Project name: e81f11883001f20

Status: done

Started: 2025-12-30 21:36:16
Settings
Chain sequence(s) A: SGLQQYLKATTNCQVTNAQIQALATKITSGKTSAYDKAVAIFNWVRDNISYSFYYNTKRGAVGTLNAKSGNCVDTTHLLIALSRAAGIPARYRHGTCKFTSGNTYGHVWAQIWVDGKWYAADATSSRNSFGVINNWNTATYTLKGTYASLSF
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]                                                (00:00:01)
[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 A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:02:04)
[INFO]       Auto_mut: Residue number 53 from chain A and a score of 2.352 (phenylalanine)         
                       selected for automated muatation                                            (00:02:05)
[INFO]       Auto_mut: Residue number 54 from chain A and a score of 1.398 (tyrosine) selected for 
                       automated muatation                                                         (00:02:05)
[INFO]       Auto_mut: Residue number 52 from chain A and a score of 1.289 (serine) selected for   
                       automated muatation                                                         (00:02:05)
[INFO]       Auto_mut: Residue number 132 from chain A and a score of 1.128 (valine) selected for  
                       automated muatation                                                         (00:02:05)
[INFO]       Auto_mut: Residue number 55 from chain A and a score of 1.060 (tyrosine) selected for 
                       automated muatation                                                         (00:02:05)
[INFO]       Auto_mut: Residue number 51 from chain A and a score of 0.860 (tyrosine) selected for 
                       automated muatation                                                         (00:02:05)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (tyrosine) into glutamic acid       (00:02:05)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (phenylalanine) into glutamic acid  
                       Mutating residue number 53 from chain A (phenylalanine) into glutamic acid  (00:02:05)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (phenylalanine) into aspartic acid  
                       Mutating residue number 53 from chain A (phenylalanine) into aspartic acid  (00:02:05)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (phenylalanine) into arginine       (00:03:02)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (tyrosine) into lysine              (00:03:06)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (phenylalanine) into lysine         (00:03:06)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (tyrosine) into aspartic acid       (00:04:10)
[INFO]       Auto_mut: Mutating residue number 52 from chain A (serine) into glutamic acid         (00:04:18)
[INFO]       Auto_mut: Mutating residue number 52 from chain A (serine) into aspartic acid         (00:04:33)
[INFO]       Auto_mut: Mutating residue number 52 from chain A (serine) into lysine                (00:05:14)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (tyrosine) into arginine            (00:05:22)
[INFO]       Auto_mut: Mutating residue number 52 from chain A (serine) into arginine              (00:05:26)
[INFO]       Auto_mut: Mutating residue number 132 from chain A (valine) into glutamic acid        (00:06:24)
[INFO]       Auto_mut: Mutating residue number 132 from chain A (valine) into aspartic acid        (00:06:28)
[INFO]       Auto_mut: Mutating residue number 55 from chain A (tyrosine) into glutamic acid       (00:06:39)
[INFO]       Auto_mut: Mutating residue number 132 from chain A (valine) into arginine             (00:07:20)
[INFO]       Auto_mut: Mutating residue number 132 from chain A (valine) into lysine               (00:07:22)
[INFO]       Auto_mut: Mutating residue number 55 from chain A (tyrosine) into lysine              (00:07:37)
[INFO]       Auto_mut: Mutating residue number 55 from chain A (tyrosine) into aspartic acid       (00:08:25)
[INFO]       Auto_mut: Mutating residue number 51 from chain A (tyrosine) into glutamic acid       (00:08:35)
[INFO]       Auto_mut: Mutating residue number 51 from chain A (tyrosine) into aspartic acid       (00:08:56)
[INFO]       Auto_mut: Mutating residue number 55 from chain A (tyrosine) into arginine            (00:09:19)
[INFO]       Auto_mut: Mutating residue number 51 from chain A (tyrosine) into lysine              (00:09:38)
[INFO]       Auto_mut: Mutating residue number 51 from chain A (tyrosine) into arginine            (00:09:54)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (phenylalanine) into      
                       glutamic acid: Energy difference: 0.5032 kcal/mol, Difference in average    
