| Chain sequence(s) |
A: GQVRQRYLYTDDAQQTEAHLEIREDGTVGGAADQSPESLLQLKALKPGVIQILGVKTSRFLCQRPDGALYGSLHFDPEACSFRELLLEDGYNVYQSEAHGLPLHLPGNKSPHRDPAPRGPARFLPLPG
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 (00:02:07)
[INFO] AutoMutEv:Residue number 86 from chain A and a score of 1.258 (leucine) selected for
automated mutation (00:02:07)
[INFO] AutoMutEv:Residue number 99 from chain A and a score of 1.020 (leucine) selected for
automated mutation (00:02:07)
[INFO] AutoMutEv:Residue number 88 from chain A and a score of 0.786 (phenylalanine)
selected for automated mutation (00:02:07)
[INFO] AutoMutEv:Residue number 73 from chain A and a score of 0.719 (phenylalanine)
selected for automated mutation (00:02:07)
[INFO] AutoMutEv:Residue number 98 from chain A and a score of 0.504 (leucine) selected for
automated mutation (00:02:07)
[INFO] AutoMutEv:Residue number 66 from chain A and a score of 0.307 (leucine) selected for
automated mutation (00:02:07)
[INFO] AutoMutEv:Mutating residue number 86 from chain A (leucine) into methionine (00:02:07)
[INFO] AutoMutEv:Mutating residue number 99 from chain A (leucine) into methionine (00:02:07)
[INFO] AutoMutEv:Mutating residue number 88 from chain A (phenylalanine) into methionine (00:02:07)
[INFO] AutoMutEv:Mutating residue number 88 from chain A (phenylalanine) into tryptophan (00:02:13)
[INFO] AutoMutEv:Mutating residue number 88 from chain A (phenylalanine) into tyrosine (00:02:14)
[INFO] AutoMutEv:Mutating residue number 73 from chain A (phenylalanine) into methionine (00:02:15)
[INFO] AutoMutEv:Mutating residue number 73 from chain A (phenylalanine) into tryptophan (00:02:19)
[INFO] AutoMutEv:Mutating residue number 73 from chain A (phenylalanine) into tyrosine (00:02:19)
[INFO] AutoMutEv:Mutating residue number 98 from chain A (leucine) into methionine (00:02:25)
[INFO] AutoMutEv:Mutating residue number 66 from chain A (leucine) into methionine (00:02:25)
[INFO] AutoMutEv:Effect of mutation residue number 86 from chain A (leucine) into
methionine: Energy difference: 0.0394 kcal/mol, Difference in average score
from the base case: -0.0164 (00:02:44)
[INFO] AutoMutEv:Effect of mutation residue number 99 from chain A (leucine) into
methionine: Energy difference: 0.1206 kcal/mol, Difference in average score
from the base case: -0.0040 (00:02:44)
[INFO] AutoMutEv:Effect of mutation residue number 88 from chain A (phenylalanine) into
methionine: Energy difference: 0.2337 kcal/mol, Difference in average score
from the base case: -0.0283 (00:02:44)
[INFO] AutoMutEv:Effect of mutation residue number 88 from chain A (phenylalanine) into
tryptophan: Energy difference: 0.5893 kcal/mol, Difference in average score
from the base case: -0.0131 (00:02:44)
[INFO] AutoMutEv:Effect of mutation residue number 88 from chain A (phenylalanine) into
tyrosine: Energy difference: 0.3607 kcal/mol, Difference in average score
from the base case: -0.0174 (00:02:44)
[INFO] AutoMutEv:Effect of mutation residue number 73 from chain A (phenylalanine) into
methionine: Energy difference: 0.8825 kcal/mol, Difference in average score
from the base case: -0.0056 (00:02:44)
[INFO] AutoMutEv:Effect of mutation residue number 73 from chain A (phenylalanine) into
tryptophan: Energy difference: 1.5528 kcal/mol, Difference in average score
from the base case: -0.0129 (00:02:44)
[INFO] AutoMutEv:Effect of mutation residue number 73 from chain A (phenylalanine) into
tyrosine: Energy difference: 0.2790 kcal/mol, Difference in average score
from the base case: -0.0074 (00:02:44)
[INFO] AutoMutEv:Effect of mutation residue number 98 from chain A (leucine) into
methionine: Energy difference: -0.1303 kcal/mol, Difference in average
score from the base case: 0.0049 (00:02:44)
[INFO] AutoMutEv:Effect of mutation residue number 66 from chain A (leucine) into
methionine: Energy difference: 1.0241 kcal/mol, Difference in average score
from the base case: 0.0028 (00:02:44)
[INFO] Main: Simulation completed successfully. (00:02:46)
|
