| Chain sequence(s) |
B: KCNPNLHYWTAQEQHNAAGIAWIPYFGPGAEGIYTEGLMHNQNALVCGLRQLANETTQALQLFLRATTELRTYTILNRKAIDFLLRRWGGTCRILGPDCCIEPHDW
input PDB |
| Selected Chain(s) | B |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| Dynamic mode | No |
| Automated mutations | Yes |
| Downloads | Download all the data |
| Simulation log |
[INFO] Logger: Verbosity set to: 2 - [INFO] (00:00:00)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:00)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with B chain(s) selected (00:00:00)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:00)
[INFO] FoldX: Starting FoldX energy minimalization (00:00:00)
[INFO] Analysis: Starting Aggrescan3D on folded.pdb (00:01:13)
[INFO] Auto_mut: Residue number 535 from chain B and a score of 3.076 (phenylalanine)
selected for automated muatation (00:01:13)
[INFO] Auto_mut: Residue number 529 from chain B and a score of 2.477 (isoleucine) selected
for automated muatation (00:01:13)
[INFO] Auto_mut: Residue number 532 from chain B and a score of 2.353 (isoleucine) selected
for automated muatation (00:01:13)
[INFO] Auto_mut: Residue number 534 from chain B and a score of 2.353 (tyrosine) selected
for automated muatation (00:01:13)
[INFO] Auto_mut: Residue number 531 from chain B and a score of 2.274 (tryptophan) selected
for automated muatation (00:01:13)
[INFO] Auto_mut: Residue number 530 from chain B and a score of 2.179 (alanine) selected for
automated muatation (00:01:13)
[INFO] Auto_mut: Mutating residue number 535 from chain B (phenylalanine) into glutamic acid
Mutating residue number 535 from chain B (phenylalanine) into glutamic acid (00:01:13)
[INFO] Auto_mut: Mutating residue number 535 from chain B (phenylalanine) into aspartic acid
Mutating residue number 535 from chain B (phenylalanine) into aspartic acid (00:01:13)
[INFO] Auto_mut: Mutating residue number 529 from chain B (isoleucine) into glutamic acid (00:01:13)
[INFO] Auto_mut: Mutating residue number 535 from chain B (phenylalanine) into arginine (00:01:53)
[INFO] Auto_mut: Mutating residue number 529 from chain B (isoleucine) into lysine (00:01:54)
[INFO] Auto_mut: Mutating residue number 535 from chain B (phenylalanine) into lysine (00:01:57)
[INFO] Auto_mut: Mutating residue number 529 from chain B (isoleucine) into aspartic acid (00:02:38)
[INFO] Auto_mut: Mutating residue number 532 from chain B (isoleucine) into glutamic acid (00:02:42)
[INFO] Auto_mut: Mutating residue number 532 from chain B (isoleucine) into aspartic acid (00:02:49)
[INFO] Auto_mut: Mutating residue number 529 from chain B (isoleucine) into arginine (00:03:17)
[INFO] Auto_mut: Mutating residue number 532 from chain B (isoleucine) into lysine (00:03:26)
[INFO] Auto_mut: Mutating residue number 532 from chain B (isoleucine) into arginine (00:03:27)
[INFO] Auto_mut: Mutating residue number 534 from chain B (tyrosine) into glutamic acid (00:04:00)
[INFO] Auto_mut: Mutating residue number 534 from chain B (tyrosine) into aspartic acid (00:04:14)
[INFO] Auto_mut: Mutating residue number 531 from chain B (tryptophan) into glutamic acid (00:04:19)
[INFO] Auto_mut: Mutating residue number 534 from chain B (tyrosine) into lysine (00:04:41)
[INFO] Auto_mut: Mutating residue number 534 from chain B (tyrosine) into arginine (00:04:52)
[INFO] Auto_mut: Mutating residue number 531 from chain B (tryptophan) into lysine (00:05:01)
[INFO] Auto_mut: Mutating residue number 531 from chain B (tryptophan) into aspartic acid (00:05:28)
[INFO] Auto_mut: Mutating residue number 530 from chain B (alanine) into glutamic acid (00:05:34)
[INFO] Auto_mut: Mutating residue number 530 from chain B (alanine) into aspartic acid (00:06:02)
[INFO] Auto_mut: Mutating residue number 531 from chain B (tryptophan) into arginine (00:06:06)
[INFO] Auto_mut: Mutating residue number 530 from chain B (alanine) into lysine (00:06:19)
[INFO] Auto_mut: Mutating residue number 530 from chain B (alanine) into arginine (00:06:41)
[INFO] Auto_mut: Effect of mutation residue number 535 from chain B (phenylalanine) into
glutamic acid: Energy difference: 0.9361 kcal/mol, Difference in average
score from the base case: -0.1316 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 535 from chain B (phenylalanine) into
lysine: Energy difference: 0.6164 kcal/mol, Difference in average score
from the base case: -0.1468 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 535 from chain B (phenylalanine) into
