Project name: 3H3-WT

Status: done

Started: 2026-01-16 06:43:27
Settings
Chain sequence(s) H: QVQLVQSGAEVKKPGSSVKVSCKASGGSFSRLAFSWVRQAPGQGLEWMGGIIPIIGTADYAQKFQGRVTITADESTNTAYMELSSLRSEDTAVYYCARDLSSGYSDALDIWGQGSVITVSS
L: SYELTQPLSVSVSPGQTSTITCSGEALGDRYASWYQQRPGQSPILVIYQDTKRPSGIPERFSGSSSRGTATLTISGTQATDEADYYCQTWDRSTGVFGTGTKVTVL
input PDB
Selected Chain(s) H,L
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]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with all chain(s) selected           (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:02)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:02:46)
[INFO]       Auto_mut: Residue number 59 from chain H and a score of 2.363 (isoleucine) selected   
                       for automated muatation                                                     (00:02:48)
[INFO]       Auto_mut: Residue number 62 from chain H and a score of 2.284 (isoleucine) selected   
                       for automated muatation                                                     (00:02:49)
[INFO]       Auto_mut: Residue number 127 from chain L and a score of 1.574 (leucine) selected for 
                       automated muatation                                                         (00:02:49)
[INFO]       Auto_mut: Residue number 123 from chain H and a score of 1.567 (valine) selected for  
                       automated muatation                                                         (00:02:49)
[INFO]       Auto_mut: Residue number 12 from chain H and a score of 1.530 (valine) selected for   
                       automated muatation                                                         (00:02:49)
[INFO]       Auto_mut: Residue number 8 from chain L and a score of 1.496 (leucine) selected for   
                       automated muatation                                                         (00:02:49)
[INFO]       Auto_mut: Mutating residue number 59 from chain H (isoleucine) into glutamic acid     (00:02:49)
[INFO]       Auto_mut: Mutating residue number 59 from chain H (isoleucine) into aspartic acid     (00:02:49)
[INFO]       Auto_mut: Mutating residue number 62 from chain H (isoleucine) into glutamic acid     (00:02:49)
[INFO]       Auto_mut: Mutating residue number 59 from chain H (isoleucine) into lysine            (00:04:28)
[INFO]       Auto_mut: Mutating residue number 62 from chain H (isoleucine) into lysine            (00:04:28)
[INFO]       Auto_mut: Mutating residue number 59 from chain H (isoleucine) into arginine          (00:04:38)
[INFO]       Auto_mut: Mutating residue number 62 from chain H (isoleucine) into aspartic acid     (00:06:31)
[INFO]       Auto_mut: Mutating residue number 127 from chain L (leucine) into glutamic acid       (00:06:33)
[INFO]       Auto_mut: Mutating residue number 127 from chain L (leucine) into aspartic acid       (00:06:33)
[INFO]       Auto_mut: Mutating residue number 62 from chain H (isoleucine) into arginine          (00:08:07)
[INFO]       Auto_mut: Mutating residue number 127 from chain L (leucine) into lysine              (00:08:12)
[INFO]       Auto_mut: Mutating residue number 127 from chain L (leucine) into arginine            (00:08:25)
[INFO]       Auto_mut: Mutating residue number 123 from chain H (valine) into glutamic acid        (00:09:52)
[INFO]       Auto_mut: Mutating residue number 123 from chain H (valine) into aspartic acid        (00:10:10)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (valine) into glutamic acid         (00:10:14)
[INFO]       Auto_mut: Mutating residue number 123 from chain H (valine) into lysine               (00:11:48)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (valine) into lysine                (00:11:55)
[INFO]       Auto_mut: Mutating residue number 123 from chain H (valine) into arginine             (00:11:56)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (valine) into aspartic acid         (00:13:45)
