| Chain sequence(s) |
A: EVQLVESGGGLVQPGGSLRLSCAASGRTFSSYVMGWLRQAPGKEREFVAAINWGGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRPEDTAVYYCNAVSIGAGNDYWGQGTLVTVSS
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 (00:00:59)
[INFO] AutoMut: Residue number 113 from chain A and a score of 1.657 omitted from automated
mutation (excluded by the user). (00:01:00)
[INFO] AutoMut: Residue number 101 from chain A and a score of 1.531 (isoleucine) selected
for automated mutation (00:01:00)
[INFO] AutoMut: Residue number 11 from chain A and a score of 1.314 omitted from automated
mutation (excluded by the user). (00:01:00)
[INFO] AutoMut: Residue number 5 from chain A and a score of 1.210 omitted from automated
mutation (excluded by the user). (00:01:00)
[INFO] AutoMut: Residue number 10 from chain A and a score of 0.666 omitted from automated
mutation (excluded by the user). (00:01:00)
[INFO] AutoMut: Residue number 59 from chain A and a score of 0.613 (tyrosine) selected for
automated mutation (00:01:00)
[INFO] AutoMut: Residue number 112 from chain A and a score of 0.598 omitted from automated
mutation (excluded by the user). (00:01:00)
[INFO] AutoMut: Residue number 50 from chain A and a score of 0.552 (alanine) selected for
automated mutation (00:01:00)
[INFO] AutoMut: Residue number 93 from chain A and a score of 0.499 omitted from automated
mutation (excluded by the user). (00:01:00)
[INFO] AutoMut: Residue number 33 from chain A and a score of 0.476 (valine) selected for
automated mutation (00:01:00)
[INFO] AutoMut: Residue number 53 from chain A and a score of 0.374 (tryptophan) selected
for automated mutation (00:01:00)
[INFO] AutoMut: Residue number 100 from chain A and a score of 0.370 (serine) selected for
automated mutation (00:01:00)
[INFO] AutoMut: Mutating residue number 101 from chain A (isoleucine) into glutamic acid (00:01:00)
[INFO] AutoMut: Mutating residue number 101 from chain A (isoleucine) into aspartic acid (00:01:00)
[INFO] AutoMut: Mutating residue number 59 from chain A (tyrosine) into glutamic acid (00:01:00)
[INFO] AutoMut: Mutating residue number 101 from chain A (isoleucine) into arginine (00:01:05)
[INFO] AutoMut: Mutating residue number 101 from chain A (isoleucine) into lysine (00:01:07)
[INFO] AutoMut: Mutating residue number 59 from chain A (tyrosine) into aspartic acid (00:01:14)
[INFO] AutoMut: Mutating residue number 50 from chain A (alanine) into glutamic acid (00:01:16)
[INFO] AutoMut: Mutating residue number 50 from chain A (alanine) into lysine (00:01:23)
[INFO] AutoMut: Mutating residue number 59 from chain A (tyrosine) into lysine (00:01:27)
[INFO] AutoMut: Mutating residue number 50 from chain A (alanine) into aspartic acid (00:01:29)
[INFO] AutoMut: Mutating residue number 59 from chain A (tyrosine) into arginine (00:01:32)
[INFO] AutoMut: Mutating residue number 50 from chain A (alanine) into arginine (00:01:37)
[INFO] AutoMut: Mutating residue number 33 from chain A (valine) into glutamic acid (00:01:44)
[INFO] AutoMut: Mutating residue number 33 from chain A (valine) into aspartic acid (00:01:55)
[INFO] AutoMut: Mutating residue number 33 from chain A (valine) into lysine (00:01:56)
[INFO] AutoMut: Mutating residue number 33 from chain A (valine) into arginine (00:02:04)
[INFO] AutoMut: Mutating residue number 53 from chain A (tryptophan) into glutamic acid (00:02:08)
[INFO] AutoMut: Mutating residue number 53 from chain A (tryptophan) into lysine (00:02:16)
[INFO] AutoMut: Mutating residue number 53 from chain A (tryptophan) into aspartic acid (00:02:23)
[INFO] AutoMut: Mutating residue number 100 from chain A (serine) into glutamic acid (00:02:24)
[INFO] AutoMut: Mutating residue number 100 from chain A (serine) into aspartic acid (00:02:24)
[INFO] AutoMut: Mutating residue number 53 from chain A (tryptophan) into arginine (00:02:31)
[INFO] AutoMut: Mutating residue number 100 from chain A (serine) into arginine (00:02:32)
[INFO] AutoMut: Mutating residue number 100 from chain A (serine) into lysine (00:02:32)
[INFO] AutoMut: Effect of mutation residue number 101 from chain A (isoleucine) into
glutamic acid: Energy difference: 0.1691 kcal/mol, Difference in average
