Project name: 3H3_PDB2

Status: done

Started: 2026-01-15 08:41:13
Settings
Chain sequence(s) A: QVQLVQSGAEVKKPGSSVKVSCKASGGSFSRLAFSWVRQAPGQGLEWMGGIIPIIGTADYAQKFQGRVTITADESTNTAYMELSSLRSEDTAVYYCARDLSSGYSDALDIWGQGSVITVSS
B: SYELTQPLSVSVSPGQTSTITCSGEALGDRYASWYQQRPGQSPILVIYQDTKRPSGIPERFSGSSSRGTATLTISGTQATDEADYYCQTWDRSTGVFGTGTKVTVL
input PDB
Selected Chain(s) A,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 all chain(s) selected           (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:02:50)
[INFO]       Auto_mut: Residue number 55 from chain A and a score of 2.477 (isoleucine) selected   
                       for automated muatation                                                     (00:02:52)
[INFO]       Auto_mut: Residue number 54 from chain A and a score of 1.672 (isoleucine) selected   
                       for automated muatation                                                     (00:02:52)
[INFO]       Auto_mut: Residue number 106 from chain B and a score of 1.274 (leucine) selected for 
                       automated muatation                                                         (00:02:52)
[INFO]       Auto_mut: Residue number 52 from chain A and a score of 1.245 (isoleucine) selected   
                       for automated muatation                                                     (00:02:52)
[INFO]       Auto_mut: Residue number 116 from chain A and a score of 1.072 (valine) selected for  
                       automated muatation                                                         (00:02:52)
[INFO]       Auto_mut: Residue number 8 from chain B and a score of 1.063 (leucine) selected for   
                       automated muatation                                                         (00:02:52)
[INFO]       Auto_mut: Mutating residue number 55 from chain A (isoleucine) into glutamic acid     (00:02:52)
[INFO]       Auto_mut: Mutating residue number 55 from chain A (isoleucine) into aspartic acid     (00:02:52)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (isoleucine) into glutamic acid     (00:02:52)
[INFO]       Auto_mut: Mutating residue number 55 from chain A (isoleucine) into arginine          (00:04:18)
[INFO]       Auto_mut: Mutating residue number 55 from chain A (isoleucine) into lysine            (00:04:21)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (isoleucine) into lysine            (00:04:24)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (isoleucine) into aspartic acid     (00:05:52)
[INFO]       Auto_mut: Mutating residue number 106 from chain B (leucine) into glutamic acid       (00:05:56)
[INFO]       Auto_mut: Mutating residue number 106 from chain B (leucine) into aspartic acid       (00:06:06)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (isoleucine) into arginine          (00:07:21)
[INFO]       Auto_mut: Mutating residue number 106 from chain B (leucine) into lysine              (00:07:23)
[INFO]       Auto_mut: Mutating residue number 106 from chain B (leucine) into arginine            (00:07:30)
[INFO]       Auto_mut: Mutating residue number 52 from chain A (isoleucine) into glutamic acid     (00:08:49)
[INFO]       Auto_mut: Mutating residue number 52 from chain A (isoleucine) into aspartic acid     (00:08:56)
[INFO]       Auto_mut: Mutating residue number 116 from chain A (valine) into glutamic acid        (00:09:06)
[INFO]       Auto_mut: Mutating residue number 52 from chain A (isoleucine) into lysine            (00:10:21)
[INFO]       Auto_mut: Mutating residue number 52 from chain A (isoleucine) into arginine          (00:10:25)
[INFO]       Auto_mut: Mutating residue number 116 from chain A (valine) into lysine               (00:10:33)
[INFO]       Auto_mut: Mutating residue number 116 from chain A (valine) into aspartic acid        (00:12:07)
[INFO]       Auto_mut: Mutating residue number 8 from chain B (leucine) into glutamic acid         (00:12:09)
[INFO]       Auto_mut: Mutating residue number 8 from chain B (leucine) into aspartic acid         (00:12:24)
[INFO]       Auto_mut: Mutating residue number 116 from chain A (valine) into arginine             (00:13:31)
[INFO]       Auto_mut: Mutating residue number 8 from chain B (leucine) into lysine                (00:13:52)
[INFO]       Auto_mut: Mutating residue number 8 from chain B (leucine) into arginine              (00:14:00)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: -0.0251 kcal/mol, Difference in average   
                       score from the base case: -0.0457                                           (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain A (isoleucine) into lysine: 
                       Energy difference: -0.1521 kcal/mol, Difference in average score from the   
                       base case: -0.0544                                                          (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 0.4444 kcal/mol, Difference in average    