                       score from the base case: -0.0655                                           (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (phenylalanine) into      
                       lysine: Energy difference: 0.4705 kcal/mol, Difference in average score     
                       from the base case: -0.0609                                                 (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (phenylalanine) into      
                       aspartic acid: Energy difference: 0.3314 kcal/mol, Difference in average    
                       score from the base case: -0.0561                                           (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (phenylalanine) into      
                       arginine: Energy difference: 0.4359 kcal/mol, Difference in average score   
                       from the base case: -0.0692                                                 (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 4.1799 kcal/mol, Difference in average score from  
                       the base case: -0.0402                                                      (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (tyrosine) into lysine:   
                       Energy difference: 4.1196 kcal/mol, Difference in average score from the    
                       base case: -0.0414                                                          (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 4.0637 kcal/mol, Difference in average score from  
                       the base case: -0.0264                                                      (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (tyrosine) into arginine: 
                       Energy difference: 3.8006 kcal/mol, Difference in average score from the    
                       base case: -0.0447                                                          (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain A (serine) into glutamic    
                       acid: Energy difference: -0.6072 kcal/mol, Difference in average score from 
                       the base case: -0.0355                                                      (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain A (serine) into lysine:     
                       Energy difference: -0.6898 kcal/mol, Difference in average score from the   
                       base case: -0.0322                                                          (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain A (serine) into aspartic    
                       acid: Energy difference: -0.2760 kcal/mol, Difference in average score from 
                       the base case: -0.0268                                                      (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain A (serine) into arginine:   
                       Energy difference: -1.0206 kcal/mol, Difference in average score from the   
                       base case: -0.0280                                                          (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 132 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.5736 kcal/mol, Difference in average score from 
                       the base case: -0.0695                                                      (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 132 from chain A (valine) into lysine:    
                       Energy difference: -0.9790 kcal/mol, Difference in average score from the   
                       base case: -0.0639                                                          (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 132 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.6128 kcal/mol, Difference in average score from 
                       the base case: -0.0606                                                      (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 132 from chain A (valine) into arginine:  
                       Energy difference: -0.8928 kcal/mol, Difference in average score from the   
                       base case: -0.0663                                                          (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 0.3803 kcal/mol, Difference in average score from  
                       the base case: -0.0592                                                      (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain A (tyrosine) into lysine:   
                       Energy difference: -0.5549 kcal/mol, Difference in average score from the   
                       base case: -0.0442                                                          (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 0.1112 kcal/mol, Difference in average score from  
