| Chain sequence(s) |
A: TSESGELHGLTTEEEFVEGIYKVEIDTKSYWKALGISPFHEHAEVVFTANDSGPRRYTIAALLSPYSYSTTAVVTNPKE
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] (00:00:00)
[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 A chain(s) selected (00:00:00)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:00)
[INFO] FoldX: Starting FoldX energy minimization (00:00:00)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:00:46)
[INFO] AutoMutEv:Residue number 73 from chain A and a score of 2.098 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 66 from chain A and a score of 1.834 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 20 from chain A and a score of 1.782 (isoleucine) selected
for automated mutation (00:00:47)
[INFO] AutoMutEv:Residue number 74 from chain A and a score of 1.526 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 39 from chain A and a score of 1.520 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 47 from chain A and a score of 1.386 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 46 from chain A and a score of 1.254 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 72 from chain A and a score of 1.139 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 67 from chain A and a score of 1.086 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 10 from chain A and a score of 0.957 (leucine) selected for
automated mutation (00:00:47)
[INFO] AutoMutEv:Residue number 62 from chain A and a score of 0.953 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 21 from chain A and a score of 0.919 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 68 from chain A and a score of 0.776 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 65 from chain A and a score of 0.623 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 64 from chain A and a score of 0.597 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 69 from chain A and a score of 0.473 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 71 from chain A and a score of 0.449 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 48 from chain A and a score of 0.386 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 34 from chain A and a score of 0.375 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 38 from chain A and a score of 0.189 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 19 from chain A and a score of 0.157 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 57 from chain A and a score of 0.133 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 58 from chain A and a score of 0.071 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 27 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 31 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 43 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 49 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 50 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 59 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 61 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 63 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 70 from chain A and a score of -0.035 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 37 from chain A and a score of -0.041 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 36 from chain A and a score of -0.057 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Residue number 1 from chain A and a score of -0.119 omitted from automated
mutation (excluded by the user). (00:00:47)
[INFO] AutoMutEv:Mutating residue number 20 from chain A (isoleucine) into threonine (00:00:47)
[INFO] AutoMutEv:Mutating residue number 20 from chain A (isoleucine) into methionine (00:00:47)
[INFO] AutoMutEv:Mutating residue number 20 from chain A (isoleucine) into leucine (00:00:47)
[INFO] AutoMutEv:Mutating residue number 10 from chain A (leucine) into methionine (00:00:51)
[INFO] AutoMutEv:Effect of mutation residue number 20 from chain A (isoleucine) into
threonine: Energy difference: 0.5079 kcal/mol, Difference in average score
from the base case: -0.0955 (00:00:57)
[INFO] AutoMutEv:Effect of mutation residue number 20 from chain A (isoleucine) into
methionine: Energy difference: 0.1370 kcal/mol, Difference in average score
from the base case: -0.0534 (00:00:57)
[INFO] AutoMutEv:Effect of mutation residue number 20 from chain A (isoleucine) into
leucine: Energy difference: -0.2298 kcal/mol, Difference in average score
from the base case: -0.0347 (00:00:57)
[INFO] AutoMutEv:Effect of mutation residue number 10 from chain A (leucine) into
methionine: Energy difference: -0.7104 kcal/mol, Difference in average
score from the base case: -0.0289 (00:00:57)
[INFO] Main: Simulation completed successfully. (00:00:59)
|
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 | T | A | -0.1191 | |
| 2 | S | A | -0.2952 | |
| 3 | E | A | -0.4755 | |
| 4 | S | A | -0.4359 | |
| 5 | G | A | -1.0252 | |
| 6 | E | A | -1.8622 | |
| 7 | L | A | -0.7864 | |
| 8 | H | A | -1.2615 | |
| 9 | G | A | -0.5332 | |
| 10 | L | A | 0.9565 | |
| 11 | T | A | -0.4739 | |
| 12 | T | A | -1.6557 | |
| 13 | E | A | -3.0890 | |
| 14 | E | A | -3.1494 | |
| 15 | E | A | -2.8300 | |
| 16 | F | A | -1.4105 | |
| 17 | V | A | -0.4070 | |
| 18 | E | A | -1.4737 | |
| 19 | G | A | 0.1566 | |
| 20 | I | A | 1.7820 | |
| 21 | Y | A | 0.9187 | |
| 22 | K | A | -0.8987 | |
| 23 | V | A | -1.1874 | |
| 24 | E | A | -2.7699 | |
| 25 | I | A | -2.3521 | |
| 26 | D | A | -3.0362 | |
| 27 | T | A | 0.0000 | |
| 28 | K | A | -2.3174 | |
| 29 | S | A | -1.6264 | |
| 30 | Y | A | -0.6749 | |
| 31 | W | A | 0.0000 | |
| 32 | K | A | -1.4857 | |
| 33 | A | A | -0.3703 | |
| 34 | L | A | 0.3753 | |
| 35 | G | A | -0.3721 | |
| 36 | I | A | -0.0568 | |
| 37 | S | A | -0.0410 | |
| 38 | P | A | 0.1894 | |
| 39 | F | A | 1.5204 | |
| 40 | H | A | -0.7195 | |
| 41 | E | A | -2.5273 | |
| 42 | H | A | -2.5944 | |
| 43 | A | A | 0.0000 | |
| 44 | E | A | -2.3401 | |
| 45 | V | A | -0.3914 | |
| 46 | V | A | 1.2539 | |
| 47 | F | A | 1.3860 | |
| 48 | T | A | 0.3858 | |
| 49 | A | A | 0.0000 | |
| 50 | N | A | 0.0000 | |
| 51 | D | A | -2.1829 | |
| 52 | S | A | -1.5527 | |
| 53 | G | A | -1.3884 | |
| 54 | P | A | -1.8862 | |
| 55 | R | A | -1.8555 | |
| 56 | R | A | -1.8377 | |
| 57 | Y | A | 0.1329 | |
| 58 | T | A | 0.0711 | |
| 59 | I | A | 0.0000 | |
| 60 | A | A | -0.2933 | |
| 61 | A | A | 0.0000 | |
| 62 | L | A | 0.9533 | |
| 63 | L | A | 0.0000 | |
| 64 | S | A | 0.5969 | |
| 65 | P | A | 0.6232 | |
| 66 | Y | A | 1.8339 | |
| 67 | S | A | 1.0857 | |
| 68 | Y | A | 0.7764 | |
| 69 | S | A | 0.4727 | |
| 70 | T | A | -0.0351 | |
| 71 | T | A | 0.4485 | |
| 72 | A | A | 1.1388 | |
| 73 | V | A | 2.0980 | |
| 74 | V | A | 1.5260 | |
| 75 | T | A | -0.2391 | |
| 76 | N | A | -1.9587 | |
| 77 | P | A | -2.0627 | |
| 78 | K | A | -3.0151 | |
| 79 | E | A | -2.8114 |
Automated mutations analysis - evolutionary conserved mutations
In the automated mutations mode, the server selects aggregation prone resides
and each selected residue is mutated based off an evolutionary approach.
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 |
|||
| LM10A | -0.7104 | -0.0289 | View | CSV | PDB |
| IL20A | -0.2298 | -0.0347 | View | CSV | PDB |
| IM20A | 0.137 | -0.0534 | 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