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 |
|---|---|---|---|---|
| 14 | G | A | -1.2202 | |
| 15 | Q | A | -1.3553 | |
| 16 | V | A | -1.0825 | |
| 17 | R | A | -2.7306 | |
| 18 | Q | A | -2.3186 | |
| 19 | R | A | -1.5844 | |
| 20 | Y | A | -0.5414 | |
| 21 | L | A | 0.0000 | |
| 22 | Y | A | -0.8080 | |
| 23 | T | A | 0.0000 | |
| 24 | D | A | -2.4254 | |
| 25 | D | A | -3.2410 | |
| 26 | A | A | -2.9366 | |
| 27 | Q | A | -3.1800 | |
| 28 | Q | A | -2.7890 | |
| 29 | T | A | -2.3658 | |
| 30 | E | A | -3.3494 | |
| 31 | A | A | -2.4305 | |
| 32 | H | A | -1.5090 | |
| 33 | L | A | 0.0000 | |
| 34 | E | A | -1.5279 | |
| 35 | I | A | 0.0000 | |
| 36 | R | A | -3.7272 | |
| 37 | E | A | -3.9769 | |
| 38 | D | A | -3.3426 | |
| 39 | G | A | 0.0000 | |
| 40 | T | A | -1.6750 | |
| 41 | V | A | 0.0000 | |
| 42 | G | A | -0.8744 | |
| 43 | G | A | -1.4379 | |
| 44 | A | A | -1.3962 | |
| 45 | A | A | -1.5241 | |
| 46 | D | A | -2.6214 | |
| 47 | Q | A | -1.9359 | |
| 48 | S | A | -1.3237 | |
| 49 | P | A | -0.9316 | |
| 50 | E | A | -1.5211 | |
| 51 | S | A | 0.0000 | |
| 52 | L | A | -0.6874 | |
| 53 | L | A | 0.0000 | |
| 54 | Q | A | -0.9822 | |
| 55 | L | A | -1.1276 | |
| 56 | K | A | -1.0251 | |
| 57 | A | A | -0.8467 | |
| 58 | L | A | -0.5496 | |
| 59 | K | A | -1.8323 | |
| 60 | P | A | -1.3707 | |
| 61 | G | A | -1.5842 | |
| 62 | V | A | -1.6413 | |
| 63 | I | A | -0.7373 | |
| 64 | Q | A | 0.0000 | |
| 65 | I | A | 0.0000 | |
| 66 | L | A | 0.3072 | |
| 67 | G | A | 0.0000 | |
| 68 | V | A | -0.1731 | |
| 69 | K | A | -1.6596 | |
| 70 | T | A | -1.6297 | |
| 71 | S | A | -0.4647 | |
| 72 | R | A | -0.4077 | |
| 73 | F | A | 0.7192 | |
| 74 | L | A | 0.0000 | |
| 75 | C | A | 0.0000 | |
| 76 | Q | A | 0.0000 | |
| 77 | R | A | -2.4045 | |
| 78 | P | A | -2.2410 | |
| 79 | D | A | -2.4215 | |
| 80 | G | A | -1.6251 | |
| 81 | A | A | -1.1696 | |
| 82 | L | A | 0.0000 | |
| 83 | Y | A | -0.5869 | |
| 84 | G | A | 0.0000 | |
| 85 | S | A | 0.2645 | |
| 86 | L | A | 1.2578 | |
| 87 | H | A | 0.2980 | |
| 88 | F | A | 0.7861 | |
| 89 | D | A | -0.8691 | |
| 90 | P | A | -1.2326 | |
| 91 | E | A | -2.6756 | |
| 92 | A | A | -1.8358 | |
| 93 | C | A | 0.0000 | |
| 94 | S | A | 0.0000 | |
| 95 | F | A | 0.0000 | |
| 96 | R | A | -2.6419 | |
| 97 | E | A | -1.0850 | |
| 98 | L | A | 0.5044 | |
| 99 | L | A | 1.0204 | |
| 100 | L | A | -0.3307 | |
| 101 | E | A | -2.1292 | |
| 102 | D | A | -2.4395 | |
| 103 | G | A | -1.3568 | |
| 104 | Y | A | -0.4655 | |
| 105 | N | A | 0.0511 | |
| 106 | V | A | 0.0000 | |
| 107 | Y | A | 0.0000 | |
| 108 | Q | A | -1.7071 | |
| 109 | S | A | 0.0000 | |
| 110 | E | A | -3.2181 | |
| 111 | A | A | -2.2804 | |
| 112 | H | A | -1.9768 | |
| 113 | G | A | -1.7055 | |
| 114 | L | A | -1.4491 | |
| 115 | P | A | -1.1683 | |
| 116 | L | A | 0.0000 | |
| 117 | H | A | -0.6903 | |
| 118 | L | A | -0.5200 | |
| 119 | P | A | -0.9043 | |
| 120 | G | A | -1.5253 | |
| 121 | N | A | -1.8390 | |
| 122 | K | A | -3.2298 | |
| 123 | S | A | -2.2431 | |
| 124 | P | A | -2.5286 | |
| 125 | H | A | -2.8147 | |
| 126 | R | A | -3.6343 | |
| 127 | D | A | -3.6617 | |
| 128 | P | A | -2.2404 | |
| 129 | A | A | -1.1759 | |
| 130 | P | A | -1.3366 | |
| 131 | R | A | -2.0295 | |
| 132 | G | A | -1.4516 | |
| 133 | P | A | -1.0857 | |
| 134 | A | A | 0.0000 | |
| 135 | R | A | -1.4199 | |
| 136 | F | A | 0.0000 | |
| 137 | L | A | 0.0097 | |
| 138 | P | A | -0.1140 | |
| 139 | L | A | -0.0465 | |
| 140 | P | A | -1.0289 | |
| 141 | G | A | -1.5299 |
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 |
|||
| LM86A | 0.0394 | -0.0164 | View | CSV | PDB |
| FM88A | 0.2337 | -0.0283 | View | CSV | PDB |
| FY88A | 0.3607 | -0.0174 | View | CSV | PDB |
| LM99A | 0.1206 | -0.004 | View | CSV | PDB |
| FY73A | 0.279 | -0.0074 | View | CSV | PDB |
| FW73A | 1.5528 | -0.0129 | View | CSV | PDB |
| LM98A | -0.1303 | 0.0049 | View | CSV | PDB |
| LM66A | 1.0241 | 0.0028 | 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