Project name: 3H3-I51T-1

Status: done

Started: 2026-01-16 01:05:00
Settings
Chain sequence(s) A: QVQLVQSGAEVKKPGSSVKVSCKASGGSFSRLAFSWVRQAPGQGLEWMGGTIPIIGTADYAQKFQGRVTITADESTNTAYMELSSLRSEDTAVYYCARDLSSGYSDALDIWGQGSVITVSS
B: SYELTQPLSVSVSPGQTSTITCSGEALGDRYASWYQQRPGQSPILVIYQDTKRPSGIPERFSGSSSRGTATLTISGTQATDEADYYCQTWDRSTGVFGTGTKVTVL
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]                                                (00:00:00)
[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                                          (00:02:47)
[INFO]       Auto_mut: Residue number 55 from chain A and a score of 2.115 (isoleucine) selected   
                       for automated muatation                                                     (00:02:49)
[INFO]       Auto_mut: Residue number 106 from chain B and a score of 1.573 (leucine) selected for 
                       automated muatation                                                         (00:02:49)
[INFO]       Auto_mut: Residue number 11 from chain A and a score of 1.514 (valine) selected for   
                       automated muatation                                                         (00:02:49)
[INFO]       Auto_mut: Residue number 8 from chain B and a score of 1.491 (leucine) selected for   
                       automated muatation                                                         (00:02:49)
[INFO]       Auto_mut: Residue number 54 from chain A and a score of 1.389 (isoleucine) selected   
                       for automated muatation                                                     (00:02:49)
[INFO]       Auto_mut: Residue number 116 from chain A and a score of 1.336 (valine) selected for  
                       automated muatation                                                         (00:02:49)
[INFO]       Auto_mut: Mutating residue number 55 from chain A (isoleucine) into glutamic acid     (00:02:49)
[INFO]       Auto_mut: Mutating residue number 55 from chain A (isoleucine) into aspartic acid     (00:02:49)
[INFO]       Auto_mut: Mutating residue number 106 from chain B (leucine) into glutamic acid       (00:02:49)
[INFO]       Auto_mut: Mutating residue number 55 from chain A (isoleucine) into lysine            (00:04:14)
[INFO]       Auto_mut: Mutating residue number 55 from chain A (isoleucine) into arginine          (00:04:14)
[INFO]       Auto_mut: Mutating residue number 106 from chain B (leucine) into lysine              (00:04:19)
[INFO]       Auto_mut: Mutating residue number 106 from chain B (leucine) into aspartic acid       (00:05:48)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (valine) into glutamic acid         (00:05:57)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (valine) into aspartic acid         (00:05:58)
[INFO]       Auto_mut: Mutating residue number 106 from chain B (leucine) into arginine            (00:07:17)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (valine) into arginine              (00:07:28)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (valine) into lysine                (00:07:29)
[INFO]       Auto_mut: Mutating residue number 8 from chain B (leucine) into glutamic acid         (00:08:50)
[INFO]       Auto_mut: Mutating residue number 8 from chain B (leucine) into aspartic acid         (00:08:56)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (isoleucine) into glutamic acid     (00:08:58)
[INFO]       Auto_mut: Mutating residue number 8 from chain B (leucine) into lysine                (00:10:17)
[INFO]       Auto_mut: Mutating residue number 8 from chain B (leucine) into arginine              (00:10:18)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (isoleucine) into lysine            (00:10:28)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (isoleucine) into aspartic acid     (00:11:51)
[INFO]       Auto_mut: Mutating residue number 116 from chain A (valine) into glutamic acid        (00:11:57)
[INFO]       Auto_mut: Mutating residue number 116 from chain A (valine) into aspartic acid        (00:12:01)
[INFO]       Auto_mut: Mutating residue number 116 from chain A (valine) into lysine               (00:13:23)
[INFO]       Auto_mut: Mutating residue number 116 from chain A (valine) into arginine             (00:13:26)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (isoleucine) into arginine          (00:13:29)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 0.2016 kcal/mol, Difference in average    
                       score from the base case: -0.0245                                           (00:15:09)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain A (isoleucine) into lysine: 
                       Energy difference: -0.0874 kcal/mol, Difference in average score from the   
                       base case: -0.0250                                                          (00:15:09)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 0.4367 kcal/mol, Difference in average    
                       score from the base case: -0.0221                                           (00:15:09)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain A (isoleucine) into         
