| Chain sequence(s) |
B: EVQLVESGGGLVQAGGFLRLSCELRGSIFNQYAMAWFRQAPGKEREFVAGMGAVPHYGEFVKGRFTISRDNAKSTVYLQMSSLKPEDTAIYFCARSKSTYISYNSNGYDYWGRGTQVTVSSA
input PDB |
| Selected Chain(s) | B |
| 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 B 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 (00:00:58)
[INFO] Auto_mut: Residue number 54 from chain B and a score of 1.818 (valine) selected for
automated muatation (00:00:59)
[INFO] Auto_mut: Residue number 100 from chain B and a score of 1.277 (tyrosine) selected
for automated muatation (00:00:59)
[INFO] Auto_mut: Residue number 101 from chain B and a score of 0.997 (isoleucine) selected
for automated muatation (00:00:59)
[INFO] Auto_mut: Residue number 28 from chain B and a score of 0.986 (isoleucine) selected
for automated muatation (00:00:59)
[INFO] Auto_mut: Residue number 53 from chain B and a score of 0.968 (alanine) selected for
automated muatation (00:00:59)
[INFO] Auto_mut: Residue number 11 from chain B and a score of 0.913 (leucine) selected for
automated muatation (00:00:59)
[INFO] Auto_mut: Mutating residue number 54 from chain B (valine) into glutamic acid (00:00:59)
[INFO] Auto_mut: Mutating residue number 54 from chain B (valine) into aspartic acid (00:00:59)
[INFO] Auto_mut: Mutating residue number 100 from chain B (tyrosine) into glutamic acid (00:00:59)
[INFO] Auto_mut: Mutating residue number 54 from chain B (valine) into arginine (00:01:29)
[INFO] Auto_mut: Mutating residue number 54 from chain B (valine) into lysine (00:01:30)
[INFO] Auto_mut: Mutating residue number 100 from chain B (tyrosine) into lysine (00:01:34)
[INFO] Auto_mut: Mutating residue number 100 from chain B (tyrosine) into aspartic acid (00:02:08)
[INFO] Auto_mut: Mutating residue number 101 from chain B (isoleucine) into glutamic acid (00:02:11)
[INFO] Auto_mut: Mutating residue number 101 from chain B (isoleucine) into aspartic acid (00:02:18)
[INFO] Auto_mut: Mutating residue number 100 from chain B (tyrosine) into arginine (00:02:38)
[INFO] Auto_mut: Mutating residue number 101 from chain B (isoleucine) into lysine (00:02:47)
[INFO] Auto_mut: Mutating residue number 101 from chain B (isoleucine) into arginine (00:02:53)
[INFO] Auto_mut: Mutating residue number 28 from chain B (isoleucine) into glutamic acid (00:03:16)
[INFO] Auto_mut: Mutating residue number 28 from chain B (isoleucine) into aspartic acid (00:03:22)
[INFO] Auto_mut: Mutating residue number 53 from chain B (alanine) into glutamic acid (00:03:27)
[INFO] Auto_mut: Mutating residue number 28 from chain B (isoleucine) into lysine (00:03:49)
[INFO] Auto_mut: Mutating residue number 28 from chain B (isoleucine) into arginine (00:03:54)
[INFO] Auto_mut: Mutating residue number 53 from chain B (alanine) into lysine (00:03:59)
[INFO] Auto_mut: Mutating residue number 53 from chain B (alanine) into aspartic acid (00:04:30)
[INFO] Auto_mut: Mutating residue number 11 from chain B (leucine) into glutamic acid (00:04:33)
[INFO] Auto_mut: Mutating residue number 11 from chain B (leucine) into aspartic acid (00:04:37)
[INFO] Auto_mut: Mutating residue number 53 from chain B (alanine) into arginine (00:05:00)
[INFO] Auto_mut: Mutating residue number 11 from chain B (leucine) into lysine (00:05:04)
[INFO] Auto_mut: Mutating residue number 11 from chain B (leucine) into arginine (00:05:06)
[INFO] Auto_mut: Effect of mutation residue number 54 from chain B (valine) into glutamic
acid: Energy difference: -0.2446 kcal/mol, Difference in average score from
the base case: -0.0598 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 54 from chain B (valine) into lysine:
Energy difference: -0.6227 kcal/mol, Difference in average score from the
base case: -0.0779 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 54 from chain B (valine) into aspartic
acid: Energy difference: 0.1895 kcal/mol, Difference in average score from
the base case: -0.0659 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 54 from chain B (valine) into arginine:
