| Chain sequence(s) |
B: QVQLVESGGGLVQPGGSLRLSCAASGFPFSSYGMGWVRQAPGKGLEWVSGINWSGGSTGYADSVKGRFTISRDNAKNTLYLQMNSLRAEDTAVYYCADGLLFSYDDWGQGTQVTVSS
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 101 from chain B and a score of 3.171 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 102 from chain B and a score of 2.781 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 100 from chain B and a score of 2.561 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 103 from chain B and a score of 1.279 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 33 from chain B and a score of 1.026 (glycine) selected for
automated mutation (00:00:49)
[INFO] AutoMutEv:Residue number 11 from chain B and a score of 0.897 (leucine) selected for
automated mutation (00:00:49)
[INFO] AutoMutEv:Residue number 32 from chain B and a score of 0.846 (tyrosine) selected for
automated mutation (00:00:49)
[INFO] AutoMutEv:Residue number 5 from chain B and a score of 0.801 (valine) selected for
automated mutation (00:00:49)
[INFO] AutoMutEv:Residue number 104 from chain B and a score of 0.276 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 45 from chain B and a score of 0.202 (leucine) selected for
automated mutation (00:00:49)
[INFO] AutoMutEv:Residue number 52 from chain B and a score of 0.172 (asparagine) selected
for automated mutation (00:00:49)
[INFO] AutoMutEv:Mutating residue number 33 from chain B (glycine) into glutamic acid (00:00:49)
[INFO] AutoMutEv:Mutating residue number 33 from chain B (glycine) into asparagine (00:00:49)
[INFO] AutoMutEv:Mutating residue number 32 from chain B (tyrosine) into histidine (00:00:49)
[INFO] AutoMutEv:Mutating residue number 11 from chain B (leucine) into methionine (00:00:53)
[INFO] AutoMutEv:Mutating residue number 32 from chain B (tyrosine) into cysteine (00:00:55)
[INFO] AutoMutEv:Mutating residue number 33 from chain B (glycine) into aspartic acid (00:00:55)
[INFO] AutoMutEv:Mutating residue number 32 from chain B (tyrosine) into tryptophan (00:00:59)
[INFO] AutoMutEv:Mutating residue number 5 from chain B (valine) into alanine (00:01:00)
[INFO] AutoMutEv:Mutating residue number 45 from chain B (leucine) into methionine (00:01:01)
[INFO] AutoMutEv:Mutating residue number 5 from chain B (valine) into threonine (00:01:05)
[INFO] AutoMutEv:Mutating residue number 5 from chain B (valine) into methionine (00:01:05)
[INFO] AutoMutEv:Mutating residue number 52 from chain B (asparagine) into arginine (00:01:06)
[INFO] AutoMutEv:Mutating residue number 52 from chain B (asparagine) into glutamic acid (00:01:10)
[INFO] AutoMutEv:Mutating residue number 52 from chain B (asparagine) into aspartic acid (00:01:19)
[INFO] AutoMutEv:Effect of mutation residue number 33 from chain B (glycine) into glutamic
acid: Energy difference: 0.2944 kcal/mol, Difference in average score from
the base case: -0.0098 (00:01:25)
[INFO] AutoMutEv:Effect of mutation residue number 33 from chain B (glycine) into aspartic
acid: Energy difference: 2.1050 kcal/mol, Difference in average score from
the base case: -0.0095 (00:01:25)
