| Chain sequence(s) |
A: GSPWSLSCRKEQGKFYDHLLRDCISCASICGQHPKQCAYFCENKLR
input PDB |
| Selected Chain(s) | A |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| 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 minimalization (00:00:00)
[INFO] Analysis: Starting Aggrescan3D on folded.pdb (00:00:27)
[INFO] Auto_mut: Residue number 69 from chain A and a score of 1.116 (leucine) selected for
automated muatation (00:00:27)
[INFO] Auto_mut: Residue number 68 from chain A and a score of 0.896 (serine) selected for
automated muatation (00:00:27)
[INFO] Auto_mut: Residue number 82 from chain A and a score of 0.738 (leucine) selected for
automated muatation (00:00:27)
[INFO] Auto_mut: Residue number 67 from chain A and a score of 0.442 (tryptophan) selected
for automated muatation (00:00:27)
[INFO] Auto_mut: Residue number 83 from chain A and a score of 0.102 (leucine) selected for
automated muatation (00:00:27)
[INFO] Auto_mut: Residue number 92 from chain A and a score of -0.115 (isoleucine) selected
for automated muatation (00:00:27)
[INFO] Auto_mut: Mutating residue number 69 from chain A (leucine) into glutamic acid (00:00:27)
[INFO] Auto_mut: Mutating residue number 69 from chain A (leucine) into aspartic acid (00:00:27)
[INFO] Auto_mut: Mutating residue number 68 from chain A (serine) into glutamic acid (00:00:27)
[INFO] Auto_mut: Mutating residue number 69 from chain A (leucine) into arginine (00:00:42)
[INFO] Auto_mut: Mutating residue number 68 from chain A (serine) into lysine (00:00:43)
[INFO] Auto_mut: Mutating residue number 69 from chain A (leucine) into lysine (00:00:44)
[INFO] Auto_mut: Mutating residue number 68 from chain A (serine) into aspartic acid (00:01:02)
[INFO] Auto_mut: Mutating residue number 82 from chain A (leucine) into glutamic acid (00:01:06)
[INFO] Auto_mut: Mutating residue number 82 from chain A (leucine) into aspartic acid (00:01:06)
[INFO] Auto_mut: Mutating residue number 68 from chain A (serine) into arginine (00:01:17)
[INFO] Auto_mut: Mutating residue number 82 from chain A (leucine) into arginine (00:01:22)
[INFO] Auto_mut: Mutating residue number 82 from chain A (leucine) into lysine (00:01:24)
[INFO] Auto_mut: Mutating residue number 67 from chain A (tryptophan) into glutamic acid (00:01:36)
[INFO] Auto_mut: Mutating residue number 67 from chain A (tryptophan) into aspartic acid (00:01:42)
[INFO] Auto_mut: Mutating residue number 83 from chain A (leucine) into glutamic acid (00:01:46)
[INFO] Auto_mut: Mutating residue number 67 from chain A (tryptophan) into lysine (00:01:54)
[INFO] Auto_mut: Mutating residue number 67 from chain A (tryptophan) into arginine (00:01:57)
[INFO] Auto_mut: Mutating residue number 83 from chain A (leucine) into lysine (00:02:04)
[INFO] Auto_mut: Mutating residue number 83 from chain A (leucine) into aspartic acid (00:02:18)
[INFO] Auto_mut: Mutating residue number 92 from chain A (isoleucine) into glutamic acid (00:02:20)
[INFO] Auto_mut: Mutating residue number 92 from chain A (isoleucine) into aspartic acid (00:02:30)
[INFO] Auto_mut: Mutating residue number 83 from chain A (leucine) into arginine (00:02:35)
[INFO] Auto_mut: Mutating residue number 92 from chain A (isoleucine) into lysine (00:02:41)
[INFO] Auto_mut: Mutating residue number 92 from chain A (isoleucine) into arginine (00:02:49)
[INFO] Auto_mut: Effect of mutation residue number 69 from chain A (leucine) into glutamic
acid: Energy difference: 0.2397 kcal/mol, Difference in average score from
the base case: -0.2299 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 69 from chain A (leucine) into lysine:
Energy difference: 0.3742 kcal/mol, Difference in average score from the
base case: -0.2182 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 69 from chain A (leucine) into aspartic
acid: Energy difference: 0.0260 kcal/mol, Difference in average score from
the base case: -0.2298 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 69 from chain A (leucine) into arginine:
Energy difference: 0.3192 kcal/mol, Difference in average score from the
base case: -0.2031 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 68 from chain A (serine) into glutamic
acid: Energy difference: 1.1758 kcal/mol, Difference in average score from
the base case: -0.1152 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 68 from chain A (serine) into lysine:
Energy difference: -0.3875 kcal/mol, Difference in average score from the
base case: -0.1300 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 68 from chain A (serine) into aspartic
acid: Energy difference: -0.0287 kcal/mol, Difference in average score from
the base case: -0.1067 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 68 from chain A (serine) into arginine:
Energy difference: -0.3309 kcal/mol, Difference in average score from the
base case: -0.1376 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 82 from chain A (leucine) into glutamic
acid: Energy difference: -0.2182 kcal/mol, Difference in average score from
the base case: -0.1814 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 82 from chain A (leucine) into lysine:
