Project name: 3H3-VL-Backmutation

Status: done

Started: 2026-01-16 05:02:28
Settings
Chain sequence(s) A: QVQLVQSGAEVKKPGSSVKVSCKASGGSFSRLAISWVRQAPGQGLEWMGGIIPIIGTADYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARDLSSGYSDALDIWGQGSVITVSS
B: SYELTQPLSVSVSPGQTSTITCSGEALGDRYACWYQQKPGQSPVLVIYQDTKRPSGIPERFSGSNSGNTATLTISGTQAMDEADYYCQTWDRSTGVFGTGTKVTVL
input PDB
Selected Chain(s) A,B
Distance of aggregation 5 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 all 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                                          (00:01:58)
[INFO]       Auto_mut: Residue number 55 from chain A and a score of 2.223 (isoleucine) selected   
                       for automated muatation                                                     (00:02:00)
[INFO]       Auto_mut: Residue number 54 from chain A and a score of 1.981 (isoleucine) selected   
                       for automated muatation                                                     (00:02:00)
[INFO]       Auto_mut: Residue number 106 from chain B and a score of 1.565 (leucine) selected for 
                       automated muatation                                                         (00:02:00)
[INFO]       Auto_mut: Residue number 8 from chain B and a score of 1.508 (leucine) selected for   
                       automated muatation                                                         (00:02:00)
[INFO]       Auto_mut: Residue number 11 from chain A and a score of 1.500 (valine) selected for   
                       automated muatation                                                         (00:02:00)
[INFO]       Auto_mut: Residue number 5 from chain A and a score of 1.257 (valine) selected for    
                       automated muatation                                                         (00:02:00)
[INFO]       Auto_mut: Mutating residue number 55 from chain A (isoleucine) into glutamic acid     (00:02:00)
[INFO]       Auto_mut: Mutating residue number 55 from chain A (isoleucine) into aspartic acid     (00:02:00)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (isoleucine) into glutamic acid     (00:02:00)
[INFO]       Auto_mut: Mutating residue number 55 from chain A (isoleucine) into arginine          (00:02:46)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (isoleucine) into lysine            (00:02:48)
[INFO]       Auto_mut: Mutating residue number 55 from chain A (isoleucine) into lysine            (00:02:49)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (isoleucine) into aspartic acid     (00:03:37)
[INFO]       Auto_mut: Mutating residue number 106 from chain B (leucine) into glutamic acid       (00:03:40)
[INFO]       Auto_mut: Mutating residue number 106 from chain B (leucine) into aspartic acid       (00:03:49)
[INFO]       Auto_mut: Mutating residue number 106 from chain B (leucine) into lysine              (00:04:28)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (isoleucine) into arginine          (00:04:28)
[INFO]       Auto_mut: Mutating residue number 106 from chain B (leucine) into arginine            (00:04:35)
[INFO]       Auto_mut: Mutating residue number 8 from chain B (leucine) into glutamic acid         (00:05:21)
[INFO]       Auto_mut: Mutating residue number 8 from chain B (leucine) into aspartic acid         (00:05:24)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (valine) into glutamic acid         (00:05:25)
[INFO]       Auto_mut: Mutating residue number 8 from chain B (leucine) into lysine                (00:06:09)
[INFO]       Auto_mut: Mutating residue number 8 from chain B (leucine) into arginine              (00:06:11)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (valine) into lysine                (00:06:12)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (valine) into aspartic acid         (00:07:06)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (valine) into glutamic acid          (00:07:12)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (valine) into aspartic acid          (00:07:15)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (valine) into arginine              (00:07:52)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (valine) into lysine                 (00:08:00)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (valine) into arginine               (00:08:12)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 0.1261 kcal/mol, Difference in average    
                       score from the base case: -0.0233                                           (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain A (isoleucine) into lysine: 
                       Energy difference: -0.1832 kcal/mol, Difference in average score from the   
                       base case: -0.0250                                                          (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 0.6340 kcal/mol, Difference in average    
