 506 518 523 573 585 636 |
A |
3 |
211 216 250 285 299 345 346 347 355 441 445 453 459 502 512 529 551 578 588 591... |
A |
2 |
287 303 321 324 354 454 480 505 522 535 569 596 603 622 629 630 632 |
A |
1 |
195 196 197 200 201 204 205 210 212 213 215 217 218 242 245 247 251 253 254 255... |
Relative amino acid conservation using ConSurf
(Show brief version)
|
Chain |
Color |
Residues |
A |
9 |
199 203 221 222 223 224 225 226 227 228 231 232 233 234 238 239 240 300 327 328 329 332 333 334 336 337 338 339 360 363 364 365 366 367 368 369 370 372 373 374 375 377 378 380 386 388 392 396 397 399 400 401 402 403 404 405 406 410 411 417 418 428 431 455 458 462 467 471 472 473 474 476 477 489 491 492 494 495 497 519 520 531 532 537 538 539 541 545 558 561 563 580 592 601 604 614 639 644 646 |
A |
8 |
198 229 230 235 237 241 243 244 248 291 302 319 330 341 343 356 358 384 385 389 394 395 398 407 408 415 425 429 442 447 451 452 457 463 466 481 493 496 498 507 508 509 510 548 568 572 574 583 586 590 594 595 611 642 650 656 |
A |
7 |
219 249 288 290 295 340 387 390 393 419 422 460 465 479 483 490 511 515 516 517 521 526 534 536 540 544 552 559 560 565 567 576 577 593 599 602 613 617 626 643 655 657 |
A |
6 |
208 209 252 257 258 259 260 261 262 280 281 282 283 284 292 298 301 362 371 379 381 382 383 391 409 421 427 432 436 437 438 446 456 464 468 469 470 475 484 485 486 487 513 530 533 542 562 575 600 612 616 623 624 625 633 634 635 638 652 659 660 |
A |
5 |
214 220 236 246 293 294 304 320 331 335 348 350 352 376 413 416 423 440 444 448 488 514 524 527 543 546 553 570 571 579 581 598 605 607 608 609 619 641 647 654 658 |
A |
4 |
202 206 207 289 325 424 435 449 450 461 482 499 506 518 523 573 585 636 |
A |
3 |
211 216 250 285 299 345 346 347 355 441 445 453 459 502 512 529 551 578 588 591 597 620 628 637 649 |
A |
2 |
287 303 321 324 354 454 480 505 522 535 569 596 603 622 629 630 632 |
A |
1 |
195 196 197 200 201 204 205 210 212 213 215 217 218 242 245 247 251 253 254 255 256 286 296 297 322 323 326 342 344 349 351 353 357 359 361 412 414 420 426 430 433 434 439 443 478 500 501 503 504 525 528 547 549 550 554 555 556 557 564 566 582 584 587 589 606 610 615 618 621 627 631 640 645 648 651 653 |
Analysis of docking models from CAPRI
POLYVIEW-3D provides an option for analyzing the docking models in the
CAPRI format
obtained by different programs or web-servers for
protein-protein docking. In addition to visualization of
docking models, POLYVIEW-3D performs their analysis and
assessment. In particular, when a custom PDB file with multiple
models of a protein complex (e.g., generated by the
ClusPro
server) submitted to POLYVIEW-3D using the
Docking models option, it
triggers SPPIDER predictions to perform for all chains
in the model. Unbound structures of these chains are used to
predict putative interaction interfaces, which are then
compared to the interfaces observed in each model. The
fraction of residues within the interface in a given model
that overlaps with SPPIDER predictions (averaged over both
chains) provides a simple score to rank these models. In
addition, the surface area and average hydrophobicity for
each interface within these models are computed to provide
a basis for further analysis and model ranking. Models can
be then re-ranked according to these values and sent to
refine image rendering.
The table below includes the output of the POLYVIEW-3D assessment of
docking models for the system used as CAPRI target #9, and
described in more details in
Example 2 of the
Advanced examples section. The
two chains were submitted to the ClusPro server, in order
to obtain 10 best ranking models of the protein complex
(download results).