                       score from the base case: -0.0429                                           (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain A (isoleucine) into         
                       arginine: Energy difference: -0.0993 kcal/mol, Difference in average score  
                       from the base case: -0.0485                                                 (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 0.6423 kcal/mol, Difference in average    
                       score from the base case: -0.0432                                           (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (isoleucine) into lysine: 
                       Energy difference: 0.7052 kcal/mol, Difference in average score from the    
                       base case: -0.0360                                                          (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 0.8568 kcal/mol, Difference in average    
                       score from the base case: -0.0463                                           (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (isoleucine) into         
                       arginine: Energy difference: 0.8446 kcal/mol, Difference in average score   
                       from the base case: -0.0470                                                 (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 106 from chain B (leucine) into glutamic  
                       acid: Energy difference: 0.0862 kcal/mol, Difference in average score from  
                       the base case: -0.0354                                                      (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 106 from chain B (leucine) into lysine:   
                       Energy difference: -0.0421 kcal/mol, Difference in average score from the   
                       base case: -0.0338                                                          (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 106 from chain B (leucine) into aspartic  
                       acid: Energy difference: 0.6001 kcal/mol, Difference in average score from  
                       the base case: -0.0349                                                      (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 106 from chain B (leucine) into arginine: 
                       Energy difference: -0.7782 kcal/mol, Difference in average score from the   
                       base case: -0.0312                                                          (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 1.5334 kcal/mol, Difference in average    
                       score from the base case: -0.0293                                           (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain A (isoleucine) into lysine: 
                       Energy difference: 0.6112 kcal/mol, Difference in average score from the    
                       base case: -0.0203                                                          (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 2.3274 kcal/mol, Difference in average    
                       score from the base case: -0.0187                                           (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain A (isoleucine) into         
                       arginine: Energy difference: -0.0324 kcal/mol, Difference in average score  
                       from the base case: -0.0143                                                 (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 116 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.0458 kcal/mol, Difference in average score from 
                       the base case: -0.0351                                                      (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 116 from chain A (valine) into lysine:    
                       Energy difference: -0.2415 kcal/mol, Difference in average score from the   
                       base case: -0.0354                                                          (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 116 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.5656 kcal/mol, Difference in average score from  
                       the base case: -0.0366                                                      (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 116 from chain A (valine) into arginine:  
                       Energy difference: -0.4850 kcal/mol, Difference in average score from the   
                       base case: -0.0404                                                          (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain B (leucine) into glutamic    
                       acid: Energy difference: -0.2466 kcal/mol, Difference in average score from 
                       the base case: -0.0371                                                      (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain B (leucine) into lysine:     
