| Chain sequence(s) |
A: MQNIFLANAADVGGSFSKHWELFSEMEGENQMKLANRSSEVEYKNGQEYVMLESASNTHSYKLDVWRYKHVNFVEFSLVPWPSLDTGMQVAATMRMSAERGNVAKGYKLHG
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 (00:00:01)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:01:43)
[INFO] AutoMut: Residue number 79 from chain A and a score of 1.159 (valine) selected for
automated mutation (00:01:44)
[INFO] AutoMut: Residue number 5 from chain A and a score of 0.814 (phenylalanine) selected
for automated mutation (00:01:44)
[INFO] AutoMut: Residue number 6 from chain A and a score of 0.788 (leucine) selected for
automated mutation (00:01:44)
[INFO] AutoMut: Residue number 78 from chain A and a score of 0.718 omitted from automated
mutation (excluded by the user). (00:01:44)
[INFO] AutoMut: Residue number 65 from chain A and a score of 0.592 (valine) selected for
automated mutation (00:01:44)
[INFO] AutoMut: Residue number 12 from chain A and a score of 0.584 (valine) selected for
automated mutation (00:01:44)
[INFO] AutoMut: Residue number 16 from chain A and a score of 0.573 (phenylalanine)
selected for automated mutation (00:01:44)
[INFO] AutoMut: Mutating residue number 79 from chain A (valine) into aspartic acid (00:01:44)
[INFO] AutoMut: Mutating residue number 79 from chain A (valine) into glutamic acid (00:01:44)
[INFO] AutoMut: Mutating residue number 5 from chain A (phenylalanine) into glutamic acid (00:01:44)
[INFO] AutoMut: Mutating residue number 79 from chain A (valine) into arginine (00:01:48)
[INFO] AutoMut: Mutating residue number 79 from chain A (valine) into lysine (00:01:51)
[INFO] AutoMut: Mutating residue number 5 from chain A (phenylalanine) into lysine (00:01:58)
[INFO] AutoMut: Mutating residue number 5 from chain A (phenylalanine) into aspartic acid (00:02:11)
[INFO] AutoMut: Mutating residue number 6 from chain A (leucine) into glutamic acid (00:02:13)
[INFO] AutoMut: Mutating residue number 6 from chain A (leucine) into lysine (00:02:20)
[INFO] AutoMut: Mutating residue number 5 from chain A (phenylalanine) into arginine (00:02:20)
[INFO] AutoMut: Mutating residue number 6 from chain A (leucine) into aspartic acid (00:02:27)
[INFO] AutoMut: Mutating residue number 6 from chain A (leucine) into arginine (00:02:33)
[INFO] AutoMut: Mutating residue number 65 from chain A (valine) into glutamic acid (00:02:34)
[INFO] AutoMut: Mutating residue number 65 from chain A (valine) into aspartic acid (00:02:36)
[INFO] AutoMut: Mutating residue number 12 from chain A (valine) into glutamic acid (00:02:40)
[INFO] AutoMut: Mutating residue number 65 from chain A (valine) into lysine (00:02:41)
[INFO] AutoMut: Mutating residue number 65 from chain A (valine) into arginine (00:02:42)
[INFO] AutoMut: Mutating residue number 12 from chain A (valine) into aspartic acid (00:02:51)
[INFO] AutoMut: Mutating residue number 12 from chain A (valine) into lysine (00:02:51)
[INFO] AutoMut: Mutating residue number 16 from chain A (phenylalanine) into glutamic acid
Mutating residue number 16 from chain A (phenylalanine) into glutamic acid (00:02:52)
[INFO] AutoMut: Mutating residue number 12 from chain A (valine) into arginine (00:03:01)
[INFO] AutoMut: Mutating residue number 16 from chain A (phenylalanine) into aspartic acid
Mutating residue number 16 from chain A (phenylalanine) into aspartic acid (00:03:05)
[INFO] AutoMut: Mutating residue number 16 from chain A (phenylalanine) into lysine (00:03:12)
[INFO] AutoMut: Mutating residue number 16 from chain A (phenylalanine) into arginine (00:03:15)
[INFO] AutoMut: Effect of mutation residue number 79 from chain A (valine) into glutamic
acid: Energy difference: 0.2625 kcal/mol, Difference in average score from
the base case: -0.1143 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 79 from chain A (valine) into lysine:
Energy difference: -0.0978 kcal/mol, Difference in average score from the
base case: -0.1096 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 79 from chain A (valine) into aspartic