[INFO] AutoMutEv:Effect of mutation residue number 33 from chain B (glycine) into
asparagine: Energy difference: 1.2276 kcal/mol, Difference in average score
from the base case: -0.0064 (00:01:25)
[INFO] AutoMutEv:Effect of mutation residue number 11 from chain B (leucine) into
methionine: Energy difference: -0.1494 kcal/mol, Difference in average
score from the base case: -0.0132 (00:01:25)
[INFO] AutoMutEv:Effect of mutation residue number 32 from chain B (tyrosine) into
histidine: Energy difference: 0.6905 kcal/mol, Difference in average score
from the base case: -0.0164 (00:01:25)
[INFO] AutoMutEv:Effect of mutation residue number 32 from chain B (tyrosine) into cysteine:
Energy difference: 1.8725 kcal/mol, Difference in average score from the
base case: -0.0011 (00:01:25)
[INFO] AutoMutEv:Effect of mutation residue number 32 from chain B (tyrosine) into
tryptophan: Energy difference: -0.7960 kcal/mol, Difference in average
score from the base case: -0.0155 (00:01:25)
[INFO] AutoMutEv:Effect of mutation residue number 5 from chain B (valine) into threonine:
Energy difference: 0.1871 kcal/mol, Difference in average score from the
base case: -0.0386 (00:01:25)
[INFO] AutoMutEv:Effect of mutation residue number 5 from chain B (valine) into alanine:
Energy difference: 0.6671 kcal/mol, Difference in average score from the
base case: -0.0508 (00:01:25)
[INFO] AutoMutEv:Effect of mutation residue number 5 from chain B (valine) into methionine:
Energy difference: -0.3784 kcal/mol, Difference in average score from the
base case: -0.0240 (00:01:25)
[INFO] AutoMutEv:Effect of mutation residue number 45 from chain B (leucine) into
methionine: Energy difference: 0.4173 kcal/mol, Difference in average score
from the base case: -0.0111 (00:01:25)
[INFO] AutoMutEv:Effect of mutation residue number 52 from chain B (asparagine) into
arginine: Energy difference: 0.3229 kcal/mol, Difference in average score
from the base case: -0.0478 (00:01:25)
[INFO] AutoMutEv:Effect of mutation residue number 52 from chain B (asparagine) into
glutamic acid: Energy difference: 0.4848 kcal/mol, Difference in average
score from the base case: -0.0307 (00:01:25)
[INFO] AutoMutEv:Effect of mutation residue number 52 from chain B (asparagine) into
aspartic acid: Energy difference: 0.3923 kcal/mol, Difference in average
score from the base case: -0.0028 (00:01:25)
[INFO] Main: Simulation completed successfully. (00:01:29)
|
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 | Q | B | -1.4466 | |
| 2 | V | B | -1.1028 | |
| 3 | Q | B | -1.2162 | |
| 4 | L | B | 0.0000 | |
| 5 | V | B | 0.8010 | |
| 6 | E | B | 0.0000 | |
| 7 | S | B | -0.6159 | |
| 8 | G | B | -1.0367 | |
| 9 | G | B | -0.8286 | |
| 10 | G | B | -0.0674 | |
| 11 | L | B | 0.8974 | |
| 12 | V | B | 0.0000 | |
| 13 | Q | B | -1.5496 | |
| 14 | P | B | -1.8855 | |
| 15 | G | B | -1.5865 | |
| 16 | G | B | -1.0593 | |
| 17 | S | B | -1.3268 | |
| 18 | L | B | -0.9221 | |
| 19 | R | B | -2.1202 | |
| 20 | L | B | 0.0000 | |
| 21 | S | B | -0.4067 | |
| 22 | C | B | 0.0000 | |
| 23 | A | B | -0.2760 | |