Energy difference: -0.8285 kcal/mol, Difference in average score from the
base case: -0.0685 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 100 from chain B (tyrosine) into glutamic
acid: Energy difference: -0.5651 kcal/mol, Difference in average score from
the base case: -0.0696 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 100 from chain B (tyrosine) into lysine:
Energy difference: 0.0467 kcal/mol, Difference in average score from the
base case: -0.0669 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 100 from chain B (tyrosine) into aspartic
acid: Energy difference: -0.7384 kcal/mol, Difference in average score from
the base case: -0.0694 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 100 from chain B (tyrosine) into
arginine: Energy difference: 0.0917 kcal/mol, Difference in average score
from the base case: -0.0715 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 101 from chain B (isoleucine) into
glutamic acid: Energy difference: 2.5631 kcal/mol, Difference in average
score from the base case: -0.0042 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 101 from chain B (isoleucine) into
lysine: Energy difference: 4.1115 kcal/mol, Difference in average score
from the base case: -0.0081 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 101 from chain B (isoleucine) into
aspartic acid: Energy difference: 3.2286 kcal/mol, Difference in average
score from the base case: -0.0057 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 101 from chain B (isoleucine) into
arginine: Energy difference: 4.8834 kcal/mol, Difference in average score
from the base case: -0.0156 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 28 from chain B (isoleucine) into
glutamic acid: Energy difference: 0.0302 kcal/mol, Difference in average
score from the base case: -0.0651 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 28 from chain B (isoleucine) into lysine:
Energy difference: -0.3465 kcal/mol, Difference in average score from the
base case: -0.0613 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 28 from chain B (isoleucine) into
aspartic acid: Energy difference: -0.0287 kcal/mol, Difference in average
score from the base case: -0.0662 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 28 from chain B (isoleucine) into
arginine: Energy difference: -0.2703 kcal/mol, Difference in average score
from the base case: -0.0650 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 53 from chain B (alanine) into glutamic
acid: Energy difference: -0.8530 kcal/mol, Difference in average score from
the base case: -0.0270 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 53 from chain B (alanine) into lysine:
Energy difference: -0.2293 kcal/mol, Difference in average score from the
base case: -0.0422 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 53 from chain B (alanine) into aspartic
acid: Energy difference: -0.4026 kcal/mol, Difference in average score from
the base case: -0.0269 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 53 from chain B (alanine) into arginine:
Energy difference: -0.3487 kcal/mol, Difference in average score from the
base case: -0.0201 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 11 from chain B (leucine) into glutamic
acid: Energy difference: 0.5350 kcal/mol, Difference in average score from
the base case: -0.0573 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 11 from chain B (leucine) into lysine:
Energy difference: -0.2124 kcal/mol, Difference in average score from the
base case: -0.0537 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 11 from chain B (leucine) into aspartic
acid: Energy difference: 0.7444 kcal/mol, Difference in average score from
the base case: -0.0589 (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 11 from chain B (leucine) into arginine:
Energy difference: -0.4140 kcal/mol, Difference in average score from the
base case: -0.0571 (00:05:44)
[INFO] Main: Simulation completed successfully. (00:05:49)