acid: Energy difference: 0.1329 kcal/mol, Difference in average score from
the base case: -0.1141 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 79 from chain A (valine) into arginine:
Energy difference: -0.1286 kcal/mol, Difference in average score from the
base case: -0.1157 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 5 from chain A (phenylalanine) into
glutamic acid: Energy difference: 0.7549 kcal/mol, Difference in average
score from the base case: -0.0649 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 5 from chain A (phenylalanine) into
lysine: Energy difference: 0.8647 kcal/mol, Difference in average score
from the base case: -0.0640 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 5 from chain A (phenylalanine) into
aspartic acid: Energy difference: 0.5160 kcal/mol, Difference in average
score from the base case: -0.0623 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 5 from chain A (phenylalanine) into
arginine: Energy difference: 0.5238 kcal/mol, Difference in average score
from the base case: -0.0733 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 6 from chain A (leucine) into glutamic
acid: Energy difference: 1.8528 kcal/mol, Difference in average score from
the base case: -0.0470 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 6 from chain A (leucine) into lysine:
Energy difference: 1.5875 kcal/mol, Difference in average score from the
base case: -0.0279 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 6 from chain A (leucine) into aspartic
acid: Energy difference: 1.4639 kcal/mol, Difference in average score from
the base case: -0.0619 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 6 from chain A (leucine) into arginine:
Energy difference: 1.1012 kcal/mol, Difference in average score from the
base case: -0.0433 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 65 from chain A (valine) into glutamic
acid: Energy difference: 1.7700 kcal/mol, Difference in average score from
the base case: -0.0347 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 65 from chain A (valine) into lysine:
Energy difference: 0.8703 kcal/mol, Difference in average score from the
base case: -0.0367 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 65 from chain A (valine) into aspartic
acid: Energy difference: 2.4320 kcal/mol, Difference in average score from
the base case: -0.0204 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 65 from chain A (valine) into arginine:
Energy difference: 1.1813 kcal/mol, Difference in average score from the
base case: -0.0517 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 12 from chain A (valine) into glutamic
acid: Energy difference: -0.6342 kcal/mol, Difference in average score from
the base case: -0.1254 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 12 from chain A (valine) into lysine:
Energy difference: -0.8006 kcal/mol, Difference in average score from the
base case: -0.1387 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 12 from chain A (valine) into aspartic
acid: Energy difference: -2.2820 kcal/mol, Difference in average score from
the base case: -0.1280 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 12 from chain A (valine) into arginine:
Energy difference: -0.7598 kcal/mol, Difference in average score from the
base case: -0.1428 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 16 from chain A (phenylalanine) into
glutamic acid: Energy difference: 0.8917 kcal/mol, Difference in average
score from the base case: -0.0798 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 16 from chain A (phenylalanine) into
lysine: Energy difference: 1.3024 kcal/mol, Difference in average score
from the base case: -0.0933 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 16 from chain A (phenylalanine) into
aspartic acid: Energy difference: 1.2140 kcal/mol, Difference in average
score from the base case: -0.0833 (00:04:12)