aspartic acid: Energy difference: 1.1954 kcal/mol, Difference in average
score from the base case: -0.1349 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 535 from chain B (phenylalanine) into
arginine: Energy difference: 0.3002 kcal/mol, Difference in average score
from the base case: -0.1642 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 529 from chain B (isoleucine) into
glutamic acid: Energy difference: -2.9332 kcal/mol, Difference in average
score from the base case: -0.1128 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 529 from chain B (isoleucine) into
lysine: Energy difference: -2.0710 kcal/mol, Difference in average score
from the base case: -0.1223 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 529 from chain B (isoleucine) into
aspartic acid: Energy difference: -1.7893 kcal/mol, Difference in average
score from the base case: -0.1194 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 529 from chain B (isoleucine) into
arginine: Energy difference: -2.0557 kcal/mol, Difference in average score
from the base case: -0.1278 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 532 from chain B (isoleucine) into
glutamic acid: Energy difference: 1.1822 kcal/mol, Difference in average
score from the base case: -0.0361 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 532 from chain B (isoleucine) into
lysine: Energy difference: 0.8177 kcal/mol, Difference in average score
from the base case: -0.0433 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 532 from chain B (isoleucine) into
aspartic acid: Energy difference: 1.5814 kcal/mol, Difference in average
score from the base case: -0.0312 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 532 from chain B (isoleucine) into
arginine: Energy difference: 0.9752 kcal/mol, Difference in average score
from the base case: -0.0762 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 534 from chain B (tyrosine) into glutamic
acid: Energy difference: -0.0240 kcal/mol, Difference in average score from
the base case: -0.1008 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 534 from chain B (tyrosine) into lysine:
Energy difference: -0.0346 kcal/mol, Difference in average score from the
base case: -0.1017 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 534 from chain B (tyrosine) into aspartic
acid: Energy difference: 0.0846 kcal/mol, Difference in average score from
the base case: -0.0960 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 534 from chain B (tyrosine) into
arginine: Energy difference: 0.1958 kcal/mol, Difference in average score
from the base case: -0.0968 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 531 from chain B (tryptophan) into
glutamic acid: Energy difference: 1.3623 kcal/mol, Difference in average
score from the base case: -0.0956 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 531 from chain B (tryptophan) into
lysine: Energy difference: 0.8936 kcal/mol, Difference in average score
from the base case: -0.0968 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 531 from chain B (tryptophan) into
aspartic acid: Energy difference: 1.5213 kcal/mol, Difference in average
score from the base case: -0.0908 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 531 from chain B (tryptophan) into
arginine: Energy difference: 0.8058 kcal/mol, Difference in average score
from the base case: -0.0939 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 530 from chain B (alanine) into glutamic
acid: Energy difference: -0.0659 kcal/mol, Difference in average score from
the base case: -0.0700 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 530 from chain B (alanine) into lysine:
Energy difference: -0.6360 kcal/mol, Difference in average score from the
base case: -0.0754 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 530 from chain B (alanine) into aspartic
acid: Energy difference: -0.0466 kcal/mol, Difference in average score from
the base case: -0.0749 (00:07:25)
[INFO] Auto_mut: Effect of mutation residue number 530 from chain B (alanine) into arginine:
Energy difference: -0.8442 kcal/mol, Difference in average score from the
base case: -0.0696 (00:07:25)
[INFO] Main: Simulation completed successfully. (00:07:31)
|
The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.
| residue index | residue name | chain | Aggrescan3D score | mutation |
|---|---|---|---|---|
| residue index | residue name | chain | Aggrescan3D score | |
| 511 | C | B | -0.4776 | |
| 512 | N | B | -1.4682 | |
