Project name: 3H3

Status: done

Started: 2026-01-15 08:06:14
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                                        (00:00:00)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:03:02)
[INFO]       Auto_mut: Residue number 55 from chain A and a score of 2.244 (isoleucine) selected   
                       for automated muatation                                                     (00:03:03)
[INFO]       Auto_mut: Residue number 106 from chain B and a score of 1.290 (leucine) selected for 
                       automated muatation                                                         (00:03:03)
[INFO]       Auto_mut: Residue number 54 from chain A and a score of 1.276 (isoleucine) selected   
                       for automated muatation                                                     (00:03:03)
[INFO]       Auto_mut: Residue number 116 from chain A and a score of 1.146 (valine) selected for  
                       automated muatation                                                         (00:03:03)
[INFO]       Auto_mut: Residue number 52 from chain A and a score of 1.096 (isoleucine) selected   
                       for automated muatation                                                     (00:03:03)
[INFO]       Auto_mut: Residue number 8 from chain B and a score of 0.972 (leucine) selected for   
                       automated muatation                                                         (00:03:03)
[INFO]       Auto_mut: Mutating residue number 55 from chain A (isoleucine) into glutamic acid     (00:03:03)
[INFO]       Auto_mut: Mutating residue number 55 from chain A (isoleucine) into aspartic acid     (00:03:03)
[INFO]       Auto_mut: Mutating residue number 106 from chain B (leucine) into glutamic acid       (00:03:03)
[INFO]       Auto_mut: Mutating residue number 55 from chain A (isoleucine) into arginine          (00:04:32)
[INFO]       Auto_mut: Mutating residue number 106 from chain B (leucine) into lysine              (00:04:34)
[INFO]       Auto_mut: Mutating residue number 55 from chain A (isoleucine) into lysine            (00:04:35)
[INFO]       Auto_mut: Mutating residue number 106 from chain B (leucine) into aspartic acid       (00:06:08)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (isoleucine) into glutamic acid     (00:06:20)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (isoleucine) into aspartic acid     (00:06:20)
[INFO]       Auto_mut: Mutating residue number 106 from chain B (leucine) into arginine            (00:07:38)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (isoleucine) into lysine            (00:07:58)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (isoleucine) into arginine          (00:07:59)
[INFO]       Auto_mut: Mutating residue number 116 from chain A (valine) into glutamic acid        (00:09:15)
[INFO]       Auto_mut: Mutating residue number 116 from chain A (valine) into aspartic acid        (00:09:40)
[INFO]       Auto_mut: Mutating residue number 52 from chain A (isoleucine) into glutamic acid     (00:09:43)
[INFO]       Auto_mut: Mutating residue number 116 from chain A (valine) into lysine               (00:10:48)
[INFO]       Auto_mut: Mutating residue number 116 from chain A (valine) into arginine             (00:11:10)
[INFO]       Auto_mut: Mutating residue number 52 from chain A (isoleucine) into lysine            (00:11:19)
[INFO]       Auto_mut: Mutating residue number 52 from chain A (isoleucine) into aspartic acid     (00:12:53)
[INFO]       Auto_mut: Mutating residue number 8 from chain B (leucine) into glutamic acid         (00:12:57)
[INFO]       Auto_mut: Mutating residue number 8 from chain B (leucine) into aspartic acid         (00:13:06)
[INFO]       Auto_mut: Mutating residue number 52 from chain A (isoleucine) into arginine          (00:14:25)
[INFO]       Auto_mut: Mutating residue number 8 from chain B (leucine) into lysine                (00:14:30)
[INFO]       Auto_mut: Mutating residue number 8 from chain B (leucine) into arginine              (00:14:35)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 0.1397 kcal/mol, Difference in average    
                       score from the base case: -0.0527                                           (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain A (isoleucine) into lysine: 
                       Energy difference: -0.1378 kcal/mol, Difference in average score from the   
                       base case: -0.0568                                                          (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 0.6548 kcal/mol, Difference in average    
                       score from the base case: -0.0519                                           (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain A (isoleucine) into         
