| Chain sequence(s) |
B: EVQLVESGGGLVQPGGSLRLSCAASGRTFSYNPMGWFRQAPGKGRELVAAISRTGGSTYYPDSVEGRFTISRDNAKRMVYLQMNSLRAEDTAVYYCAAAGVRAEDGRVRTLPSEYTFWGQGTQVTVSS
input PDB |
| Selected Chain(s) | B |
| 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 B 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 (00:00:48)
[INFO] AutoMutEv:Residue number 112 from chain B and a score of 1.274 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 12 from chain B and a score of 1.021 (leucine) selected for
automated mutation (00:00:49)
[INFO] AutoMutEv:Residue number 111 from chain B and a score of 0.531 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 6 from chain B and a score of 0.215 (valine) selected for
automated mutation (00:00:49)
[INFO] AutoMutEv:Residue number 117 from chain B and a score of 0.137 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 60 from chain B and a score of 0.104 (tyrosine) selected for
automated mutation (00:00:49)
[INFO] AutoMutEv:Residue number 119 from chain B and a score of 0.103 (tryptophan) selected
for automated mutation (00:00:49)
[INFO] AutoMutEv:Residue number 114 from chain B and a score of 0.098 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 3 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 5 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 21 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 23 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 25 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 30 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 33 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 34 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 35 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 36 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 37 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 38 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 39 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 48 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 49 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 50 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 51 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 52 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 53 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 65 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 68 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 69 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 71 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 80 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 82 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 84 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 87 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 91 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 93 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 95 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 96 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 97 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 98 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 99 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 100 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 110 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 116 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 125 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 127 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 11 from chain B and a score of -0.019 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 13 from chain B and a score of -0.029 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 113 from chain B and a score of -0.050 omitted from
automated mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 32 from chain B and a score of -0.078 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 115 from chain B and a score of -0.107 omitted from
automated mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 118 from chain B and a score of -0.126 omitted from
automated mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Mutating residue number 12 from chain B (leucine) into methionine (00:00:49)
[INFO] AutoMutEv:Mutating residue number 6 from chain B (valine) into threonine (00:00:49)
[INFO] AutoMutEv:Mutating residue number 6 from chain B (valine) into alanine (00:00:49)
[INFO] AutoMutEv:Mutating residue number 6 from chain B (valine) into methionine (00:00:53)
[INFO] AutoMutEv:Mutating residue number 60 from chain B (tyrosine) into histidine (00:00:53)
[INFO] AutoMutEv:Mutating residue number 60 from chain B (tyrosine) into cysteine (00:00:54)
[INFO] AutoMutEv:Mutating residue number 60 from chain B (tyrosine) into tryptophan (00:00:59)
[INFO] AutoMutEv:Mutating residue number 119 from chain B (tryptophan) into arginine (00:01:00)
[INFO] AutoMutEv:Effect of mutation residue number 12 from chain B (leucine) into
methionine: Energy difference: -0.0683 kcal/mol, Difference in average
score from the base case: -0.0139 (00:01:07)
[INFO] AutoMutEv:Effect of mutation residue number 6 from chain B (valine) into threonine:
Energy difference: 0.7575 kcal/mol, Difference in average score from the
