Project name: db7599cf9a8ab0a

Status: done

Started: 2025-02-07 20:53:27
Settings
Chain sequence(s) A: ALDTNYCRSSTEKNCCVRQLRIDFRKDLGWKWIHEPKGYHANRCKGPCPRIWSLDTQYSKKLALENQHNPGASAAPKCVPQALEPLPIVYEKGRKPKREQLSNMIVRSCKCS
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                                          (00:01:58)
[INFO]       Auto_mut: Residue number 51 from chain A and a score of 1.302 (isoleucine) selected   
                       for automated muatation                                                     (00:01:59)
[INFO]       Auto_mut: Residue number 52 from chain A and a score of 0.383 (tryptophan) selected   
                       for automated muatation                                                     (00:01:59)
[INFO]       Auto_mut: Residue number 53 from chain A and a score of -0.113 (serine) selected for  
                       automated muatation                                                         (00:01:59)
[INFO]       Auto_mut: Mutating residue number 51 from chain A (isoleucine) into glutamic acid     (00:01:59)
[INFO]       Auto_mut: Mutating residue number 51 from chain A (isoleucine) into lysine            (00:01:59)
[INFO]       Auto_mut: Mutating residue number 51 from chain A (isoleucine) into aspartic acid     (00:01:59)
[INFO]       Auto_mut: Mutating residue number 51 from chain A (isoleucine) into arginine          (00:03:18)
[INFO]       Auto_mut: Mutating residue number 52 from chain A (tryptophan) into glutamic acid     (00:03:19)
[INFO]       Auto_mut: Mutating residue number 52 from chain A (tryptophan) into lysine            (00:03:26)
[INFO]       Auto_mut: Mutating residue number 52 from chain A (tryptophan) into aspartic acid     (00:04:19)
[INFO]       Auto_mut: Mutating residue number 52 from chain A (tryptophan) into arginine          (00:04:35)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (serine) into glutamic acid         (00:04:36)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (serine) into lysine                (00:05:19)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (serine) into aspartic acid         (00:05:49)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (serine) into arginine              (00:05:56)
[INFO]       Auto_mut: Effect of mutation residue number 51 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: -2.2658 kcal/mol, Difference in average   
                       score from the base case: -0.0793                                           (00:07:13)
[INFO]       Auto_mut: Effect of mutation residue number 51 from chain A (isoleucine) into lysine: 
                       Energy difference: -1.7321 kcal/mol, Difference in average score from the   
                       base case: -0.0884                                                          (00:07:13)
[INFO]       Auto_mut: Effect of mutation residue number 51 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: -2.1381 kcal/mol, Difference in average   
                       score from the base case: -0.0986                                           (00:07:13)
[INFO]       Auto_mut: Effect of mutation residue number 51 from chain A (isoleucine) into         
                       arginine: Energy difference: -1.5460 kcal/mol, Difference in average score  
                       from the base case: -0.0932                                                 (00:07:13)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain A (tryptophan) into         
                       glutamic acid: Energy difference: 3.9922 kcal/mol, Difference in average    
                       score from the base case: 0.0043                                            (00:07:13)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain A (tryptophan) into lysine: 
                       Energy difference: 2.6365 kcal/mol, Difference in average score from the    
                       base case: 0.0022                                                           (00:07:13)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain A (tryptophan) into         
                       aspartic acid: Energy difference: 4.4540 kcal/mol, Difference in average    
                       score from the base case: 0.0056                                            (00:07:13)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain A (tryptophan) into         
                       arginine: Energy difference: 2.5973 kcal/mol, Difference in average score   
                       from the base case: -0.0114                                                 (00:07:13)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (serine) into glutamic    
                       acid: Energy difference: -1.5415 kcal/mol, Difference in average score from 
                       the base case: -0.0161                                                      (00:07:13)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (serine) into lysine:     
                       Energy difference: -1.2519 kcal/mol, Difference in average score from the   
                       base case: -0.0083                                                          (00:07:13)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (serine) into aspartic    
                       acid: Energy difference: -0.4694 kcal/mol, Difference in average score from 
                       the base case: -0.0026                                                      (00:07:13)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (serine) into arginine:   
                       Energy difference: -1.0793 kcal/mol, Difference in average score from the   
                       base case: -0.0311                                                          (00:07:13)
[INFO]       Main:     Simulation completed successfully.                                          (00:07:16)
Show buried residues
Minimal score value
-4.1363
Maximal score value
1.3025
Average score
-1.5133
Total score value
-169.4855
Download the table (csv)