                       the base case: -0.0507                                                      (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain A (tyrosine) into arginine: 
                       Energy difference: -0.8443 kcal/mol, Difference in average score from the   
                       base case: -0.0469                                                          (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 51 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 1.8020 kcal/mol, Difference in average score from  
                       the base case: -0.0614                                                      (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 51 from chain A (tyrosine) into lysine:   
                       Energy difference: 0.8834 kcal/mol, Difference in average score from the    
                       base case: -0.0487                                                          (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 51 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 2.0779 kcal/mol, Difference in average score from  
                       the base case: -0.0609                                                      (00:10:54)
[INFO]       Auto_mut: Effect of mutation residue number 51 from chain A (tyrosine) into arginine: 
                       Energy difference: 0.2719 kcal/mol, Difference in average score from the    
                       base case: -0.0419                                                          (00:10:54)
[INFO]       Main:     Simulation completed successfully.                                          (00:10:59)
Show buried residues
Minimal score value
-2.6848
Maximal score value
2.3518
Average score
-0.5479
Total score value
-83.2835
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 S A -0.8286
2 G A -0.9121
3 L A -0.8316
4 Q A -1.7635
5 Q A -1.8960
6 Y A -1.0027
7 L A -0.9798
8 K A -2.0174
9 A A -1.0439
10 T A -0.6978
11 T A -0.3057
12 N A -0.7576
13 C A 0.0000
14 Q A -0.8399
15 V A 0.0000
16 T A -0.7929
17 N A -0.8087
18 A A -0.6770
19 Q A -1.1085
20 I A 0.0000
21 Q A -1.1031
22 A A -0.8891
23 L A -0.7310
24 A A 0.0000
25 T A -1.2074
26 K A -1.7665
27 I A -0.8184
28 T A -1.2266
29 S A -1.2370
30 G A -1.3756
31 K A -1.5274
32 T A -0.9365
33 S A -1.0356
34 A A -0.8196
35 Y A -0.6890
36 D A -1.6297
37 K A -1.1456
38 A A 0.0000
39 V A -0.1562
40 A A -0.3990
41 I A 0.0000
42 F A 0.0000
43 N A -0.9133
44 W A -0.7373
45 V A 0.0000
46 R A -1.6715
47 D A -2.4295
48 N A -1.9965
49 I A 0.0000
50 S A -0.5495
51 Y A 0.8600
52 S A 1.2888
53 F A 2.3518
54 Y A 1.3979
55 Y A 1.0597
56 N A -0.6528
57 T A -1.3521
58 K A -2.4406
59 R A -2.6848
60 G A 0.0000
61 A A 0.0000
62 V A -0.9103
63 G A -1.5304
64 T A 0.0000
65 L A 0.0000
66 N A -1.8988
67 A A -1.4502
68 K A -1.8083
69 S A -0.8368
70 G A 0.0000
71 N A 0.0000
72 C A 0.0000
73 V A 0.0000
74 D A 0.0000
75 T A 0.0000
76 T A 0.0000
77 H A 0.0000
78 L A 0.0000
79 L A 0.0000
80 I A 0.0000
81 A A 0.0000
82 L A 0.0000
83 S A 0.0000
84 R A 0.0000
85 A A -0.5256
86 A A -0.2674
87 G A -0.5460
88 I A 0.0000
89 P A -0.3787
90 A A 0.0000
91 R A -0.2138
92 Y A 0.0000
93 R A -0.3535
94 H A 0.0000
95 G A 0.0000
96 T A -0.2850
97 C A 0.0000
98 K A -1.7415
99 F A -1.1918
100 T A -1.0757
101 S A -0.9291
102 G A -1.3155
103 N A -1.4625
104 T A -0.8679
105 Y A 0.0107
106 G A -0.3191
107 H A 0.0000
108 V A 0.0000
109 W A 0.0000
110 A A 0.0000
111 Q A -0.2342
112 I A 0.0000
113 W A -0.5196
114 V A 0.0000
115 D A -2.2656
116 G A -2.0060
117 K A -2.1497
118 W A -0.8127
119 Y A -0.0639
120 A A 0.4073
121 A A 0.0000
122 D A 0.0000
123 A A 0.0000
124 T A -0.4138
125 S A -1.0261
126 S A -1.6544
127 R A -1.8250
128 N A 0.0000
129 S A -0.1793
130 F A 0.0000
131 G A 0.7103
132 V A 1.1284
133 I A 0.0160
134 N A -1.0131
135 N A -1.0740
136 W A 0.0000
137 N A -1.4249
138 T A -0.5294
139 A A -0.3891
140 T A -0.3317
141 Y A -0.1757
142 T A -0.0780
143 L A 0.1116
144 K A -1.2794
145 G A -0.5756
146 T A -0.2096
147 Y A -0.0944
148 A A -0.4729
149 S A -0.4137
150 L A 0.0000
151 S A -0.1234
152 F A 0.0020
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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
VK132A -0.979 -0.0639 View CSV PDB
VR132A -0.8928 -0.0663 View CSV PDB
YR55A -0.8443 -0.0469 View CSV PDB
YK55A -0.5549 -0.0442 View CSV PDB
SR52A -1.0206 -0.028 View CSV PDB
SE52A -0.6072 -0.0355 View CSV PDB
FD53A 0.3314 -0.0561 View CSV PDB
FR53A 0.4359 -0.0692 View CSV PDB
YR51A 0.2719 -0.0419 View CSV PDB
YK51A 0.8834 -0.0487 View CSV PDB
YR54A 3.8006 -0.0447 View CSV PDB
YK54A 4.1196 -0.0414 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018