                       arginine: Energy difference: -0.1679 kcal/mol, Difference in average score  
                       from the base case: -0.0591                                                 (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 106 from chain B (leucine) into glutamic  
                       acid: Energy difference: 0.1578 kcal/mol, Difference in average score from  
                       the base case: -0.0414                                                      (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 106 from chain B (leucine) into lysine:   
                       Energy difference: -0.1037 kcal/mol, Difference in average score from the   
                       base case: -0.0397                                                          (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 106 from chain B (leucine) into aspartic  
                       acid: Energy difference: 0.5967 kcal/mol, Difference in average score from  
                       the base case: -0.0409                                                      (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 106 from chain B (leucine) into arginine: 
                       Energy difference: -0.2615 kcal/mol, Difference in average score from the   
                       base case: -0.0416                                                          (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 0.8852 kcal/mol, Difference in average    
                       score from the base case: -0.0298                                           (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (isoleucine) into lysine: 
                       Energy difference: 1.0038 kcal/mol, Difference in average score from the    
                       base case: -0.0324                                                          (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 1.1158 kcal/mol, Difference in average    
                       score from the base case: -0.0349                                           (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (isoleucine) into         
                       arginine: Energy difference: -0.2552 kcal/mol, Difference in average score  
                       from the base case: -0.0453                                                 (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 116 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.0343 kcal/mol, Difference in average score from  
                       the base case: -0.0435                                                      (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 116 from chain A (valine) into lysine:    
                       Energy difference: -0.2604 kcal/mol, Difference in average score from the   
                       base case: -0.0330                                                          (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 116 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.7897 kcal/mol, Difference in average score from  
                       the base case: -0.0456                                                      (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 116 from chain A (valine) into arginine:  
                       Energy difference: 0.1130 kcal/mol, Difference in average score from the    
                       base case: -0.0523                                                          (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 1.5444 kcal/mol, Difference in average    
                       score from the base case: -0.0338                                           (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain A (isoleucine) into lysine: 
                       Energy difference: -0.3468 kcal/mol, Difference in average score from the   
                       base case: -0.0254                                                          (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 1.9367 kcal/mol, Difference in average    
                       score from the base case: -0.0255                                           (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain A (isoleucine) into         
                       arginine: Energy difference: -0.6868 kcal/mol, Difference in average score  
                       from the base case: -0.0065                                                 (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain B (leucine) into glutamic    
                       acid: Energy difference: -0.4068 kcal/mol, Difference in average score from 
                       the base case: -0.0450                                                      (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain B (leucine) into lysine:     