                       Energy difference: -0.0039 kcal/mol, Difference in average score from the   
                       base case: -0.0299                                                          (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain B (leucine) into aspartic    
                       acid: Energy difference: -0.0701 kcal/mol, Difference in average score from 
                       the base case: -0.0369                                                      (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain B (leucine) into arginine:   
                       Energy difference: -0.3905 kcal/mol, Difference in average score from the   
                       base case: -0.0377                                                          (00:15:54)
[INFO]       Main:     Simulation completed successfully.                                          (00:16:00)
Show buried residues
Minimal score value
-2.9569
Maximal score value
2.4768
Average score
-0.6052
Total score value
-137.3703
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 -1.6050
2 V A 0.0000
3 Q A -1.2490
4 L A 0.0000
5 V A 0.0845
6 Q A 0.0000
7 S A -0.5563
8 G A -0.4926
9 A A 0.1916
10 E A -0.2260
11 V A 0.8418
12 K A -1.0361
13 K A -2.1353
14 P A -2.0020
15 G A -1.4912
16 S A -1.2204
17 S A -1.3875
18 V A 0.0000
19 K A -2.1188
20 V A 0.0000
21 S A -0.6042
22 C A 0.0000
23 K A -0.9559
24 A A 0.0000
25 S A -1.1128
26 G A -1.3136
27 G A -1.3692
28 S A -1.3452
29 F A 0.0000
30 S A -0.7167
31 R A -1.0350
32 L A -0.5347
33 A A 0.1788
34 F A 0.0000
35 S A 0.0000
36 W A 0.0000
37 V A 0.0000
38 R A -0.3399
39 Q A -0.5825
40 A A -0.9504
41 P A -0.9531
42 G A -1.2482
43 Q A -1.6795
44 G A -1.0938
45 L A 0.0000
46 E A -0.8002
47 W A 0.0000
48 M A 0.0000
49 G A 0.0000
50 G A -0.1332
51 I A 0.0000
52 I A 1.2451
53 P A 0.0000
54 I A 1.6723
55 I A 2.4768
56 G A 0.8914
57 T A 0.5353
58 A A -0.0414
59 D A -0.9482
60 Y A -1.1196
61 A A 0.0000
62 Q A -2.5314
63 K A -2.7429
64 F A 0.0000
65 Q A -2.4942
66 G A -1.6485
67 R A -1.4134
68 V A 0.0000
69 T A -0.8953
70 I A 0.0000
71 T A -0.4023
72 A A -0.5667
73 D A -1.7703
74 E A -2.3288
75 S A -1.5036
76 T A -1.3739
77 N A -1.8437
78 T A 0.0000
79 A A 0.0000
80 Y A -0.6341
81 M A 0.0000
82 E A -1.4913
83 L A 0.0000
84 S A -1.1210
85 S A -1.0913
86 L A 0.0000
87 R A -2.6892
88 S A -2.2358
89 E A -2.4582
90 D A 0.0000
91 T A -0.6838
92 A A 0.0000
93 V A 0.5297
94 Y A 0.0000
95 Y A 0.0000
96 C A 0.0000
97 A A 0.0000
98 R A -0.3165
99 D A 0.0000
100 L A -0.1104
101 S A -0.5610
102 S A -0.1883
103 G A -0.0994
104 Y A 0.8328
105 S A 0.0000
106 D A -0.6541
107 A A 0.0000
108 L A 0.0000
109 D A -0.0953
110 I A -0.1525
111 W A 0.0000
112 G A 0.0000
113 Q A -1.1536
114 G A -0.4468
115 S A 0.0000
116 V A 1.0717
117 I A 0.0000
118 T A -0.0948
119 V A 0.0000
120 S A -1.0350
121 S A -0.7603
1 S B -0.9309
2 Y B -1.1921
3 E B -2.1257
4 L B 0.0000
5 T B -0.3715
6 Q B 0.0000
7 P B 0.4439
8 L B 1.0626
9 S B 0.0722
10 V B -0.0342
11 S B -0.0584
12 V B 0.0000
13 S B -0.3288
14 P B -0.8594
15 G B -1.4440
16 Q B -1.6924
17 T B -1.0342
18 S B 0.0000
19 T B -0.0849
20 I B 0.0000
21 T B -0.1597
22 C B 0.0000
23 S B -1.1246
24 G B -1.7573
25 E B -2.9569
26 A B -2.2115
27 L B 0.0000
28 G B -2.5755
29 D B -2.7934
30 R B -1.8197
31 Y B 0.1103
32 A B 0.0000
33 S B 0.0000
34 W B 0.0000
35 Y B 0.0000
36 Q B 0.0000
37 Q B 0.0000
38 R B -2.0589
39 P B -1.6622
40 G B -1.5965
41 Q B -1.9509
42 S B -0.9943
43 P B 0.0000
44 I B 0.7783
45 L B 0.0000
46 V B 0.0000
47 I B 0.0000
48 Y B -0.6744
49 Q B -0.4483
50 D B -0.6941
51 T B -1.0694
52 K B -1.9596
53 R B -1.9512
54 P B -0.8785
55 S B -0.7715
56 G B -0.8660
57 I B -0.7413
58 P B -1.3424
59 E B -2.2409
60 R B -1.4216
61 F B 0.0000
62 S B -1.1191
63 G B 0.0000
64 S B -0.5028
65 S B -0.7741
66 S B -1.4659
67 R B -2.5991
68 G B -2.1280
69 T B -1.1554
70 A B 0.0000
71 T B -0.2583
72 L B 0.0000
73 T B -0.2455
74 I B 0.0000
75 S B -1.1680
76 G B -1.3406
77 T B 0.0000
78 Q B -1.2591
79 A B -0.5113
80 T B -0.7897
81 D B 0.0000
82 E B -1.5725
83 A B 0.0000
84 D B -1.5105
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 -1.0932
91 D B -2.3204
92 R B -2.3065
93 S B -1.3622
94 T B -1.0575
95 G B 0.0000
96 V B 0.0000
97 F B 0.0000
98 G B 0.0000
99 T B -0.3656
100 G B 0.0000
101 T B 0.0000
102 K B -1.4646
103 V B 0.0000
104 T B -0.4396
105 V B 0.0085
106 L B 1.2739
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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
LR106B -0.7782 -0.0312 View CSV PDB
VR116A -0.485 -0.0404 View CSV PDB
IK55A -0.1521 -0.0544 View CSV PDB
LR8B -0.3905 -0.0377 View CSV PDB
IR55A -0.0993 -0.0485 View CSV PDB
LE8B -0.2466 -0.0371 View CSV PDB
VK116A -0.2415 -0.0354 View CSV PDB
LK106B -0.0421 -0.0338 View CSV PDB
IR52A -0.0324 -0.0143 View CSV PDB
IE54A 0.6423 -0.0432 View CSV PDB
IR54A 0.8446 -0.047 View CSV PDB
IK52A 0.6112 -0.0203 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018