base case: -0.0154 (00:01:07)
[INFO] AutoMutEv:Effect of mutation residue number 6 from chain B (valine) into alanine:
Energy difference: 1.1323 kcal/mol, Difference in average score from the
base case: -0.0129 (00:01:07)
[INFO] AutoMutEv:Effect of mutation residue number 6 from chain B (valine) into methionine:
Energy difference: -0.1207 kcal/mol, Difference in average score from the
base case: -0.0027 (00:01:07)
[INFO] AutoMutEv:Effect of mutation residue number 60 from chain B (tyrosine) into
histidine: Energy difference: 1.2329 kcal/mol, Difference in average score
from the base case: -0.0233 (00:01:07)
[INFO] AutoMutEv:Effect of mutation residue number 60 from chain B (tyrosine) into cysteine:
Energy difference: 1.7211 kcal/mol, Difference in average score from the
base case: -0.0066 (00:01:07)
[INFO] AutoMutEv:Effect of mutation residue number 60 from chain B (tyrosine) into
tryptophan: Energy difference: -0.8314 kcal/mol, Difference in average
score from the base case: -0.0019 (00:01:07)
[INFO] AutoMutEv:Effect of mutation residue number 119 from chain B (tryptophan) into
arginine: Energy difference: 1.8409 kcal/mol, Difference in average score
from the base case: -0.0429 (00:01:07)
[INFO] Main: Simulation completed successfully. (00:01:10)
|
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 |
|---|---|---|---|---|
| 2 | E | B | -2.6620 | |
| 3 | V | B | 0.0000 | |
| 4 | Q | B | -1.7940 | |
| 5 | L | B | 0.0000 | |
| 6 | V | B | 0.2151 | |
| 7 | E | B | -0.3044 | |
| 8 | S | B | -0.8786 | |
| 9 | G | B | -1.2588 | |
| 10 | G | B | -0.8318 | |
| 11 | G | B | -0.0190 | |
| 12 | L | B | 1.0214 | |
| 13 | V | B | -0.0295 | |
| 14 | Q | B | -1.3278 | |
| 15 | P | B | -1.5290 | |
| 16 | G | B | -1.3710 | |
| 17 | G | B | -0.8766 | |
| 18 | S | B | -1.0895 | |
| 19 | L | B | -1.0303 | |
| 20 | R | B | -2.2822 | |
| 21 | L | B | 0.0000 | |
| 22 | S | B | -0.5877 | |
| 23 | C | B | 0.0000 | |
| 24 | A | B | -0.5109 | |
| 25 | A | B | 0.0000 | |
| 26 | S | B | -1.5344 | |
| 27 | G | B | -2.2471 | |
| 28 | R | B | -2.6509 | |
| 29 | T | B | -1.7268 | |
| 30 | F | B | 0.0000 | |
| 31 | S | B | -0.6714 | |
| 32 | Y | B | -0.0782 | |
| 33 | N | B | 0.0000 | |
| 34 | P | B | 0.0000 | |
| 35 | M | B | 0.0000 | |
| 36 | G | B | 0.0000 | |
| 37 | W | B | 0.0000 | |
| 38 | F | B | 0.0000 | |
| 39 | R | B | 0.0000 | |
| 40 | Q | B | -1.7760 | |
| 41 | A | B | -1.5572 | |
| 42 | P | B | -1.1967 | |
| 43 | G | B | -1.6803 | |
| 44 | K | B | -2.6989 | |
| 45 | G | B | -2.3836 | |
| 46 | R | B | -2.5185 | |
| 47 | E | B | -2.1743 | |
| 48 | L | B | 0.0000 | |
| 49 | V | B | 0.0000 | |
| 50 | A | B | 0.0000 | |
| 51 | A | B | 0.0000 | |
| 52 | I | B | 0.0000 | |
| 53 | S | B | 0.0000 | |
| 54 | R | B | -1.1508 | |
| 55 | T | B | -0.8047 | |
| 56 | G | B | -0.9511 | |
| 57 | G | B | -0.9807 | |
| 58 | S | B | -0.7504 | |
| 59 | T | B | -0.2192 | |
| 60 | Y | B | 0.1041 | |
| 61 | Y | B | -0.7574 | |
| 62 | P | B | -1.4870 | |
| 63 | D | B | -2.5538 | |
| 64 | S | B | -1.6375 | |
| 65 | V | B | 0.0000 | |
| 66 | E | B | -2.6586 | |
| 67 | G | B | -1.7356 | |
| 68 | R | B | 0.0000 | |
| 69 | F | B | 0.0000 | |
| 70 | T | B | -0.8651 | |
| 71 | I | B | 0.0000 | |
| 72 | S | B | -0.5256 | |
| 73 | R | B | -0.9707 | |
| 74 | D | B | -1.3933 | |
| 75 | N | B | -1.5082 | |
| 76 | A | B | -1.3241 | |
| 77 | K | B | -2.4187 | |
| 78 | R | B | -1.9706 | |
| 79 | M | B | -1.0227 | |
| 80 | V | B | 0.0000 | |
| 81 | Y | B | -0.6625 | |
| 82 | L | B | 0.0000 | |
| 83 | Q | B | -1.5935 | |
| 84 | M | B | 0.0000 | |
| 85 | N | B | -1.2863 | |
| 86 | S | B | -1.1343 | |
| 87 | L | B | 0.0000 | |
| 88 | R | B | -2.2484 | |
| 89 | A | B | -1.7384 | |
| 90 | E | B | -2.2188 | |
| 91 | D | B | 0.0000 | |
| 92 | T | B | -0.8411 | |
| 93 | A | B | 0.0000 | |
| 94 | V | B | -0.5941 | |
| 95 | Y | B | 0.0000 | |
| 96 | Y | B | 0.0000 | |
| 97 | C | B | 0.0000 | |
| 98 | A | B | 0.0000 | |
| 99 | A | B | 0.0000 | |
| 100 | A | B | 0.0000 | |
| 101 | G | B | -0.6504 | |
| 102 | V | B | -0.6089 | |
| 103 | R | B | -2.2470 | |
| 104 | A | B | -2.0248 | |
| 105 | E | B | -2.7851 | |
| 106 | D | B | -2.4001 | |
| 107 | G | B | -2.0657 | |
| 108 | R | B | -2.3453 | |
| 109 | V | B | -0.6278 | |
| 110 | R | B | 0.0000 | |
| 111 | T | B | 0.5311 | |
| 112 | L | B | 1.2745 | |
| 113 | P | B | -0.0503 | |
| 114 | S | B | 0.0979 | |
| 115 | E | B | -0.1070 | |
| 116 | Y | B | 0.0000 | |
| 117 | T | B | 0.1370 | |
| 118 | F | B | -0.1258 | |
| 119 | W | B | 0.1031 | |
| 120 | G | B | -0.4268 | |
| 121 | Q | B | -1.1151 | |
| 122 | G | B | -0.8059 | |
| 123 | T | B | -0.9376 | |
| 124 | Q | B | -1.0567 | |
| 125 | V | B | 0.0000 | |
| 126 | T | B | -0.2980 | |
| 127 | V | B | 0.0000 | |
| 128 | S | B | -0.8031 | |
| 129 | S | B | -0.7229 |
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 |
|||
| LM12B | -0.0683 | -0.0139 | View | CSV | PDB |
| YW60B | -0.8314 | -0.0019 | View | CSV | PDB |
| VM6B | -0.1207 | -0.0027 | View | CSV | PDB |
| WR119B | 1.8409 | -0.0429 | View | CSV | PDB |
| VT6B | 0.7575 | -0.0154 | View | CSV | PDB |
| YH60B | 1.2329 | -0.0233 | 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