[INFO]       Auto_mut: Mutating residue number 8 from chain L (leucine) into glutamic acid         (00:13:48)
[INFO]       Auto_mut: Mutating residue number 8 from chain L (leucine) into aspartic acid         (00:14:17)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (valine) into arginine              (00:15:26)
[INFO]       Auto_mut: Mutating residue number 8 from chain L (leucine) into lysine                (00:15:57)
[INFO]       Auto_mut: Mutating residue number 8 from chain L (leucine) into arginine              (00:16:10)
[INFO]       Auto_mut: Effect of mutation residue number 59 from chain H (isoleucine) into         
                       glutamic acid: Energy difference: 0.2637 kcal/mol, Difference in average    
                       score from the base case: -0.0275                                           (00:18:12)
[INFO]       Auto_mut: Effect of mutation residue number 59 from chain H (isoleucine) into lysine: 
                       Energy difference: -0.0572 kcal/mol, Difference in average score from the   
                       base case: -0.0288                                                          (00:18:12)
[INFO]       Auto_mut: Effect of mutation residue number 59 from chain H (isoleucine) into         
                       aspartic acid: Energy difference: 0.6565 kcal/mol, Difference in average    
                       score from the base case: -0.0257                                           (00:18:12)
[INFO]       Auto_mut: Effect of mutation residue number 59 from chain H (isoleucine) into         
                       arginine: Energy difference: -0.5342 kcal/mol, Difference in average score  
                       from the base case: -0.0227                                                 (00:18:12)
[INFO]       Auto_mut: Effect of mutation residue number 62 from chain H (isoleucine) into         
                       glutamic acid: Energy difference: 0.8423 kcal/mol, Difference in average    
                       score from the base case: -0.0201                                           (00:18:12)
[INFO]       Auto_mut: Effect of mutation residue number 62 from chain H (isoleucine) into lysine: 
                       Energy difference: 0.3861 kcal/mol, Difference in average score from the    
                       base case: -0.0202                                                          (00:18:12)
[INFO]       Auto_mut: Effect of mutation residue number 62 from chain H (isoleucine) into         
                       aspartic acid: Energy difference: 1.0401 kcal/mol, Difference in average    
                       score from the base case: -0.0196                                           (00:18:12)
[INFO]       Auto_mut: Effect of mutation residue number 62 from chain H (isoleucine) into         
                       arginine: Energy difference: 0.4373 kcal/mol, Difference in average score   
                       from the base case: -0.0209                                                 (00:18:12)
[INFO]       Auto_mut: Effect of mutation residue number 127 from chain L (leucine) into glutamic  
                       acid: Energy difference: 0.6524 kcal/mol, Difference in average score from  
                       the base case: -0.0186                                                      (00:18:12)
[INFO]       Auto_mut: Effect of mutation residue number 127 from chain L (leucine) into lysine:   
                       Energy difference: -0.1247 kcal/mol, Difference in average score from the   
                       base case: -0.0176                                                          (00:18:12)
[INFO]       Auto_mut: Effect of mutation residue number 127 from chain L (leucine) into aspartic  
                       acid: Energy difference: 0.8874 kcal/mol, Difference in average score from  
                       the base case: -0.0184                                                      (00:18:12)
[INFO]       Auto_mut: Effect of mutation residue number 127 from chain L (leucine) into arginine: 