                       score from the base case: -0.0225                                           (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain A (isoleucine) into         
                       arginine: Energy difference: -0.4204 kcal/mol, Difference in average score  
                       from the base case: -0.0284                                                 (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 0.8328 kcal/mol, Difference in average    
                       score from the base case: -0.0216                                           (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (isoleucine) into lysine: 
                       Energy difference: 0.2177 kcal/mol, Difference in average score from the    
                       base case: -0.0204                                                          (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 1.0787 kcal/mol, Difference in average    
                       score from the base case: -0.0252                                           (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (isoleucine) into         
                       arginine: Energy difference: 0.0705 kcal/mol, Difference in average score   
                       from the base case: -0.0211                                                 (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 106 from chain B (leucine) into glutamic  
                       acid: Energy difference: 0.0418 kcal/mol, Difference in average score from  
                       the base case: -0.0205                                                      (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 106 from chain B (leucine) into lysine:   
                       Energy difference: -0.0774 kcal/mol, Difference in average score from the   
                       base case: -0.0198                                                          (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 106 from chain B (leucine) into aspartic  
                       acid: Energy difference: 0.5283 kcal/mol, Difference in average score from  
                       the base case: -0.0205                                                      (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 106 from chain B (leucine) into arginine: 
                       Energy difference: -0.1221 kcal/mol, Difference in average score from the   
                       base case: -0.0207                                                          (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain B (leucine) into glutamic    
                       acid: Energy difference: -0.3949 kcal/mol, Difference in average score from 
                       the base case: -0.0215                                                      (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain B (leucine) into lysine:     
                       Energy difference: -0.1221 kcal/mol, Difference in average score from the   
                       base case: -0.0187                                                          (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain B (leucine) into aspartic    
                       acid: Energy difference: -0.2181 kcal/mol, Difference in average score from 
                       the base case: -0.0213                                                      (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain B (leucine) into arginine:   
                       Energy difference: -0.2398 kcal/mol, Difference in average score from the   
                       base case: -0.0218                                                          (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (valine) into glutamic    
                       acid: Energy difference: 0.4963 kcal/mol, Difference in average score from  
                       the base case: -0.0260                                                      (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (valine) into lysine:     
                       Energy difference: 0.0657 kcal/mol, Difference in average score from the    
                       base case: -0.0247                                                          (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (valine) into aspartic    
                       acid: Energy difference: 0.1626 kcal/mol, Difference in average score from  
                       the base case: -0.0254                                                      (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (valine) into arginine:   
                       Energy difference: 0.0154 kcal/mol, Difference in average score from the    
                       base case: -0.0254                                                          (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (valine) into glutamic     
                       acid: Energy difference: 0.4321 kcal/mol, Difference in average score from  
                       the base case: -0.0140                                                      (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (valine) into lysine:      
