| Chain sequence(s) |
A: MHSDCIFKKEQAMCLEKIQRANELMGFNDSSPGCPGMWDNITCWKPAHVGEMVLVSCPELFRIFNPDQDMGVVSRNCTEDGWSEPFPHYFDACGFDEYESETGDQD
input PDB |
| Selected Chain(s) | A |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| pH calculations | No |
| alphaCutter usage | No |
| Dynamic mode | No |
| Automated mutations | Yes |
| Downloads | Download all the data |
| Simulation log |
[INFO] Logger: Verbosity set to: 2 - [INFO] (00:00:01)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:01)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with A chain(s) selected (00:00:01)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:01)
[INFO] FoldX: Starting FoldX energy minimization (00:00:01)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:01:32)
[INFO] AutoMut: Residue number 54 from chain A and a score of 1.856 (leucine) selected for
automated mutation (00:01:32)
[INFO] AutoMut: Residue number 63 from chain A and a score of 1.503 (isoleucine) selected
for automated mutation (00:01:32)
[INFO] AutoMut: Residue number 64 from chain A and a score of 1.405 (phenylalanine)
selected for automated mutation (00:01:32)
[INFO] AutoMut: Residue number 55 from chain A and a score of 1.097 (valine) selected for
automated mutation (00:01:32)
[INFO] AutoMut: Residue number 72 from chain A and a score of 0.965 (valine) selected for
automated mutation (00:01:32)
[INFO] AutoMut: Residue number 86 from chain A and a score of 0.962 (phenylalanine)
selected for automated mutation (00:01:32)
[INFO] AutoMut: Residue number 74 from chain A and a score of 0.950 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 52 from chain A and a score of 0.395 (methionine) selected
for automated mutation (00:01:32)
[INFO] AutoMut: Residue number 56 from chain A and a score of 0.311 (serine) selected for
automated mutation (00:01:32)
[INFO] AutoMut: Residue number 1 from chain A and a score of 0.204 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 87 from chain A and a score of 0.200 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 24 from chain A and a score of 0.188 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 25 from chain A and a score of 0.024 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 75 from chain A and a score of 0.017 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 14 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 34 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 42 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 44 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 46 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 47 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 53 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 57 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 60 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 61 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 71 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 73 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 77 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 89 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 92 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 93 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 95 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 38 from chain A and a score of -0.129 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 43 from chain A and a score of -0.139 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Residue number 37 from chain A and a score of -0.198 omitted from automated
mutation (excluded by the user). (00:01:32)
[INFO] AutoMut: Mutating residue number 54 from chain A (leucine) into glutamic acid (00:01:32)
[INFO] AutoMut: Mutating residue number 54 from chain A (leucine) into arginine (00:01:32)
[INFO] AutoMut: Mutating residue number 63 from chain A (isoleucine) into aspartic acid (00:01:32)
[INFO] AutoMut: Mutating residue number 54 from chain A (leucine) into lysine (00:01:38)
[INFO] AutoMut: Mutating residue number 63 from chain A (isoleucine) into glutamic acid (00:01:39)
[INFO] AutoMut: Mutating residue number 63 from chain A (isoleucine) into arginine (00:01:43)
[INFO] AutoMut: Mutating residue number 54 from chain A (leucine) into aspartic acid (00:01:49)