                       arginine: Energy difference: 0.0963 kcal/mol, Difference in average score   
                       from the base case: -0.0258                                                 (00:15:09)
[INFO]       Auto_mut: Effect of mutation residue number 106 from chain B (leucine) into glutamic  
                       acid: Energy difference: -0.3999 kcal/mol, Difference in average score from 
                       the base case: -0.0207                                                      (00:15:09)
[INFO]       Auto_mut: Effect of mutation residue number 106 from chain B (leucine) into lysine:   
                       Energy difference: -0.8760 kcal/mol, Difference in average score from the   
                       base case: -0.0200                                                          (00:15:09)
[INFO]       Auto_mut: Effect of mutation residue number 106 from chain B (leucine) into aspartic  
                       acid: Energy difference: -0.3003 kcal/mol, Difference in average score from 
                       the base case: -0.0206                                                      (00:15:10)
[INFO]       Auto_mut: Effect of mutation residue number 106 from chain B (leucine) into arginine: 
                       Energy difference: -0.8327 kcal/mol, Difference in average score from the   
                       base case: -0.0208                                                          (00:15:10)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (valine) into glutamic    
                       acid: Energy difference: 0.3339 kcal/mol, Difference in average score from  
                       the base case: -0.0249                                                      (00:15:10)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (valine) into lysine:     
                       Energy difference: -0.0425 kcal/mol, Difference in average score from the   
                       base case: -0.0251                                                          (00:15:10)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (valine) into aspartic    
                       acid: Energy difference: 0.6495 kcal/mol, Difference in average score from  
                       the base case: -0.0250                                                      (00:15:10)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (valine) into arginine:   
                       Energy difference: -0.3051 kcal/mol, Difference in average score from the   
                       base case: -0.0261                                                          (00:15:10)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain B (leucine) into glutamic    
                       acid: Energy difference: -0.3487 kcal/mol, Difference in average score from 
                       the base case: -0.0220                                                      (00:15:10)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain B (leucine) into lysine:     
                       Energy difference: -0.1156 kcal/mol, Difference in average score from the   
                       base case: -0.0212                                                          (00:15:10)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain B (leucine) into aspartic    
                       acid: Energy difference: -0.1174 kcal/mol, Difference in average score from 
                       the base case: -0.0219                                                      (00:15:10)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain B (leucine) into arginine:   
                       Energy difference: -0.2596 kcal/mol, Difference in average score from the   
                       base case: -0.0223                                                          (00:15:10)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 1.0217 kcal/mol, Difference in average    
                       score from the base case: -0.0148                                           (00:15:10)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (isoleucine) into lysine: 
                       Energy difference: 1.0428 kcal/mol, Difference in average score from the    
                       base case: -0.0170                                                          (00:15:10)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 1.1226 kcal/mol, Difference in average    
                       score from the base case: -0.0229                                           (00:15:10)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (isoleucine) into         
                       arginine: Energy difference: -0.0104 kcal/mol, Difference in average score  
                       from the base case: -0.0181                                                 (00:15:10)
[INFO]       Auto_mut: Effect of mutation residue number 116 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.0658 kcal/mol, Difference in average score from  