                       Energy difference: 0.2565 kcal/mol, Difference in average score from the    
                       base case: -0.0138                                                          (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (valine) into aspartic     
                       acid: Energy difference: 0.4848 kcal/mol, Difference in average score from  
                       the base case: -0.0173                                                      (00:09:14)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (valine) into arginine:    
                       Energy difference: 0.1977 kcal/mol, Difference in average score from the    
                       base case: -0.0140                                                          (00:09:14)
[INFO]       Main:     Simulation completed successfully.                                          (00:09:19)
Show buried residues
Minimal score value
-1.9341
Maximal score value
2.2231
Average score
-0.2191
Total score value
-49.7309
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 Q A -1.1579
2 V A -0.2897
3 Q A -1.1145
4 L A 0.0000
5 V A 1.2569
6 Q A 0.0000
7 S A -0.1652
8 G A -0.4700
9 A A -0.0868
10 E A -0.7570
11 V A 1.4997
12 K A -0.3537
13 K A -1.7884
14 P A -0.5111
15 G A -0.5240
16 S A -0.1553
17 S A -0.0905
18 V A 0.0000
19 K A -1.8376
20 V A 0.0000
21 S A -0.0130
22 C A 0.0000
23 K A -1.0927
24 A A 0.0000
25 S A -0.1665
26 G A -0.5313
27 G A -0.5906
28 S A -0.2981
29 F A 0.0000
30 S A -0.2329
31 R A -1.8203
32 L A -0.1508
33 A A 0.0000
34 I A 0.0000
35 S A 0.0000
36 W A 0.0000
37 V A 0.0000
38 R A -0.2429
39 Q A -0.1660
40 A A -0.0601
41 P A -0.3428
42 G A -0.7346
43 Q A -1.3065
44 G A -0.3488
45 L A 0.0000
46 E A -0.3295
47 W A 0.0000
48 M A 0.0000
49 G A 0.0000
50 G A 0.0000
51 I A 0.0000
52 I A 0.2736
53 P A 0.0000
54 I A 1.9809
55 I A 2.2231
56 G A -0.1052
57 T A -0.1548
58 A A -0.1167
59 D A -0.5356
60 Y A 0.2027
61 A A 0.0000
62 Q A -1.5173
63 K A -1.9249
64 F A 0.0000
65 Q A -1.2840
66 G A -0.7736
67 R A -0.5512
68 V A 0.0000
69 T A -0.0603
70 I A 0.0000
71 T A -0.0415
72 A A -0.1502
73 D A -1.0256
74 E A -1.3636
75 S A -0.4475
76 T A -0.1085
77 S A -0.1990
78 T A -0.1747
79 A A 0.0000
80 Y A 0.2545
81 M A 0.0000
82 E A -1.1741
83 L A 0.0000
84 S A -0.1322
85 S A -0.2764
86 L A 0.0000
87 R A -1.8842
88 S A -0.8937
89 E A -1.8588
90 D A 0.0000
91 T A -0.0163
92 A A 0.0000
93 V A 0.5299
94 Y A 0.0000
95 Y A 0.0000
96 C A 0.0000
97 A A 0.0000
98 R A -0.2417
99 D A 0.0000
100 L A 0.5496
101 S A -0.0042
102 S A -0.1632
103 G A -0.0704
104 Y A 0.0934
105 S A -0.1852
106 D A 0.0000
107 A A 0.0000
108 L A 0.0000
109 D A -0.2456
110 I A 0.2939
111 W A 0.1774
112 G A 0.0000
113 Q A -1.2096
114 G A -0.2798
115 S A 0.0000
116 V A 1.2153
117 I A 0.0000
118 T A 0.1801
119 V A 0.0000
120 S A -0.2002
121 S A -0.2418
1 S B -0.1799
2 Y B -0.2004
3 E B -1.7865
4 L B 0.0000
5 T B -0.0709
6 Q B 0.0000
7 P B 0.1752
8 L B 1.5079
9 S B 0.1021
10 V B 0.2593
11 S B -0.1573
12 V B 0.0000
13 S B -0.0430
14 P B -0.3259
15 G B -0.7268
16 Q B -1.2029
17 T B -0.2959
18 S B 0.0000
19 T B -0.0731
20 I B 0.0000
21 T B -0.0382
22 C B 0.0000
23 S B -0.1116
24 G B -0.4210
25 E B -1.8249
26 A B -0.3967
27 L B 0.0000
28 G B -0.6246
29 D B -1.9178
30 R B -0.5794
31 Y B 1.1377
32 A B 0.0000
33 C B 0.0000
34 W B 0.0000
35 Y B 0.0000
36 Q B -0.1629
37 Q B 0.0000
38 K B -0.4772
39 P B -0.4223
40 G B -0.6967
41 Q B -1.0725
42 S B -0.2257
43 P B 0.0000
44 V B 1.1994
45 L B 0.0000
46 V B 0.0000
47 I B 0.0000
48 Y B 0.1583
49 Q B -0.1115
50 D B -0.3293
51 T B -0.3618
52 K B -1.4086
53 R B -1.1427
54 P B -0.2506
55 S B -0.3058
56 G B -0.4571
57 I B 0.1368
58 P B -0.4246
59 E B -1.9016
60 R B -0.6590
61 F B 0.0000
62 S B -0.1551
63 G B -0.1302
64 S B -0.2572
65 N B -0.2818
66 S B -0.3643
67 G B -0.6977
68 N B -0.9601
69 T B -0.1988
70 A B 0.0000
71 T B -0.0184
72 L B 0.0000
73 T B -0.0264
74 I B 0.0000
75 S B -0.1837
76 G B -0.1939
77 T B 0.0000
78 Q B -0.5761
79 A B 0.1444
80 M B 1.0642
81 D B 0.0000
82 E B -0.8730
83 A B 0.0000
84 D B -0.7459
85 Y B 0.0000
86 Y B 0.0000
87 C B 0.0000
88 Q B 0.0000
89 T B 0.0000
90 W B 0.0000
91 D B -0.7553
92 R B -1.9341
93 S B -0.4115
94 T B -0.0353
95 G B 0.0000
96 V B 0.2473
97 F B 0.2265
98 G B 0.0000
99 T B -0.0790
100 G B -0.0577
101 T B 0.0000
102 K B -1.1882
103 V B 0.0000
104 T B -0.0004
105 V B 0.4659
106 L B 1.5646
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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
IR55A -0.4204 -0.0284 View CSV PDB
LE8B -0.3949 -0.0215 View CSV PDB
IK55A -0.1832 -0.025 View CSV PDB
LR8B -0.2398 -0.0218 View CSV PDB
LR106B -0.1221 -0.0207 View CSV PDB
LK106B -0.0774 -0.0198 View CSV PDB
VR11A 0.0154 -0.0254 View CSV PDB
VK11A 0.0657 -0.0247 View CSV PDB
IR54A 0.0705 -0.0211 View CSV PDB
IK54A 0.2177 -0.0204 View CSV PDB
VR5A 0.1977 -0.014 View CSV PDB
VK5A 0.2565 -0.0138 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018