[INFO] AutoMut: Mutating residue number 63 from chain A (isoleucine) into lysine (00:01:52)
[INFO] AutoMut: Mutating residue number 64 from chain A (phenylalanine) into glutamic acid
Mutating residue number 64 from chain A (phenylalanine) into glutamic acid (00:01:53)
[INFO] AutoMut: Mutating residue number 64 from chain A (phenylalanine) into lysine (00:01:54)
[INFO] AutoMut: Mutating residue number 55 from chain A (valine) into glutamic acid (00:02:02)
[INFO] AutoMut: Mutating residue number 55 from chain A (valine) into arginine (00:02:06)
[INFO] AutoMut: Mutating residue number 55 from chain A (valine) into lysine (00:02:10)
[INFO] AutoMut: Mutating residue number 64 from chain A (phenylalanine) into aspartic acid
Mutating residue number 64 from chain A (phenylalanine) into aspartic acid (00:02:12)
[INFO] AutoMut: Mutating residue number 64 from chain A (phenylalanine) into arginine (00:02:19)
[INFO] AutoMut: Mutating residue number 55 from chain A (valine) into aspartic acid (00:02:24)
[INFO] AutoMut: Mutating residue number 72 from chain A (valine) into aspartic acid (00:02:27)
[INFO] AutoMut: Mutating residue number 86 from chain A (phenylalanine) into lysine (00:02:31)
[INFO] AutoMut: Mutating residue number 72 from chain A (valine) into arginine (00:02:33)
[INFO] AutoMut: Mutating residue number 72 from chain A (valine) into glutamic acid (00:02:35)
[INFO] AutoMut: Mutating residue number 72 from chain A (valine) into lysine (00:02:41)
[INFO] AutoMut: Mutating residue number 86 from chain A (phenylalanine) into glutamic acid
Mutating residue number 86 from chain A (phenylalanine) into glutamic acid (00:02:42)
[INFO] AutoMut: Mutating residue number 86 from chain A (phenylalanine) into aspartic acid
Mutating residue number 86 from chain A (phenylalanine) into aspartic acid (00:02:43)
[INFO] AutoMut: Mutating residue number 86 from chain A (phenylalanine) into arginine (00:02:50)
[INFO] AutoMut: Mutating residue number 52 from chain A (methionine) into glutamic acid (00:02:53)
[INFO] AutoMut: Mutating residue number 52 from chain A (methionine) into arginine (00:02:54)
[INFO] AutoMut: Mutating residue number 56 from chain A (serine) into glutamic acid (00:03:02)
[INFO] AutoMut: Mutating residue number 52 from chain A (methionine) into lysine (00:03:02)
[INFO] AutoMut: Mutating residue number 56 from chain A (serine) into aspartic acid (00:03:08)
[INFO] AutoMut: Mutating residue number 56 from chain A (serine) into lysine (00:03:13)
[INFO] AutoMut: Mutating residue number 56 from chain A (serine) into arginine (00:03:16)
[INFO] AutoMut: Mutating residue number 52 from chain A (methionine) into aspartic acid (00:03:24)
[INFO] AutoMut: Effect of mutation residue number 54 from chain A (leucine) into glutamic
acid: Energy difference: 0.4631 kcal/mol, Difference in average score from
the base case: -0.1139 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 54 from chain A (leucine) into lysine:
Energy difference: 0.0088 kcal/mol, Difference in average score from the
base case: -0.1143 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 54 from chain A (leucine) into aspartic
acid: Energy difference: 1.3191 kcal/mol, Difference in average score from
the base case: -0.0972 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 54 from chain A (leucine) into arginine:
Energy difference: 0.4830 kcal/mol, Difference in average score from the
base case: -0.1134 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 63 from chain A (isoleucine) into
glutamic acid: Energy difference: 0.2029 kcal/mol, Difference in average
score from the base case: -0.1285 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 63 from chain A (isoleucine) into lysine:
Energy difference: -0.0176 kcal/mol, Difference in average score from the
base case: -0.1096 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 63 from chain A (isoleucine) into
aspartic acid: Energy difference: 0.4642 kcal/mol, Difference in average
score from the base case: -0.1225 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 63 from chain A (isoleucine) into
arginine: Energy difference: -0.0453 kcal/mol, Difference in average score
from the base case: -0.1148 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 64 from chain A (phenylalanine) into