score from the base case: -0.1147 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 101 from chain A (isoleucine) into
lysine: Energy difference: 0.2826 kcal/mol, Difference in average score
from the base case: -0.1108 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 101 from chain A (isoleucine) into
aspartic acid: Energy difference: 0.5953 kcal/mol, Difference in average
score from the base case: -0.1088 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 101 from chain A (isoleucine) into
arginine: Energy difference: 0.5048 kcal/mol, Difference in average score
from the base case: -0.1181 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 59 from chain A (tyrosine) into glutamic
acid: Energy difference: 0.5358 kcal/mol, Difference in average score from
the base case: -0.0975 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 59 from chain A (tyrosine) into lysine:
Energy difference: 0.4038 kcal/mol, Difference in average score from the
base case: -0.0750 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 59 from chain A (tyrosine) into aspartic
acid: Energy difference: 0.5767 kcal/mol, Difference in average score from
the base case: -0.0899 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 59 from chain A (tyrosine) into arginine:
Energy difference: -1.6196 kcal/mol, Difference in average score from the
base case: -0.1054 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 50 from chain A (alanine) into glutamic
acid: Energy difference: -0.4392 kcal/mol, Difference in average score from
the base case: -0.0305 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 50 from chain A (alanine) into lysine:
Energy difference: 0.8503 kcal/mol, Difference in average score from the
base case: -0.0279 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 50 from chain A (alanine) into aspartic
acid: Energy difference: 3.8676 kcal/mol, Difference in average score from
the base case: -0.0067 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 50 from chain A (alanine) into arginine:
Energy difference: -0.5939 kcal/mol, Difference in average score from the
base case: -0.0397 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 33 from chain A (valine) into glutamic
acid: Energy difference: 1.3602 kcal/mol, Difference in average score from
the base case: -0.0299 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 33 from chain A (valine) into lysine:
Energy difference: 0.3983 kcal/mol, Difference in average score from the
base case: -0.0246 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 33 from chain A (valine) into aspartic
acid: Energy difference: 2.8797 kcal/mol, Difference in average score from
the base case: -0.0158 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 33 from chain A (valine) into arginine:
Energy difference: -0.5994 kcal/mol, Difference in average score from the
base case: -0.0388 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 53 from chain A (tryptophan) into
glutamic acid: Energy difference: 1.0925 kcal/mol, Difference in average
score from the base case: -0.0770 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 53 from chain A (tryptophan) into lysine:
Energy difference: 1.2379 kcal/mol, Difference in average score from the
base case: -0.0761 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 53 from chain A (tryptophan) into
aspartic acid: Energy difference: 1.3707 kcal/mol, Difference in average
score from the base case: -0.0920 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 53 from chain A (tryptophan) into
arginine: Energy difference: 0.7710 kcal/mol, Difference in average score
from the base case: -0.0846 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 100 from chain A (serine) into glutamic
acid: Energy difference: 0.0839 kcal/mol, Difference in average score from
the base case: -0.0121 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 100 from chain A (serine) into lysine:
Energy difference: 0.2143 kcal/mol, Difference in average score from the
base case: -0.0138 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 100 from chain A (serine) into aspartic
acid: Energy difference: -0.8172 kcal/mol, Difference in average score from