|
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 | |
| 1 | E | B | -2.3291 | |
| 2 | V | B | -1.3331 | |
| 3 | Q | B | -1.7433 | |
| 4 | L | B | -0.4780 | |
| 5 | V | B | 0.1578 | |
| 6 | E | B | -0.3832 | |
| 7 | S | B | -0.6571 | |
| 8 | G | B | -1.1961 | |
| 9 | G | B | -0.6069 | |
| 10 | G | B | -0.1007 | |
| 11 | L | B | 0.9135 | |
| 12 | V | B | 0.0000 | |
| 13 | Q | B | -1.0181 | |
| 14 | A | B | -1.2008 | |
| 15 | G | B | -0.9074 | |
| 16 | G | B | 0.0923 | |
| 17 | F | B | 0.8542 | |
| 18 | L | B | -0.1866 | |
| 19 | R | B | -1.8675 | |
| 20 | L | B | 0.0000 | |
| 21 | S | B | -0.7079 | |
| 22 | C | B | 0.0000 | |
| 23 | E | B | -0.9121 | |
| 24 | L | B | 0.0000 | |
| 25 | R | B | -1.8227 | |
| 26 | G | B | -1.4376 | |
| 27 | S | B | -0.3607 | |
| 28 | I | B | 0.9855 | |
| 29 | F | B | 0.0000 | |
| 30 | N | B | -1.3762 | |
| 31 | Q | B | -0.7476 | |
| 32 | Y | B | -0.2149 | |
| 33 | A | B | 0.0000 | |
| 34 | M | B | 0.0000 | |
| 35 | A | B | 0.0000 | |
| 36 | W | B | 0.0000 | |
| 37 | F | B | 0.0000 | |
| 38 | R | B | 0.0000 | |
| 39 | Q | B | -1.9331 | |
| 40 | A | B | -1.8291 | |
| 41 | P | B | -1.4172 | |
| 42 | G | B | -1.9469 | |
| 43 | K | B | -3.3035 | |
| 44 | E | B | -3.4676 | |
| 45 | R | B | -2.7149 | |
| 46 | E | B | -1.9759 | |
| 47 | F | B | 0.0000 | |
| 48 | V | B | 0.0000 | |
| 49 | A | B | 0.0000 | |
| 50 | G | B | 0.0000 | |
| 51 | M | B | 0.8512 | |
| 52 | G | B | 0.6521 | |
| 53 | A | B | 0.9682 | |
| 54 | V | B | 1.8179 | |
| 55 | P | B | 0.6620 | |
| 56 | H | B | 0.2560 | |
| 57 | Y | B | -0.3602 | |
| 58 | G | B | -0.8962 | |
| 59 | E | B | -2.0179 | |
| 60 | F | B | -1.1999 | |
| 61 | V | B | 0.0000 | |
| 62 | K | B | -2.2683 | |
| 63 | G | B | -1.5735 | |
| 64 | R | B | -0.9612 | |
| 65 | F | B | 0.0000 | |
| 66 | T | B | -0.6690 | |
| 67 | I | B | 0.0000 | |
| 68 | S | B | -0.3907 | |
| 69 | R | B | -1.2019 | |
| 70 | D | B | -2.0485 | |
| 71 | N | B | -2.2346 | |
| 72 | A | B | -1.7443 | |
| 73 | K | B | -2.5225 | |
| 74 | S | B | -1.7771 | |
| 75 | T | B | 0.0000 | |
| 76 | V | B | 0.0000 | |
| 77 | Y | B | -0.7340 | |
| 78 | L | B | 0.0000 | |
| 79 | Q | B | -1.1186 | |
| 80 | M | B | 0.0000 | |
| 81 | S | B | -0.2277 | |
| 82 | S | B | -0.5084 | |
| 83 | L | B | 0.0000 | |
| 84 | K | B | -2.4014 | |
| 85 | P | B | -1.9712 | |
| 86 | E | B | -2.3015 | |
| 87 | D | B | 0.0000 | |
| 88 | T | B | -0.9464 | |
| 89 | A | B | 0.0000 | |
| 90 | I | B | -0.4561 | |
| 91 | Y | B | 0.0000 | |
| 92 | F | B | -0.4335 | |
| 93 | C | B | 0.0000 | |
| 94 | A | B | 0.0000 | |
| 95 | R | B | 0.0000 | |
| 96 | S | B | 0.0000 | |
| 97 | K | B | -2.1667 | |
| 98 | S | B | -0.7892 | |
| 99 | T | B | -0.0734 | |
| 100 | Y | B | 1.2768 | |
| 101 | I | B | 0.9966 | |
| 102 | S | B | 0.1515 | |
| 103 | Y | B | 0.3878 | |
| 104 | N | B | -1.2840 | |
| 105 | S | B | -1.6186 | |
| 106 | N | B | -2.1300 | |
| 107 | G | B | -1.4241 | |
| 108 | Y | B | 0.0000 | |
| 109 | D | B | -2.2500 | |
| 110 | Y | B | -0.7965 | |
| 111 | W | B | -0.2608 | |
| 112 | G | B | -0.6148 | |
| 113 | R | B | -1.5918 | |
| 114 | G | B | 0.0000 | |
| 115 | T | B | -1.0131 | |
| 116 | Q | B | -0.8900 | |
| 117 | V | B | 0.0000 | |
| 118 | T | B | -0.3879 | |
| 119 | V | B | 0.0000 | |
| 120 | S | B | -0.5963 | |
| 121 | S | B | -0.8555 | |
| 122 | A | B | -0.3460 |
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 |
|||
| VR54B | -0.8285 | -0.0685 | View | CSV | PDB |
| VK54B | -0.6227 | -0.0779 | View | CSV | PDB |
| YD100B | -0.7384 | -0.0694 | View | CSV | PDB |
| YE100B | -0.5651 | -0.0696 | View | CSV | PDB |
| LR11B | -0.414 | -0.0571 | View | CSV | PDB |
| IK28B | -0.3465 | -0.0613 | View | CSV | PDB |
| IR28B | -0.2703 | -0.065 | View | CSV | PDB |
| LK11B | -0.2124 | -0.0537 | View | CSV | PDB |
| AE53B | -0.853 | -0.027 | View | CSV | PDB |
| AK53B | -0.2293 | -0.0422 | View | CSV | PDB |
| IR101B | 4.8834 | -0.0156 | View | CSV | PDB |
| IK101B | 4.1115 | -0.0081 | 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