                       Energy difference: -0.0570 kcal/mol, Difference in average score from the   
                       base case: -0.0186                                                          (00:18:12)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain H (valine) into glutamic   
                       acid: Energy difference: -0.2223 kcal/mol, Difference in average score from 
                       the base case: -0.0165                                                      (00:18:12)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain H (valine) into lysine:    
                       Energy difference: -0.4572 kcal/mol, Difference in average score from the   
                       base case: -0.0163                                                          (00:18:12)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain H (valine) into aspartic   
                       acid: Energy difference: -0.2997 kcal/mol, Difference in average score from 
                       the base case: -0.0176                                                      (00:18:12)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain H (valine) into arginine:  
                       Energy difference: -0.7742 kcal/mol, Difference in average score from the   
                       base case: -0.0168                                                          (00:18:12)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (valine) into glutamic    
                       acid: Energy difference: -0.1606 kcal/mol, Difference in average score from 
                       the base case: -0.0230                                                      (00:18:12)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (valine) into lysine:     
                       Energy difference: -0.5384 kcal/mol, Difference in average score from the   
                       base case: -0.0226                                                          (00:18:12)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (valine) into aspartic    
                       acid: Energy difference: 0.1658 kcal/mol, Difference in average score from  
                       the base case: -0.0228                                                      (00:18:12)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (valine) into arginine:   
                       Energy difference: -0.3184 kcal/mol, Difference in average score from the   
                       base case: -0.0237                                                          (00:18:12)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain L (leucine) into glutamic    
                       acid: Energy difference: -0.7238 kcal/mol, Difference in average score from 
                       the base case: -0.0189                                                      (00:18:12)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain L (leucine) into lysine:     
                       Energy difference: -0.3353 kcal/mol, Difference in average score from the   
                       base case: -0.0166                                                          (00:18:12)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain L (leucine) into aspartic    
                       acid: Energy difference: -0.3713 kcal/mol, Difference in average score from 
                       the base case: -0.0187                                                      (00:18:13)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain L (leucine) into arginine:   
                       Energy difference: -0.4060 kcal/mol, Difference in average score from the   
                       base case: -0.0174                                                          (00:18:13)
[INFO]       Main:     Simulation completed successfully.                                          (00:18:22)
Show buried residues
Minimal score value
-1.9527
Maximal score value
2.3626
Average score
-0.2093