glutamic acid: Energy difference: 1.7727 kcal/mol, Difference in average
score from the base case: -0.1212 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 64 from chain A (phenylalanine) into
lysine: Energy difference: 0.7586 kcal/mol, Difference in average score
from the base case: -0.0862 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 64 from chain A (phenylalanine) into
aspartic acid: Energy difference: 1.9900 kcal/mol, Difference in average
score from the base case: -0.1199 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 64 from chain A (phenylalanine) into
arginine: Energy difference: 0.2792 kcal/mol, Difference in average score
from the base case: -0.0583 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 55 from chain A (valine) into glutamic
acid: Energy difference: 1.2499 kcal/mol, Difference in average score from
the base case: -0.0329 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 55 from chain A (valine) into lysine:
Energy difference: 1.1031 kcal/mol, Difference in average score from the
base case: -0.0335 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 55 from chain A (valine) into aspartic
acid: Energy difference: 1.9609 kcal/mol, Difference in average score from
the base case: -0.0248 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 55 from chain A (valine) into arginine:
Energy difference: 0.0624 kcal/mol, Difference in average score from the
base case: -0.0700 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 72 from chain A (valine) into glutamic
acid: Energy difference: 0.9120 kcal/mol, Difference in average score from
the base case: -0.0463 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 72 from chain A (valine) into lysine:
Energy difference: -0.5390 kcal/mol, Difference in average score from the
base case: -0.0727 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 72 from chain A (valine) into aspartic
acid: Energy difference: 1.3299 kcal/mol, Difference in average score from
the base case: -0.0597 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 72 from chain A (valine) into arginine:
Energy difference: -0.0355 kcal/mol, Difference in average score from the
base case: -0.0894 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 86 from chain A (phenylalanine) into
glutamic acid: Energy difference: 0.6060 kcal/mol, Difference in average
score from the base case: -0.1419 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 86 from chain A (phenylalanine) into
lysine: Energy difference: 0.5809 kcal/mol, Difference in average score
from the base case: -0.1430 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 86 from chain A (phenylalanine) into
aspartic acid: Energy difference: 1.0079 kcal/mol, Difference in average
score from the base case: -0.1456 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 86 from chain A (phenylalanine) into
arginine: Energy difference: 0.3146 kcal/mol, Difference in average score
from the base case: -0.0922 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 52 from chain A (methionine) into
glutamic acid: Energy difference: 0.3004 kcal/mol, Difference in average
score from the base case: -0.0782 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 52 from chain A (methionine) into lysine:
Energy difference: -0.2208 kcal/mol, Difference in average score from the
base case: -0.0740 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 52 from chain A (methionine) into
aspartic acid: Energy difference: 0.8183 kcal/mol, Difference in average
score from the base case: -0.0914 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 52 from chain A (methionine) into
arginine: Energy difference: -0.1600 kcal/mol, Difference in average score
from the base case: -0.0859 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 56 from chain A (serine) into glutamic
acid: Energy difference: 0.5336 kcal/mol, Difference in average score from
the base case: -0.0390 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 56 from chain A (serine) into lysine:
Energy difference: 0.2690 kcal/mol, Difference in average score from the
base case: -0.0996 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 56 from chain A (serine) into aspartic