                       the base case: -0.0178                                                      (00:15:10)
[INFO]       Auto_mut: Effect of mutation residue number 116 from chain A (valine) into lysine:    
                       Energy difference: -0.2226 kcal/mol, Difference in average score from the   
                       base case: -0.0139                                                          (00:15:10)
[INFO]       Auto_mut: Effect of mutation residue number 116 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.8044 kcal/mol, Difference in average score from  
                       the base case: -0.0180                                                      (00:15:10)
[INFO]       Auto_mut: Effect of mutation residue number 116 from chain A (valine) into arginine:  
                       Energy difference: 0.1149 kcal/mol, Difference in average score from the    
                       base case: -0.0185                                                          (00:15:10)
[INFO]       Main:     Simulation completed successfully.                                          (00:15:16)
Show buried residues
Minimal score value
-2.0414
Maximal score value
2.1152
Average score
-0.2473
Total score value
-56.1263
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 -1.1641
2 V A -0.3217
3 Q A -1.1632
4 L A 0.0000
5 V A 1.3242
6 Q A 0.0000
7 S A -0.1605
8 G A -0.4690
9 A A -0.0573
10 E A -0.6862
11 V A 1.5137
12 K A -0.3532
13 K A -1.7854
14 P A -0.4957
15 G A -0.5140
16 S A -0.1433
17 S A -0.0972
18 V A 0.0000
19 K A -1.8226
20 V A 0.0000
21 S A -0.0148
22 C A 0.0000
23 K A -1.0581
24 A A 0.0000
25 S A -0.1654
26 G A -0.5444
27 G A -0.5922
28 S A -0.2964
29 F A 0.0000
30 S A -0.2900
31 R A -1.8231
32 L A -0.1676
33 A A 0.1525
34 F A 0.0000
35 S A 0.0000
36 W A 0.0000
37 V A 0.0000
38 R A -0.2087
39 Q A -0.1614
40 A A -0.0597
41 P A -0.3419
42 G A -0.7345
43 Q A -1.3062
44 G A -0.3471
45 L A 0.0000
46 E A -0.3418
47 W A 0.0000
48 M A 0.0000
49 G A 0.0000
50 G A -0.0499
51 T A 0.0000
52 I A 0.8020
53 P A 0.0000
54 I A 1.3895
55 I A 2.1152
56 G A -0.1066
57 T A -0.1533
58 A A -0.1992
59 D A -0.9946
60 Y A 0.1229
61 A A 0.0000
62 Q A -1.5153
63 K A -1.9234
64 F A 0.0000
65 Q A -1.2852
66 G A -0.7812
67 R A -0.5780
68 V A 0.0000
69 T A -0.0505
70 I A 0.0000
71 T A -0.0351
72 A A -0.1403
73 D A -0.9803
74 E A -1.3511
75 S A -0.4349
76 T A -0.2001
77 N A -0.7266
78 T A 0.0000
79 A A 0.0000
80 Y A 0.2254
81 M A 0.0000
82 E A -1.0803
83 L A 0.0000
84 S A -0.1350
85 S A -0.2440
86 L A 0.0000
87 R A -1.8843
88 S A -0.8945
89 E A -1.8589
90 D A 0.0000
91 T A -0.0186
92 A A 0.0000
93 V A 0.5470
94 Y A 0.0000
95 Y A 0.0000
96 C A 0.0000
97 A A 0.0000
98 R A -0.2224
99 D A 0.0000
100 L A 0.2033
101 S A -0.1999
102 S A -0.2864
103 G A -0.2772
104 Y A 1.2374
105 S A 0.0000
106 D A -1.0141
107 A A 0.0000
108 L A 0.0000
109 D A -0.2733
110 I A 0.2552
111 W A 0.1702
112 G A 0.0000
113 Q A -1.2090
114 G A -0.2770
115 S A 0.0000
116 V A 1.3357
117 I A 0.0000
118 T A 0.1792
119 V A 0.0000
120 S A -0.1937
121 S A -0.2406
1 S B 0.0006
2 Y B 0.9214
3 E B -1.5602
4 L B 0.0000
5 T B -0.0709
6 Q B 0.0000
7 P B 0.1896
8 L B 1.4906
9 S B -0.0319
10 V B 0.2272
11 S B -0.1590
12 V B 0.0000
13 S B 0.0137
14 P B -0.3610
15 G B -0.7535
16 Q B -1.2986
17 T B -0.3173
18 S B 0.0000
19 T B -0.0731
20 I B 0.0000
21 T B -0.0480
22 C B 0.0000
23 S B -0.1153
24 G B -0.4280
25 E B -1.8308
26 A B -0.3392
27 L B 0.0000
28 G B -0.6052
29 D B -1.9981
30 R B -1.2729
31 Y B 0.3815
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 -1.0502
39 P B -0.5301
40 G B -0.7395
41 Q B -1.2962
42 S B -0.2827
43 P B 0.0000
44 I B 0.9705
45 L B 0.0000
46 V B 0.0000
47 I B 0.0000
48 Y B 0.1212
49 Q B -0.1652
50 D B -0.3714
51 T B -0.4107
52 K B -1.5795
53 R B -1.0262
54 P B -0.2199
55 S B -0.3051
56 G B -0.4646
57 I B 0.0960
58 P B -0.4213
59 E B -1.9060
60 R B -0.6931
61 F B 0.0000
62 S B -0.1299
63 G B -0.1242
64 S B -0.2186
65 S B -0.1554
66 S B -0.5509
67 R B -1.9016
68 G B -0.4250
69 T B -0.0451
70 A B 0.0000
71 T B -0.0195
72 L B 0.0000
73 T B -0.0263
74 I B 0.0000
75 S B -0.1888
76 G B -0.1973
77 T B 0.0000
78 Q B -0.7748
79 A B -0.1020
80 T B -0.0601
81 D B 0.0000
82 E B -1.1210
83 A B 0.0000
84 D B -0.5217
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 -0.0813
91 D B -1.3307
92 R B -2.0414
93 S B -0.3873
94 T B -0.0229
95 G B 0.0000
96 V B 0.0000
97 F B 0.0000
98 G B 0.0000
99 T B -0.0795
100 G B -0.0604
101 T B 0.0000
102 K B -1.3645
103 V B 0.0000
104 T B 0.0001
105 V B 0.4713
106 L B 1.5730
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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 -0.8327 -0.0208 View CSV PDB
LK106B -0.876 -0.02 View CSV PDB
VR11A -0.3051 -0.0261 View CSV PDB
LE8B -0.3487 -0.022 View CSV PDB
LR8B -0.2596 -0.0223 View CSV PDB
IK55A -0.0874 -0.025 View CSV PDB
VK11A -0.0425 -0.0251 View CSV PDB
VK116A -0.2226 -0.0139 View CSV PDB
IR54A -0.0104 -0.0181 View CSV PDB
VE116A 0.0658 -0.0178 View CSV PDB
IR55A 0.0963 -0.0258 View CSV PDB
ID54A 1.1226 -0.0229 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018