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
mutation
1 A A -0.4816
2 L A 0.0000
3 D A -1.5422
4 T A -1.7689
5 N A -1.9704
6 Y A -0.9716
7 C A 0.0000
8 R A -2.6041
9 S A -1.3571
10 S A -1.1210
11 T A -0.9778
12 E A -1.4331
13 K A -2.2265
14 N A -1.4709
15 C A 0.0000
16 C A 0.0000
17 V A 0.0000
18 R A -2.5090
19 Q A -2.5817
20 L A -1.7513
21 R A -2.6432
22 I A -2.0326
23 D A 0.0000
24 F A 0.0000
25 R A -3.6641
26 K A -3.6452
27 D A -2.9426
28 L A -1.3334
29 G A -1.8505
30 W A -1.5221
31 K A -2.2211
32 W A -1.0816
33 I A 0.0000
34 H A -2.2855
35 E A -2.7541
36 P A -2.1235
37 K A -3.1492
38 G A -2.4823
39 Y A 0.0000
40 H A -1.9985
41 A A 0.0000
42 N A 0.0000
43 R A -2.4884
44 C A -2.2023
45 K A -2.8271
46 G A -1.8516
47 P A -1.4078
48 C A 0.0000
49 P A -0.6486
50 R A -0.9563
51 I A 1.3025
52 W A 0.3825
53 S A -0.1128
54 L A -0.7928
55 D A -1.2446
56 T A -1.1142
57 Q A -1.5075
58 Y A -0.2515
59 S A 0.0000
60 K A -1.7776
61 K A -2.3874
62 L A -1.6460
63 A A 0.0000
64 L A -1.8785
65 E A -3.1532
66 N A -2.7491
67 Q A -2.9683
68 H A -2.7163
69 N A -2.7839
70 P A -1.9925
71 G A -1.4170
72 A A -1.0402
73 S A -1.0408
74 A A -0.6689
75 A A -1.3361
76 P A 0.0000
77 K A -1.9576
78 C A 0.0000
79 V A -1.1766
80 P A -1.4192
81 Q A -1.4494
82 A A -0.8757
83 L A -0.5017
84 E A -0.9981
85 P A -1.1751
86 L A 0.0000
87 P A -1.7374
88 I A 0.0000
89 V A -2.6558
90 Y A -2.9947
91 E A -4.1137
92 K A -3.9668
93 G A -3.2456
94 R A -4.0261
95 K A -4.1363
96 P A -3.4340
97 K A -3.6195
98 R A -3.4864
99 E A -2.9329
100 Q A -2.4473
101 L A -1.3631
102 S A -1.2161
103 N A -1.3220
104 M A -0.7875
105 I A -0.6983
106 V A 0.0000
107 R A -1.4470
108 S A 0.0000
109 C A 0.0000
110 K A -1.4139
111 C A 0.0000
112 S A -1.1147
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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
ID51A -2.1381 -0.0986 View CSV PDB
IE51A -2.2658 -0.0793 View CSV PDB
SR53A -1.0793 -0.0311 View CSV PDB
SE53A -1.5415 -0.0161 View CSV PDB
WR52A 2.5973 -0.0114 View CSV PDB
WK52A 2.6365 0.0022 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018