the base case: -0.0103 (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 100 from chain A (serine) into arginine:
Energy difference: -0.4126 kcal/mol, Difference in average score from the
base case: -0.0308 (00:02:52)
[INFO] Main: Simulation completed successfully. (00:02:59)
|
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 | E | A | -2.4797 | |
| 2 | V | A | -1.6589 | |
| 3 | Q | A | -1.5238 | |
| 4 | L | A | 0.0000 | |
| 5 | V | A | 1.2096 | |
| 6 | E | A | 0.0000 | |
| 7 | S | A | -0.1446 | |
| 8 | G | A | -0.6329 | |
| 9 | G | A | 0.0984 | |
| 10 | G | A | 0.6665 | |
| 11 | L | A | 1.3139 | |
| 12 | V | A | 0.0000 | |
| 13 | Q | A | -1.5404 | |
| 14 | P | A | -1.8633 | |
| 15 | G | A | -1.5731 | |
| 16 | G | A | -1.0303 | |
| 17 | S | A | -1.3148 | |
| 18 | L | A | -0.9182 | |
| 19 | R | A | -2.1027 | |
| 20 | L | A | 0.0000 | |
| 21 | S | A | -0.3188 | |
| 22 | C | A | 0.0000 | |
| 23 | A | A | 0.0006 | |
| 24 | A | A | 0.0000 | |
| 25 | S | A | -1.6236 | |
| 26 | G | A | -2.2788 | |
| 27 | R | A | -2.6023 | |
| 28 | T | A | -1.4573 | |
| 29 | F | A | 0.0000 | |
| 30 | S | A | -0.9816 | |
| 31 | S | A | 0.1765 | |
| 32 | Y | A | 0.0000 | |
| 33 | V | A | 0.4761 | |
| 34 | M | A | 0.0000 | |
| 35 | G | A | 0.0000 | |
| 36 | W | A | 0.0000 | |
| 37 | L | A | -0.0244 | |
| 38 | R | A | -0.8434 | |
| 39 | Q | A | -1.7751 | |
| 40 | A | A | -1.7650 | |
| 41 | P | A | -1.4601 | |
| 42 | G | A | -1.9879 | |
| 43 | K | A | -3.3904 | |
| 44 | E | A | -3.5530 | |
| 45 | R | A | -2.7159 | |
| 46 | E | A | -1.7812 | |
| 47 | F | A | -0.0211 | |
| 48 | V | A | 0.0000 | |
| 49 | A | A | 0.0000 | |
| 50 | A | A | 0.5522 | |
| 51 | I | A | 0.0000 | |
| 52 | N | A | -0.0659 | |
| 53 | W | A | 0.3738 | |
| 54 | G | A | -0.7758 | |
| 55 | G | A | -1.0750 | |
| 56 | G | A | -0.7841 | |
| 57 | S | A | -0.2770 | |
| 58 | T | A | 0.2431 | |
| 59 | Y | A | 0.6126 | |
| 60 | Y | A | -0.2880 | |
| 61 | A | A | -1.0309 | |
| 62 | D | A | -2.2961 | |
| 63 | S | A | -1.6580 | |
| 64 | V | A | 0.0000 | |
| 65 | K | A | -2.5313 | |
| 66 | G | A | -1.8168 | |
| 67 | R | A | -1.6154 | |
| 68 | F | A | 0.0000 | |
| 69 | T | A | -0.7602 | |
| 70 | I | A | 0.0000 | |
| 71 | S | A | -0.5598 | |
| 72 | R | A | -1.2461 | |
| 73 | D | A | -1.8687 | |
| 74 | N | A | -2.4681 | |
| 75 | S | A | -1.9283 | |
| 76 | K | A | -2.4957 | |
| 77 | N | A | -2.1657 | |
| 78 | T | A | 0.0000 | |
| 79 | L | A | 0.0000 | |
| 80 | Y | A | -0.5296 | |
| 81 | L | A | 0.0000 | |
| 82 | Q | A | -1.2355 | |
| 83 | M | A | 0.0000 | |
| 84 | N | A | -1.5023 | |
| 85 | S | A | -1.4171 | |
| 86 | L | A | 0.0000 | |
| 87 | R | A | -3.0270 | |
| 88 | P | A | -2.2488 | |
| 89 | E | A | -2.5451 | |
| 90 | D | A | 0.0000 | |
| 91 | T | A | -0.6142 | |
| 92 | A | A | 0.0000 | |
| 93 | V | A | 0.4990 | |
| 94 | Y | A | 0.0000 | |
| 95 | Y | A | 0.2078 | |
| 96 | C | A | 0.0000 | |
| 97 | N | A | -0.0727 | |
| 98 | A | A | 0.0000 | |
| 99 | V | A | 0.0689 | |
| 100 | S | A | 0.3700 | |
| 101 | I | A | 1.5313 | |
| 102 | G | A | 0.2810 | |
| 103 | A | A | -0.3502 | |
| 104 | G | A | -0.9608 | |
| 105 | N | A | -1.5908 | |
| 106 | D | A | -1.7264 | |
| 107 | Y | A | -0.7997 | |
| 108 | W | A | 0.0156 | |
| 109 | G | A | 0.0087 | |
| 110 | Q | A | -0.8162 | |
| 111 | G | A | 0.1282 | |
| 112 | T | A | 0.5980 | |
| 113 | L | A | 1.6567 | |
| 114 | V | A | 0.0000 | |
| 115 | T | A | 0.2088 | |
| 116 | V | A | 0.0000 | |
| 117 | S | A | -0.8969 | |
| 118 | S | A | -0.5213 |
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 |
|||
| YR59A | -1.6196 | -0.1054 | View | CSV | PDB |
| AR50A | -0.5939 | -0.0397 | View | CSV | PDB |
| VR33A | -0.5994 | -0.0388 | View | CSV | PDB |
| AE50A | -0.4392 | -0.0305 | View | CSV | PDB |
| SR100A | -0.4126 | -0.0308 | View | CSV | PDB |
| SD100A | -0.8172 | -0.0103 | View | CSV | PDB |
| IE101A | 0.1691 | -0.1147 | View | CSV | PDB |
| IK101A | 0.2826 | -0.1108 | View | CSV | PDB |
| YK59A | 0.4038 | -0.075 | View | CSV | PDB |
| WR53A | 0.771 | -0.0846 | View | CSV | PDB |
| WE53A | 1.0925 | -0.077 | View | CSV | PDB |
| VK33A | 0.3983 | -0.0246 | 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