[INFO] AutoMut: Effect of mutation residue number 16 from chain A (phenylalanine) into
arginine: Energy difference: 0.6969 kcal/mol, Difference in average score
from the base case: -0.0787 (00:04:12)
[INFO] Main: Simulation completed successfully. (00:04:15)
|
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 | M | A | -0.1396 | |
| 2 | Q | A | -1.1344 | |
| 3 | N | A | -1.0895 | |
| 4 | I | A | 0.2440 | |
| 5 | F | A | 0.8139 | |
| 6 | L | A | 0.7878 | |
| 7 | A | A | 0.4293 | |
| 8 | N | A | -0.4798 | |
| 9 | A | A | -0.6616 | |
| 10 | A | A | -1.4837 | |
| 11 | D | A | -1.5901 | |
| 12 | V | A | 0.5840 | |
| 13 | G | A | -0.1172 | |
| 14 | G | A | -0.4519 | |
| 15 | S | A | -0.0854 | |
| 16 | F | A | 0.5731 | |
| 17 | S | A | -0.5906 | |
| 18 | K | A | -1.7664 | |
| 19 | H | A | -0.7681 | |
| 20 | W | A | -0.6254 | |
| 21 | E | A | -2.0184 | |
| 22 | L | A | -0.9078 | |
| 23 | F | A | -0.9157 | |
| 24 | S | A | -1.8912 | |
| 25 | E | A | -2.4890 | |
| 26 | M | A | -2.1858 | |
| 27 | E | A | -3.0021 | |
| 28 | G | A | -2.7356 | |
| 29 | E | A | -3.1817 | |
| 30 | N | A | -3.2571 | |
| 31 | Q | A | -3.2696 | |
| 32 | M | A | -2.0614 | |
| 33 | K | A | -2.3487 | |
| 34 | L | A | -1.3926 | |
| 35 | A | A | -1.9686 | |
| 36 | N | A | -2.6162 | |
| 37 | R | A | -3.0429 | |
| 38 | S | A | -1.9329 | |
| 39 | S | A | -1.5103 | |
| 40 | E | A | -1.7439 | |
| 41 | V | A | -0.0858 | |
| 42 | E | A | -0.8771 | |
| 43 | Y | A | -0.4011 | |
| 44 | K | A | -1.6369 | |
| 45 | N | A | -2.0203 | |
| 46 | G | A | -1.4849 | |
| 47 | Q | A | -1.4043 | |
| 48 | E | A | -1.0253 | |
| 49 | Y | A | -0.2267 | |
| 50 | V | A | 0.0814 | |
| 51 | M | A | -0.4546 | |
| 52 | L | A | -0.7061 | |
| 53 | E | A | -2.2525 | |
| 54 | S | A | -1.4220 | |
| 55 | A | A | -1.2111 | |
| 56 | S | A | -1.6453 | |
| 57 | N | A | -1.6899 | |
| 58 | T | A | -0.9809 | |
| 59 | H | A | -0.9003 | |
| 60 | S | A | -0.8708 | |
| 61 | Y | A | -0.0995 | |
| 62 | K | A | -0.1769 | |
| 63 | L | A | 0.3086 | |
| 64 | D | A | 0.0000 | |
| 65 | V | A | 0.5922 | |
| 66 | W | A | -0.1201 | |
| 67 | R | A | -0.9321 | |
| 68 | Y | A | -0.9660 | |
| 69 | K | A | -2.2427 | |
| 70 | H | A | -1.5971 | |
| 71 | V | A | -0.5681 | |
| 72 | N | A | -1.2782 | |
| 73 | F | A | -0.8807 | |
| 74 | V | A | -0.0643 | |
| 75 | E | A | -0.6427 | |
| 76 | F | A | 0.1493 | |
| 77 | S | A | 0.3711 | |
| 78 | L | A | 0.7177 | |
| 79 | V | A | 1.1594 | |
| 80 | P | A | 0.3091 | |
| 81 | W | A | 0.3098 | |
| 82 | P | A | -0.3704 | |
| 83 | S | A | -0.5508 | |
| 84 | L | A | -0.7519 | |
| 85 | D | A | -1.6978 | |
| 86 | T | A | -1.0213 | |
| 87 | G | A | -0.9149 | |
| 88 | M | A | -0.2673 | |
| 89 | Q | A | -0.5868 | |
| 90 | V | A | 0.0000 | |
| 91 | A | A | 0.1966 | |
| 92 | A | A | 0.0172 | |
| 93 | T | A | -0.3255 | |
| 94 | M | A | -0.6199 | |
| 95 | R | A | -1.7533 | |
| 96 | M | A | -0.9963 | |
| 97 | S | A | -1.4584 | |
| 98 | A | A | -1.9270 | |
| 99 | E | A | -3.0036 | |
| 100 | R | A | -3.2345 | |
| 101 | G | A | -2.0726 | |
| 102 | N | A | -1.7924 | |
| 103 | V | A | -0.0141 | |
| 104 | A | A | -0.5524 | |
| 105 | K | A | -1.6467 | |
| 106 | G | A | -1.0006 | |
| 107 | Y | A | -0.7593 | |
| 108 | K | A | -1.9159 | |
| 109 | L | A | -0.9940 | |
| 110 | H | A | -1.2902 | |
| 111 | G | A | -0.7946 |
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 |
|||
| VD12A | -2.282 | -0.128 | View | CSV | PDB |
| VK12A | -0.8006 | -0.1387 | View | CSV | PDB |
| VR79A | -0.1286 | -0.1157 | View | CSV | PDB |
| VK79A | -0.0978 | -0.1096 | View | CSV | PDB |
| FR5A | 0.5238 | -0.0733 | View | CSV | PDB |
| FD5A | 0.516 | -0.0623 | View | CSV | PDB |
| FR16A | 0.6969 | -0.0787 | View | CSV | PDB |
| FE16A | 0.8917 | -0.0798 | View | CSV | PDB |
| VR65A | 1.1813 | -0.0517 | View | CSV | PDB |
| LD6A | 1.4639 | -0.0619 | View | CSV | PDB |
| VK65A | 0.8703 | -0.0367 | View | CSV | PDB |
| LR6A | 1.1012 | -0.0433 | 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