| 24 | A | B | 0.0000 | |
| 25 | S | B | -0.9773 | |
| 26 | G | B | -0.9815 | |
| 27 | F | B | -0.4690 | |
| 28 | P | B | -0.4201 | |
| 29 | F | B | 0.0000 | |
| 30 | S | B | -0.7099 | |
| 31 | S | B | 0.0216 | |
| 32 | Y | B | 0.8461 | |
| 33 | G | B | 1.0262 | |
| 34 | M | B | 0.0000 | |
| 35 | G | B | 0.0000 | |
| 36 | W | B | 0.0000 | |
| 37 | V | B | 0.0000 | |
| 38 | R | B | 0.0000 | |
| 39 | Q | B | -0.8330 | |
| 40 | A | B | -1.3518 | |
| 41 | P | B | -0.9916 | |
| 42 | G | B | -1.4621 | |
| 43 | K | B | -2.1918 | |
| 44 | G | B | -1.0874 | |
| 45 | L | B | 0.2024 | |
| 46 | E | B | -0.6308 | |
| 47 | W | B | 0.0768 | |
| 48 | V | B | 0.0000 | |
| 49 | S | B | 0.0000 | |
| 50 | G | B | 0.1335 | |
| 51 | I | B | 0.0000 | |
| 52 | N | B | 0.1720 | |
| 53 | W | B | 0.0353 | |
| 54 | S | B | -0.5293 | |
| 55 | G | B | -0.8403 | |
| 56 | G | B | -0.7365 | |
| 57 | S | B | -0.6250 | |
| 58 | T | B | -0.4504 | |
| 59 | G | B | -0.6251 | |
| 60 | Y | B | -0.9465 | |
| 61 | A | B | -1.4386 | |
| 62 | D | B | -2.5086 | |
| 63 | S | B | -1.7319 | |
| 64 | V | B | 0.0000 | |
| 65 | K | B | -2.6582 | |
| 66 | G | B | -1.7863 | |
| 67 | R | B | -1.5553 | |
| 68 | F | B | 0.0000 | |
| 69 | T | B | -0.8809 | |
| 70 | I | B | 0.0000 | |
| 71 | S | B | -0.5919 | |
| 72 | R | B | -1.1837 | |
| 73 | D | B | -1.8856 | |
| 74 | N | B | -2.2889 | |
| 75 | A | B | -1.7373 | |
| 76 | K | B | -2.5502 | |
| 77 | N | B | -2.1736 | |
| 78 | T | B | 0.0000 | |
| 79 | L | B | 0.0000 | |
| 80 | Y | B | -0.5978 | |
| 81 | L | B | 0.0000 | |
| 82 | Q | B | -1.2413 | |
| 83 | M | B | 0.0000 | |
| 84 | N | B | -1.5007 | |
| 85 | S | B | -1.4170 | |
| 86 | L | B | 0.0000 | |
| 87 | R | B | -2.9607 | |
| 88 | A | B | -2.0722 | |
| 89 | E | B | -2.4492 | |
| 90 | D | B | 0.0000 | |
| 91 | T | B | -0.9982 | |
| 92 | A | B | 0.0000 | |
| 93 | V | B | -0.1595 | |
| 94 | Y | B | 0.0000 | |
| 95 | Y | B | 0.0968 | |
| 96 | C | B | 0.0000 | |
| 97 | A | B | 0.0000 | |
| 98 | D | B | 0.0000 | |
| 99 | G | B | 0.0000 | |
| 100 | L | B | 2.5613 | |
| 101 | L | B | 3.1711 | |
| 102 | F | B | 2.7815 | |
| 103 | S | B | 1.2794 | |
| 104 | Y | B | 0.2760 | |
| 105 | D | B | -1.3621 | |
| 106 | D | B | -1.4440 | |
| 107 | W | B | -0.4012 | |
| 108 | G | B | -0.3100 | |
| 109 | Q | B | -0.9032 | |
| 110 | G | B | -0.5177 | |
| 111 | T | B | -0.7068 | |
| 112 | Q | B | -0.9789 | |
| 113 | V | B | 0.0000 | |
| 114 | T | B | -0.4055 | |
| 115 | V | B | 0.0000 | |
| 116 | S | B | -0.6847 | |
| 117 | S | B | -0.5215 |
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 |
|||
| VM5B | -0.3784 | -0.024 | View | CSV | PDB |
| YW32B | -0.796 | -0.0155 | View | CSV | PDB |
| LM11B | -0.1494 | -0.0132 | View | CSV | PDB |
| VT5B | 0.1871 | -0.0386 | View | CSV | PDB |
| NR52B | 0.3229 | -0.0478 | View | CSV | PDB |
| NE52B | 0.4848 | -0.0307 | View | CSV | PDB |
| GE33B | 0.2944 | -0.0098 | View | CSV | PDB |
| LM45B | 0.4173 | -0.0111 | View | CSV | PDB |
| YH32B | 0.6905 | -0.0164 | View | CSV | PDB |
| GN33B | 1.2276 | -0.0064 | 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