| 513 | P | B | -1.9412 | |
| 514 | N | B | -1.7920 | |
| 515 | L | B | 0.0000 | |
| 516 | H | B | -0.1813 | |
| 517 | Y | B | 1.2319 | |
| 518 | W | B | 1.0852 | |
| 519 | T | B | 0.1594 | |
| 520 | A | B | -0.8196 | |
| 521 | Q | B | -2.2163 | |
| 522 | E | B | -3.1418 | |
| 523 | Q | B | -3.1890 | |
| 524 | H | B | -2.5843 | |
| 525 | N | B | -2.2760 | |
| 526 | A | B | -0.7835 | |
| 527 | A | B | 0.1752 | |
| 528 | G | B | 0.6130 | |
| 529 | I | B | 2.4768 | |
| 530 | A | B | 2.1790 | |
| 531 | W | B | 2.2738 | |
| 532 | I | B | 2.3533 | |
| 533 | P | B | 1.6372 | |
| 534 | Y | B | 2.3527 | |
| 535 | F | B | 3.0761 | |
| 536 | G | B | 1.7640 | |
| 537 | P | B | 0.1605 | |
| 538 | G | B | -0.6679 | |
| 539 | A | B | -0.8798 | |
| 540 | E | B | -1.7178 | |
| 541 | G | B | -0.8816 | |
| 542 | I | B | -0.2474 | |
| 543 | Y | B | 0.3294 | |
| 544 | T | B | -0.5646 | |
| 545 | E | B | -0.6964 | |
| 546 | G | B | -0.0321 | |
| 547 | L | B | 0.6145 | |
| 548 | M | B | -0.1363 | |
| 549 | H | B | -1.9536 | |
| 550 | N | B | -2.4951 | |
| 551 | Q | B | -2.3359 | |
| 552 | N | B | -2.3616 | |
| 553 | A | B | -0.7978 | |
| 554 | L | B | -0.1780 | |
| 555 | V | B | 0.0000 | |
| 556 | C | B | -0.6473 | |
| 557 | G | B | -0.1839 | |
| 558 | L | B | -0.0049 | |
| 559 | R | B | -1.3249 | |
| 560 | Q | B | -1.6021 | |
| 561 | L | B | -0.3797 | |
| 562 | A | B | -1.1726 | |
| 563 | N | B | -2.5008 | |
| 564 | E | B | -2.5593 | |
| 565 | T | B | -1.3787 | |
| 566 | T | B | -1.2284 | |
| 567 | Q | B | -1.6248 | |
| 568 | A | B | -0.3895 | |
| 569 | L | B | 0.1013 | |
| 570 | Q | B | -0.6233 | |
| 571 | L | B | 0.4007 | |
| 572 | F | B | 0.9662 | |
| 573 | L | B | 0.0806 | |
| 574 | R | B | -1.1911 | |
| 575 | A | B | -0.4165 | |
| 576 | T | B | -0.4992 | |
| 577 | T | B | -1.0070 | |
| 578 | E | B | -1.5765 | |
| 579 | L | B | -0.0635 | |
| 580 | R | B | -1.2463 | |
| 581 | T | B | 0.0039 | |
| 582 | Y | B | 0.8269 | |
| 583 | T | B | -0.1292 | |
| 584 | I | B | 0.3422 | |
| 585 | L | B | 0.0894 | |
| 586 | N | B | -1.5648 | |
| 587 | R | B | -2.5740 | |
| 588 | K | B | -2.0877 | |
| 589 | A | B | -0.9106 | |
| 590 | I | B | -0.7071 | |
| 591 | D | B | -1.8111 | |
| 592 | F | B | -0.2769 | |
| 593 | L | B | 0.9210 | |
| 594 | L | B | 0.5101 | |
| 595 | R | B | -1.5369 | |
| 596 | R | B | -1.1065 | |
| 597 | W | B | 0.5048 | |
| 598 | G | B | -0.3635 | |
| 599 | G | B | -0.8327 | |
| 600 | T | B | -0.4170 | |
| 601 | C | B | 0.0322 | |
| 602 | R | B | -0.3688 | |
| 603 | I | B | 1.8195 | |
| 604 | L | B | 1.5101 | |
| 605 | G | B | 0.1568 | |
| 606 | P | B | -0.3966 | |
| 607 | D | B | -2.0776 | |
| 608 | C | B | -0.8796 | |
| 609 | C | B | 0.2368 | |
| 610 | I | B | 1.1648 | |
| 611 | E | B | -0.7558 | |
| 612 | P | B | -1.0397 | |
| 613 | H | B | -2.1288 | |
| 614 | D | B | -1.7507 | |
| 615 | W | B | 0.0994 |
Automated mutations analysis
In the automated mutations mode, the server selects aggregation prone resides
and each selected residue is mutated to glutamic acid, lysine, aspartic acid and arginine.
The table below shows 2 best scored mutants for each mutated residue. Protein variants
are ordered according to the mutation effect they had on protein stability
(energetic effect) together with the difference in the average per-residue aggregation score
between the wild type and the mutant (in the table green values indicate a positive change,
grey are neutral, and orange/red mean destabilizing or more aggregation prone mutants).
Summary for all the mutants can be found in this
CSV file.
Mutant |
Energetic effect |
Score comparison |
|||
| IE529B | -2.9332 | -0.1128 | View | CSV | PDB |
| IR529B | -2.0557 | -0.1278 | View | CSV | PDB |
| AR530B | -0.8442 | -0.0696 | View | CSV | PDB |
| AK530B | -0.636 | -0.0754 | View | CSV | PDB |
| YK534B | -0.0346 | -0.1017 | View | CSV | PDB |
| YE534B | -0.024 | -0.1008 | View | CSV | PDB |
| FR535B | 0.3002 | -0.1642 | View | CSV | PDB |
| FK535B | 0.6164 | -0.1468 | View | CSV | PDB |
| WR531B | 0.8058 | -0.0939 | View | CSV | PDB |
| WK531B | 0.8936 | -0.0968 | View | CSV | PDB |
| IR532B | 0.9752 | -0.0762 | View | CSV | PDB |
| IK532B | 0.8177 | -0.0433 | View | CSV | PDB |
ALA alanine
ARG arginine
ASN asparagine
ASP aspartic acid
CYS cysteine
GLN glutamine
GLU glutamic acid
GLY glycine
HIS histidine
ILE isoleucine
LEU leucine
LYS lysine
MET methionine
PHE phenylalanine
PRO proline
SER serine
THR threonine
TRP tryptophan
TYR tyrosine
VAL valine