                       Energy difference: -0.0517 kcal/mol, Difference in average score from the   
                       base case: -0.0381                                                          (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain B (leucine) into aspartic    
                       acid: Energy difference: -0.1806 kcal/mol, Difference in average score from 
                       the base case: -0.0446                                                      (00:16:18)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain B (leucine) into arginine:   
                       Energy difference: -0.2328 kcal/mol, Difference in average score from the   
                       base case: -0.0398                                                          (00:16:18)
[INFO]       Main:     Simulation completed successfully.                                          (00:16:24)
Show buried residues
Minimal score value
-3.1341
Maximal score value
2.2436
Average score
-0.6246
Total score value
-141.7855
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 -1.7189
2 V A 0.0000
3 Q A -1.7795
4 L A 0.0000
5 V A -0.0856
6 Q A 0.0000
7 S A -0.6209
8 G A -0.4849
9 A A 0.1892
10 E A -0.2474
11 V A 0.8536
12 K A -1.0234
13 K A -2.1739
14 P A -2.1213
15 G A -1.5928
16 S A -1.2656
17 S A -1.4341
18 V A 0.0000
19 K A -2.1896
20 V A 0.0000
21 S A -0.7446
22 C A 0.0000
23 K A -1.6384
24 A A 0.0000
25 S A -1.4371
26 G A -1.5961
27 G A -1.4737
28 S A -1.2622
29 F A 0.0000
30 S A -0.7675
31 R A -1.2321
32 L A -0.4839
33 A A 0.2147
34 F A 0.0000
35 S A 0.0000
36 W A 0.0000
37 V A 0.0000
38 R A -0.3217
39 Q A -0.5648
40 A A -0.9267
41 P A -0.9345
42 G A -1.2477
43 Q A -1.6829
44 G A -1.0844
45 L A 0.0000
46 E A -0.7393
47 W A 0.0000
48 M A 0.0000
49 G A 0.0000
50 G A -0.2633
51 I A 0.0000
52 I A 1.0958
53 P A 0.0000
54 I A 1.2760
55 I A 2.2436
56 G A 0.8097
57 T A 0.3907
58 A A -0.2253
59 D A -1.3379
60 Y A -1.4214
61 A A 0.0000
62 Q A -2.5937
63 K A -2.7570
64 F A 0.0000
65 Q A -2.5765
66 G A -1.6822
67 R A -1.4799
68 V A 0.0000
69 T A -1.0207
70 I A 0.0000
71 T A -0.3913
72 A A -0.5783
73 D A -1.6963
74 E A -2.0027
75 S A -1.2438
76 T A -1.3428
77 N A -1.9508
78 T A 0.0000
79 A A 0.0000
80 Y A -0.7523
81 M A 0.0000
82 E A -1.6631
83 L A 0.0000
84 S A -1.2294
85 S A -1.2616
86 L A 0.0000
87 R A -3.1341
88 S A -2.4443
89 E A -2.6160
90 D A 0.0000
91 T A -0.6423
92 A A 0.0000
93 V A 0.5411
94 Y A 0.0000
95 Y A 0.0000
96 C A 0.0000
97 A A 0.0000
98 R A -0.2762
99 D A 0.0000
100 L A -0.1553
101 S A -0.4262
102 S A -0.1356
103 G A -0.0204
104 Y A 0.8902
105 S A 0.0000
106 D A -0.3388
107 A A 0.0000
108 L A 0.0000
109 D A -0.0627
110 I A -0.2217
111 W A -0.0766
112 G A 0.0000
113 Q A -1.2221
114 G A -0.3950
115 S A 0.0000
116 V A 1.1461
117 I A 0.0000
118 T A -0.1180
119 V A 0.0000
120 S A -1.0578
121 S A -0.7512
1 S B -0.6005
2 Y B -0.2712
3 E B -1.6714
4 L B 0.0000
5 T B -0.2783
6 Q B 0.0000
7 P B 0.3812
8 L B 0.9724
9 S B -0.0532
10 V B -0.1230
11 S B -0.0808
12 V B 0.0000
13 S B -0.2702
14 P B -0.8415
15 G B -1.4654
16 Q B -1.7341
17 T B -1.0591
18 S B 0.0000
19 T B -0.0951
20 I B 0.0000
21 T B -0.1672
22 C B 0.0000
23 S B -1.1899
24 G B -1.6200
25 E B -2.8420
26 A B -2.1953
27 L B 0.0000
28 G B -2.5977
29 D B -2.8413
30 R B -1.7776
31 Y B -0.1774
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 -2.0796
39 P B -1.6600
40 G B -1.5652
41 Q B -1.9654
42 S B -0.9959
43 P B 0.0000
44 I B 0.7223
45 L B 0.0000
46 V B 0.0000
47 I B 0.0000
48 Y B -0.6694
49 Q B -0.5903
50 D B -0.8064
51 T B -1.0451
52 K B -1.7258
53 R B -1.9426
54 P B -1.0768
55 S B -1.0018
56 G B -0.9768
57 I B 0.0000
58 P B -1.4577
59 E B -2.3445
60 R B -1.4918
61 F B 0.0000
62 S B -1.1449
63 G B 0.0000
64 S B -0.5447
65 S B -0.8429
66 S B -1.2832
67 R B -2.5946
68 G B -2.1551
69 T B -1.1595
70 A B 0.0000
71 T B -0.2784
72 L B 0.0000
73 T B -0.2654
74 I B 0.0000
75 S B -1.1932
76 G B -1.3593
77 T B 0.0000
78 Q B -1.2674
79 A B -0.4984
80 T B -0.7749
81 D B 0.0000
82 E B -1.5359
83 A B 0.0000
84 D B -1.6238
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 -2.3873
92 R B -2.4283
93 S B -1.4710
94 T B -1.1310
95 G B 0.0000
96 V B 0.0000
97 F B -0.1220
98 G B 0.0000
99 T B -0.4079
100 G B -0.4467
101 T B 0.0000
102 K B -1.6376
103 V B 0.0000
104 T B -0.4585
105 V B -0.0024
106 L B 1.2896
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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
LE8B -0.4068 -0.045 View CSV PDB
IR55A -0.1679 -0.0591 View CSV PDB
IK55A -0.1378 -0.0568 View CSV PDB
IR54A -0.2552 -0.0453 View CSV PDB
LR106B -0.2615 -0.0416 View CSV PDB
LD8B -0.1806 -0.0446 View CSV PDB
VK116A -0.2604 -0.033 View CSV PDB
LK106B -0.1037 -0.0397 View CSV PDB
IK52A -0.3468 -0.0254 View CSV PDB
IR52A -0.6868 -0.0065 View CSV PDB
VE116A 0.0343 -0.0435 View CSV PDB
IE54A 0.8852 -0.0298 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018