The option for model assessment had been invoked by
requesting the overlay with protein interfaces predicted by SPPIDER.
NOTE: table rows (and thus different models) can be
easily re-ordered (sorted) according to measures presented
in the columns.
In addition, the resulting page provides options to alter
the sensitivity used to identify interaction sites from
the SPPIDER initial (default) definition. It allows the user to make the
interface overlap measure either more restrictive or loose.
Analysis of docking models
(Click on the header of column to re-sort models)
|
Model |
Image |
(1) ASA, Å2 |
(2) HP index |
(3) Overlap, % |
Chain A Interface ASA, Å2 |
Chain A Interface HP |
Chain B Interface ASA, Å2 |
Chain B Interface HP |
Residues at the interface (Overlap with SPPIDER prediction, %) |
1 |
|
2436 |
1.04 |
52.42 |
1246 |
1.06±0.72 |
1190 |
1.01±0.72 |
Chain: A (54.84%)
Overlapped: 2 3 5 6 7 9 ...
Observed: 21 37 46 63 112 ...
Predicted: 1 4 8 12 13 14 ...
Chain: B (50.00%)
Overlapped: 2 3 5 6 7 9 ...
Observed: 21 37 38 46 ...
Predicted: 1 4 8 12 13 14 ...
|
2 |
|
2150 |
0.72 |
45.69 |
1081 |
0.68±0.67 |
1069 |
0.75±0.67 |
Chain: A (41.38%)
Overlapped: 1 2 3 6 41 ...
Observed: 34 36 37 38 112 ...
Predicted: 4 5 7 8 9 10 ...
Chain: B (50.00%)
Overlapped: 1 2 3 6 41 ...
Observed: 34 36 37 38 ...
Predicted: 4 5 7 8 9 10 ...
|
3 |
|
2438 |
0.95 |
32.73 |
1218 |
0.95±0.73 |
1220 |
0.95±0.74 |
Chain: A (32.14%)
Overlapped: 5 8 9 12 49 53 59 61 134
Observed: 62 63 65 66 ...
Predicted: 1 2 3 4 6 7 ...
Chain: B (33.33%)
Overlapped: 5 8 9 12 49 53 59 61 134
Observed: 62 63 65 66 67 96 97 ...
Predicted: 1 2 3 4 6 7 ...
|
4 |
|
2091 |
0.96 |
47.22 |
1050 |
0.98±0.67 |
1041 |
0.95±0.67 |
Chain: A (44.44%)
Overlapped: 3 7 10 11 15 17 18 40
Observed: 21 25 28 29 32 ...
Predicted: 1 2 4 5 6 8 9 ...
Chain: B (50.00%)
Overlapped: 3 7 10 11 15 17 ...
Observed: 21 25 28 29 32 ...
Predicted: 1 2 4 5 6 8 9 ...
|
5 |
|
2374 |
1.02 |
21.45 |
1176 |
1.00±0.74 |
1198 |
1.03±0.73 |
Chain: A (22.22%)
Overlapped: 53 59 61 134 137 139
Observed: 62 63 65 66 67 69 ...
Predicted: 1 2 3 4 5 6 7 8 ...
Chain: B (20.69%)
Overlapped: 53 59 61 134 137 139
Observed: 62 63 65 66 67 69 ...
Predicted: 1 2 3 4 5 6 7 8 ...
|
6 |
|
2479 |
0.83 |
48.34 |
1253 |
0.88±0.69 |
1226 |
0.79±0.69 |
Chain: A (51.52%)
Overlapped: 1 2 3 6 7 40 41 ...
Observed: 21 28 31 32 33 34 ...
Predicted: 4 5 8 9 10 11 12 ...
Chain: B (45.16%)
Overlapped: 1 2 3 6 10 40 146 ...
Observed: 31 32 33 34 36 37 ...
Predicted: 4 5 7 8 9 11 12 ...
|
7 |
|
1276 |
0.79 |
46.05 |
634 |
0.80±0.69 |
642 |
0.77±0.70 |
Chain: A (50.00%)
Overlapped: 1 2 3 5 6 10 41 ...
Observed: 36 161 163 174 177 ...
Predicted: 4 7 8 9 11 12 ...