Total score value
-47.5154
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 H -1.1561
2 V H -0.2184
3 Q H -0.9160
4 L H 0.0000
5 V H 1.4620
6 Q H 0.0000
7 S H -0.1664
8 G H -0.4705
9 A H -0.0300
11 E H -0.7219
12 V H 1.5299
13 K H -0.2690
14 K H -1.7797
15 P H -0.5481
16 G H -0.5290
17 S H -0.1566
18 S H -0.1694
19 V H 0.0000
20 K H -1.8150
21 V H 0.0000
22 S H -0.0056
23 C H 0.0000
24 K H -0.8899
25 A H -0.1797
26 S H -0.2002
27 G H -0.5175
28 G H -0.4412
29 S H -0.2704
30 F H 0.0000
35 S H -0.3903
36 R H -1.8547
37 L H 0.0000
38 A H 0.0000
39 F H 0.0000
40 S H 0.0000
41 W H 0.0000
42 V H 0.0000
43 R H 0.0000
44 Q H -0.1197
45 A H -0.0498
46 P H -0.3355
47 G H -0.7249
48 Q H -1.3241
49 G H -0.4542
50 L H 0.0000
51 E H -0.4276
52 W H 0.0000
53 M H 0.0000
54 G H 0.0000
55 G H -0.0469
56 I H 0.0000
57 I H 0.1989
58 P H 0.3704
59 I H 2.3626
62 I H 2.2845
63 G H -0.1230
64 T H -0.1518
65 A H -0.0771
66 D H -0.3831
67 Y H 0.0837
68 A H -0.1805
69 Q H -1.4956
70 K H -1.9104
71 F H 0.0000
72 Q H -1.2819
74 G H -0.7209
75 R H -0.3079
76 V H 0.0000
77 T H -0.1203
78 I H 0.0000
79 T H -0.0218
80 A H -0.0422
81 D H -0.4420
82 E H -0.9631
83 S H -0.3730
84 T H -0.1611
85 N H -0.4452
86 T H 0.0000
87 A H 0.0000
88 Y H 0.2714
89 M H 0.0000
90 E H -0.9984
91 L H 0.0000
92 S H -0.1217
93 S H -0.2418
94 L H 0.0000
95 R H -1.3946
96 S H -0.7813
97 E H -1.8577
98 D H 0.0000
99 T H -0.0185
100 A H 0.0000
101 V H 0.6361
102 Y H 0.0000
103 Y H 0.0000
104 C H 0.0000
105 A H 0.0000
106 R H -0.1922
107 D H 0.0000
108 L H 0.4106
109 S H -0.0910
110 S H -0.2497
111 G H 0.0674
112A Y H 0.9579
112 S H 0.0887
113 D H 0.0000
114 A H 0.0000
115 L H 0.0000
116 D H -0.2707
117 I H 0.2123
118 W H 0.0000
119 G H 0.0000
120 Q H -1.2072
121 G H -0.2646
122 S H 0.0000
123 V H 1.5672
124 I H 0.0000
125 T H 0.1736
126 V H 0.0000
127 S H -0.2297
128 S H -0.2470
1 S L -0.2129
2 Y L 0.0000
3 E L -1.8199
4 L L 0.0000
5 T L -0.0709
6 Q L 0.0000
7 P L 0.1719
8 L L 1.4962
9 S L -0.0201
11 V L 0.2231
12 S L -0.1619
13 V L 0.0000
14 S L 0.0876
15 P L -0.3502
16 G L -0.7509
17 Q L -1.3083
18 T L -0.3031
19 S L 0.0000
20 T L -0.0691
21 I L 0.0000
22 T L -0.0402
23 C L 0.0000
24 S L -0.0832
25 G L -0.4408
26 E L -1.8136
27 A L -0.2866
28 L L 0.0000
29 G L -0.9823
36 D L -1.9031
37 R L -0.4113
38 Y L 0.9440
39 A L 0.0000
40 S L 0.0000
41 W L 0.0000
42 Y L 0.0000
43 Q L 0.0000
44 Q L 0.0000
45 R L -0.6167
46 P L -0.4411
47 G L -0.7243
48 Q L -1.2866
49 S L -0.2491
50 P L 0.0000
51 I L 0.5885
52 L L 0.0000
53 V L 0.0000
54 I L 0.0000
55 Y L 0.1659
56 Q L -0.0179
57 D L -0.2535
65 T L -0.2404
66 K L -0.8161
67 R L -0.9129
68 P L -0.2120
69 S L -0.3022
70 G L -0.4482
71 I L 0.2044
72 P L -0.4261
74 E L -1.9026
75 R L -0.6532
76 F L 0.0000
77 S L -0.1065
78 G L -0.1135
79 S L -0.1337
80 S L -0.1377
83 S L -0.4813
84 R L -1.9527
85 G L -0.4752
86 T L -0.0548
87 A L 0.0000
88 T L -0.0152
89 L L 0.0000
90 T L -0.0229
91 I L 0.0000
92 S L -0.2585
93 G L -0.3868
94 T L 0.0000
95 Q L -1.0637
96 A L -0.1457
97 T L -0.0605
98 D L 0.0000
99 E L -1.1871
100 A L 0.0000
101 D L -0.8989
102 Y L 0.0000
103 Y L 0.0000
104 C L 0.0000
105 Q L 0.0000
106 T L 0.0000
107 W L 0.1508
108 D L 0.0000
109 R L -1.8787
114 S L -0.5239
115 T L -0.0443
116 G L 0.0000
117 V L 0.2300
118 F L 0.0000
119 G L 0.0000
120 T L -0.0709
121 G L 0.0000
122 T L 0.0000
123 K L -1.4003
124 V L 0.0000
125 T L -0.0045
126 V L 0.4650
127 L L 1.5739
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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
IR59H -0.5342 -0.0227 View CSV PDB
VK12H -0.5384 -0.0226 View CSV PDB
LE8L -0.7238 -0.0189 View CSV PDB
VR123H -0.7742 -0.0168 View CSV PDB
VR12H -0.3184 -0.0237 View CSV PDB
LD8L -0.3713 -0.0187 View CSV PDB
IK59H -0.0572 -0.0288 View CSV PDB
VK123H -0.4572 -0.0163 View CSV PDB
LK127L -0.1247 -0.0176 View CSV PDB
LR127L -0.057 -0.0186 View CSV PDB
IK62H 0.3861 -0.0202 View CSV PDB
IR62H 0.4373 -0.0209 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018