Energy difference: -0.7419 kcal/mol, Difference in average score from the
base case: -0.1152 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 82 from chain A (leucine) into aspartic
acid: Energy difference: 0.3370 kcal/mol, Difference in average score from
the base case: -0.1847 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 82 from chain A (leucine) into arginine:
Energy difference: -0.7919 kcal/mol, Difference in average score from the
base case: -0.1382 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 67 from chain A (tryptophan) into
glutamic acid: Energy difference: 0.5596 kcal/mol, Difference in average
score from the base case: -0.2357 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 67 from chain A (tryptophan) into lysine:
Energy difference: 0.5400 kcal/mol, Difference in average score from the
base case: -0.2126 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 67 from chain A (tryptophan) into
aspartic acid: Energy difference: 0.7789 kcal/mol, Difference in average
score from the base case: -0.2328 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 67 from chain A (tryptophan) into
arginine: Energy difference: -0.2285 kcal/mol, Difference in average score
from the base case: -0.2336 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 83 from chain A (leucine) into glutamic
acid: Energy difference: 0.9795 kcal/mol, Difference in average score from
the base case: -0.2461 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 83 from chain A (leucine) into lysine:
Energy difference: -0.0536 kcal/mol, Difference in average score from the
base case: -0.2250 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 83 from chain A (leucine) into aspartic
acid: Energy difference: 1.3876 kcal/mol, Difference in average score from
the base case: -0.2269 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 83 from chain A (leucine) into arginine:
Energy difference: -0.0265 kcal/mol, Difference in average score from the
base case: -0.2434 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 92 from chain A (isoleucine) into
glutamic acid: Energy difference: -0.2232 kcal/mol, Difference in average
score from the base case: -0.0571 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 92 from chain A (isoleucine) into lysine:
Energy difference: -0.9768 kcal/mol, Difference in average score from the
base case: -0.1035 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 92 from chain A (isoleucine) into
aspartic acid: Energy difference: -0.2238 kcal/mol, Difference in average
score from the base case: -0.0375 (00:03:08)
[INFO] Auto_mut: Effect of mutation residue number 92 from chain A (isoleucine) into
arginine: Energy difference: -1.1906 kcal/mol, Difference in average score
from the base case: -0.1005 (00:03:08)
[INFO] Main: Simulation completed successfully. (00:03:11)
|
The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.
| residue index | residue name | chain | Aggrescan3D score | mutation |
|---|---|---|---|---|
| residue index | residue name | chain | Aggrescan3D score | |
| 64 | G | A | -0.5021 | |
| 65 | S | A | -0.2916 | |
| 66 | P | A | -0.1674 | |
| 67 | W | A | 0.4424 | |
| 68 | S | A | 0.8960 | |
| 69 | L | A | 1.1162 | |
| 70 | S | A | -0.1567 | |
| 71 | C | A | -0.9610 | |
| 72 | R | A | -3.2974 | |
| 73 | K | A | -3.6496 | |
| 74 | E | A | -3.8554 | |
| 75 | Q | A | -2.9137 | |
| 76 | G | A | 0.0000 | |
| 77 | K | A | -1.7474 | |
| 78 | F | A | 0.0000 | |
| 79 | Y | A | -0.3629 | |
| 80 | D | A | -0.8106 | |
| 81 | H | A | -0.8741 | |
| 82 | L | A | 0.7375 | |
| 83 | L | A | 0.1017 | |
| 84 | R | A | -1.7247 | |
| 85 | D | A | -1.6614 | |
| 86 | C | A | -0.9562 | |
| 87 | I | A | -0.5769 | |
| 88 | S | A | -0.8504 | |
| 89 | C | A | 0.0000 | |
| 90 | A | A | -0.3803 | |
| 91 | S | A | -0.3331 | |
| 92 | I | A | -0.1150 | |
| 93 | C | A | -0.5146 | |
| 94 | G | A | -1.2012 | |
| 95 | Q | A | -1.6105 | |
| 96 | H | A | -1.3216 | |
| 97 | P | A | -1.6984 | |
| 98 | K | A | -2.7660 | |
| 99 | Q | A | -1.8723 | |
| 100 | C | A | 0.0000 | |
| 101 | A | A | -1.8919 | |
| 102 | Y | A | -0.7372 | |
| 103 | F | A | -0.5017 | |
| 104 | C | A | -1.1818 | |
| 105 | E | A | -2.4396 | |
| 106 | N | A | -2.5977 | |
| 107 | K | A | -2.2637 | |
| 108 | L | A | -0.5989 | |
| 109 | R | A | -2.0504 |
Automated mutations analysis
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 |
|||
| LR82A | -0.7919 | -0.1382 | View | CSV | PDB |
| WR67A | -0.2285 | -0.2336 | View | CSV | PDB |
| IR92A | -1.1906 | -0.1005 | View | CSV | PDB |
| IK92A | -0.9768 | -0.1035 | View | CSV | PDB |
| LK82A | -0.7419 | -0.1152 | View | CSV | PDB |
| LR83A | -0.0265 | -0.2434 | View | CSV | PDB |
| LK83A | -0.0536 | -0.225 | View | CSV | PDB |
| SK68A | -0.3875 | -0.13 | View | CSV | PDB |
| SR68A | -0.3309 | -0.1376 | View | CSV | PDB |
| LD69A | 0.026 | -0.2298 | View | CSV | PDB |
| LE69A | 0.2397 | -0.2299 | View | CSV | PDB |
| WE67A | 0.5596 | -0.2357 | 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