Chain: B (42.11%)
Overlapped: 1 2 3 5 6 10 ...
Observed: 36 161 162 163 ...
Predicted: 4 7 8 9 11 12 ...
|
8 |
|
2305 |
1.02 |
30.81 |
1165 |
1.00±0.69 |
1140 |
1.04±0.69 |
Chain: A (29.63%)
Overlapped: 6 53 56 58 59 61 134 139
Observed: 62 63 64 66 67 69 ...
Predicted: 1 2 3 4 5 7 8 9 ...
Chain: B (32.00%)
Overlapped: 6 53 56 58 59 61 134 139
Observed: 63 64 66 67 114 115 ...
Predicted: 1 2 3 4 5 7 8 9 ...
|
9 |
|
2081 |
0.89 |
51.47 |
1056 |
0.86±0.71 |
1025 |
0.91±0.70 |
Chain: A (50.00%)
Overlapped: 144 147 151 154 165 ...
Observed: 150 158 162 163 164 ...
Predicted: 1 2 3 4 5 6 7 8 9 ...
Chain: B (52.94%)
Overlapped: 144 147 151 154 165 ...
Observed: 150 158 162 163 164 ...
Predicted: 1 2 3 4 5 6 7 8 9 ...
|
10 |
|
2059 |
1.12 |
51.19 |
1032 |
1.11±0.67 |
1027 |
1.13±0.66 |
Chain: A (52.38%)
Overlapped: 3 6 7 10 11 15 17 ...
Observed: 21 25 28 29 32 33 ...
Predicted: 1 2 4 5 8 9 12 13 ...
Chain: B (50.00%)
Overlapped: 3 6 7 10 11 15 17 ...
Observed: 21 25 28 29 31 32 33 ...
Predicted: 1 2 4 5 8 9 12 13 ...
|
1 − Total solvent accessibility buried upon complex formation
2 − Mean hydrophobicity index of the interfaces
3 − Average overlap across chains between observed interfaces in a given model and predicted by SPPIDER
Annotation of residues:
Overlapped(Red) - observed and predicted to be at the interface
Observed(Blue) - located at the interface in a given model, but not predicted
Predicted(Yellow) - predicted to be at the interface, but not observed in a model
Animation of macromolecular movements
There are a number of programs and web-servers performing simulation
and analysis of macromolecular movements, for example
Analysis of Dynamics of Elastic Network Model
(AD-ENM) or
Database of Macromolecular Motions
(MolMovDB).
Motion trajectories and structural distortions may help
identify flexible and rigid regions, localize
hinges and stable domains. In this regard, POLYVIEW-3D
has a function that analyzes trajectory
quantitatively and produces both animations and
2D-trajectory images. In order to invoke this function,
the user has to chose the option
Trajectories and distortions
and submit a PDB-formatted
coordinate file with conformational changes recorded as
models.
NOTE: When this structure annotation is requested,
POLYVIEW-3D ignores the current setting of the
Type of request option in the
Image Settings
field set. In contrast to the option that animates
Models
from the Animation settings,
this option generates a movie comprising of all available
models and makes the motions reversible. Images shown
below represent two macromolecular motions as deduced by the
corresponding servers. Coordinate files were taken from
the examples available at those servers and can be downloaded here:
AD-ENM example of myosin deformation,
MolMovDB example of calmodulin hinge motion.
Low-frequency motion by AD-ENM |
Morph by the Morph Server |
|
|
Click on respective image to see options used for its rendering.
|
Along with animation, the resulting page presents 2D-plots with
trajectories of structural changes in terms of secondary
structure (SS) and relative solvent accessibility (RSA), and with
per-residue analysis of protein flexibility. The details
on the measures used to quantify conformational changes
as well as the options to customize a 2D-plot can be
found in the POLYVIEW-MM
documentation.
Below are 2D-plots produced for SS and RSA changes occurring
during the calmodulin hinge motion as interpolated by the
Morph Server.
Conformational changes in calmodulin in terms of SS |
|
Conformational changes in calmodulin in terms of RSA |
|
Last modified: Thu Feb 9 13:28:25 EST 2012
|