acid: Energy difference: 1.4040 kcal/mol, Difference in average score from
the base case: -0.0469 (00:03:39)
[INFO] AutoMut: Effect of mutation residue number 56 from chain A (serine) into arginine:
Energy difference: 0.2021 kcal/mol, Difference in average score from the
base case: -0.1043 (00:03:39)
[INFO] Main: Simulation completed successfully. (00:03:44)
|
The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.
| residue index | residue name | chain | Aggrescan4D score | mutation |
|---|---|---|---|---|
| 1 | M | A | 0.2043 | |
| 2 | H | A | -0.7447 | |
| 3 | S | A | -0.9379 | |
| 4 | D | A | -2.0928 | |
| 5 | C | A | -1.3520 | |
| 6 | I | A | -1.2469 | |
| 7 | F | A | -1.8942 | |
| 8 | K | A | -2.9749 | |
| 9 | K | A | -2.6216 | |
| 10 | E | A | -1.7997 | |
| 11 | Q | A | -1.6924 | |
| 12 | A | A | -1.0743 | |
| 13 | M | A | -0.6088 | |
| 14 | C | A | 0.0000 | |
| 15 | L | A | -0.2815 | |
| 16 | E | A | -2.1654 | |
| 17 | K | A | -2.6167 | |
| 18 | I | A | -1.7965 | |
| 19 | Q | A | -2.8849 | |
| 20 | R | A | -3.1928 | |
| 21 | A | A | -1.8070 | |
| 22 | N | A | -1.8666 | |
| 23 | E | A | -2.2488 | |
| 24 | L | A | 0.1882 | |
| 25 | M | A | 0.0238 | |
| 26 | G | A | -0.9095 | |
| 27 | F | A | -1.3952 | |
| 28 | N | A | -2.4953 | |
| 29 | D | A | -2.5796 | |
| 30 | S | A | -1.5880 | |
| 31 | S | A | -1.2480 | |
| 32 | P | A | -1.4509 | |
| 33 | G | A | -1.5504 | |
| 34 | C | A | 0.0000 | |
| 35 | P | A | -0.9736 | |
| 36 | G | A | -0.7142 | |
| 37 | M | A | -0.1984 | |
| 38 | W | A | -0.1289 | |
| 39 | D | A | -0.8040 | |
| 40 | N | A | -1.5627 | |
| 41 | I | A | -0.4850 | |
| 42 | T | A | 0.0000 | |
| 43 | C | A | -0.1392 | |
| 44 | W | A | 0.0000 | |
| 45 | K | A | -1.0128 | |
| 46 | P | A | 0.0000 | |
| 47 | A | A | 0.0000 | |
| 48 | H | A | -1.2314 | |
| 49 | V | A | -1.0339 | |
| 50 | G | A | -0.9621 | |
| 51 | E | A | -0.5915 | |
| 52 | M | A | 0.3948 | |
| 53 | V | A | 0.0000 | |
| 54 | L | A | 1.8562 | |
| 55 | V | A | 1.0968 | |
| 56 | S | A | 0.3112 | |
| 57 | C | A | 0.0000 | |
| 58 | P | A | -0.6733 | |
| 59 | E | A | -1.5731 | |
| 60 | L | A | 0.0000 | |
| 61 | F | A | 0.0000 | |
| 62 | R | A | -0.6537 | |
| 63 | I | A | 1.5031 | |
| 64 | F | A | 1.4051 | |
| 65 | N | A | -0.7278 | |
| 66 | P | A | -1.3240 | |
| 67 | D | A | -2.5556 | |
| 68 | Q | A | -2.2497 | |
| 69 | D | A | -2.5088 | |
| 70 | M | A | -0.2654 | |
| 71 | G | A | 0.0000 | |
| 72 | V | A | 0.9646 | |
| 73 | V | A | 0.0000 | |
| 74 | S | A | 0.9502 | |
| 75 | R | A | 0.0169 | |
| 76 | N | A | -0.8380 | |
| 77 | C | A | 0.0000 | |
| 78 | T | A | -1.8350 | |
| 79 | E | A | -2.8555 | |
| 80 | D | A | -2.6392 | |
| 81 | G | A | -1.8527 | |
| 82 | W | A | -1.0662 | |
| 83 | S | A | -1.2318 | |
| 84 | E | A | -1.5498 | |
| 85 | P | A | -0.3009 | |
| 86 | F | A | 0.9622 | |
| 87 | P | A | 0.1997 | |
| 88 | H | A | -0.6715 | |
| 89 | Y | A | 0.0000 | |
| 90 | F | A | -0.3330 | |
| 91 | D | A | -1.3476 | |
| 92 | A | A | 0.0000 | |
| 93 | C | A | 0.0000 | |
| 94 | G | A | -1.4616 | |
| 95 | F | A | 0.0000 | |
| 96 | D | A | -3.2786 | |
| 97 | E | A | -3.2521 | |
| 98 | Y | A | -2.4238 | |
| 99 | E | A | -3.8780 | |
| 100 | S | A | -3.7598 | |
| 101 | E | A | -4.0211 | |
| 102 | T | A | -2.9074 | |
| 103 | G | A | -3.1834 | |
| 104 | D | A | -3.9662 | |
| 105 | Q | A | -3.5075 | |
| 106 | D | A | -3.2437 |
Automated mutations analysis - charged mutations
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 |
|||
| VK72A | -0.539 | -0.0727 | View | CSV | PDB |
| IR63A | -0.0453 | -0.1148 | View | CSV | PDB |
| IK63A | -0.0176 | -0.1096 | View | CSV | PDB |
| MR52A | -0.16 | -0.0859 | View | CSV | PDB |
| MK52A | -0.2208 | -0.074 | View | CSV | PDB |
| VR72A | -0.0355 | -0.0894 | View | CSV | PDB |
| LK54A | 0.0088 | -0.1143 | View | CSV | PDB |
| VR55A | 0.0624 | -0.07 | View | CSV | PDB |
| SR56A | 0.2021 | -0.1043 | View | CSV | PDB |
| SK56A | 0.269 | -0.0996 | View | CSV | PDB |
| FR86A | 0.3146 | -0.0922 | View | CSV | PDB |
| FK86A | 0.5809 | -0.143 | View | CSV | PDB |
| LE54A | 0.4631 | -0.1139 | View | CSV | PDB |
| FR64A | 0.2792 | -0.0583 | View | CSV | PDB |
| FK64A | 0.7586 | -0.0862 | View | CSV | PDB |
| VK55A | 1.1031 | -0.0335 | 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