Project name: SR1

Status: done

Started: 2026-04-22 15:33:09
Settings
Chain sequence(s) H: VKLLEQSGAEVKKPGASVKVSCKASGYSFTSYGLHWVRQAPGQRLEWMGWISAGTGNTKYSQKFRGRVTFTRDTSATTAYMGLSSLRPEDTAVYYCARDPYGGGKSEFDYWGQGTLVTVSS
L: ELVMTQSPSSLSASVGDRVNIACRASQGISSALAWYQQKPGKAPRLLIYDASNLESGVPSRFSGSGSGTDFTLTISSLQPEDFAIYYCQQFNSYPLTFGGGTKVEIK
input PDB
Selected Chain(s) H,L
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]                                                (00:00:02)
[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                                          (00:01:16)
[INFO]       Auto_mut: Residue number 1 from chain H and a score of 1.660 (valine) selected for    
                       automated muatation                                                         (00:01:18)
[INFO]       Auto_mut: Residue number 12 from chain H and a score of 1.107 (valine) selected for   
                       automated muatation                                                         (00:01:18)
[INFO]       Auto_mut: Residue number 109 from chain H and a score of 0.984 (tyrosine) selected    
                       for automated muatation                                                     (00:01:18)
[INFO]       Auto_mut: Residue number 3 from chain H and a score of 0.981 (leucine) selected for   
                       automated muatation                                                         (00:01:18)
[INFO]       Auto_mut: Residue number 123 from chain H and a score of 0.972 (leucine) selected for 
                       automated muatation                                                         (00:01:18)
[INFO]       Auto_mut: Residue number 3 from chain L and a score of 0.730 (valine) selected for    
                       automated muatation                                                         (00:01:18)
[INFO]       Auto_mut: Mutating residue number 1 from chain H (valine) into glutamic acid          (00:01:18)
[INFO]       Auto_mut: Mutating residue number 1 from chain H (valine) into aspartic acid          (00:01:18)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (valine) into glutamic acid         (00:01:18)
[INFO]       Auto_mut: Mutating residue number 1 from chain H (valine) into arginine               (00:02:09)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (valine) into lysine                (00:02:16)
[INFO]       Auto_mut: Mutating residue number 1 from chain H (valine) into lysine                 (00:02:18)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (valine) into aspartic acid         (00:03:21)
[INFO]       Auto_mut: Mutating residue number 109 from chain H (tyrosine) into glutamic acid      (00:03:25)
[INFO]       Auto_mut: Mutating residue number 109 from chain H (tyrosine) into aspartic acid      (00:03:27)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (valine) into arginine              (00:04:18)
[INFO]       Auto_mut: Mutating residue number 109 from chain H (tyrosine) into arginine           (00:04:28)
[INFO]       Auto_mut: Mutating residue number 109 from chain H (tyrosine) into lysine             (00:04:31)
[INFO]       Auto_mut: Mutating residue number 3 from chain H (leucine) into glutamic acid         (00:05:22)
[INFO]       Auto_mut: Mutating residue number 3 from chain H (leucine) into aspartic acid         (00:05:42)
[INFO]       Auto_mut: Mutating residue number 123 from chain H (leucine) into glutamic acid       (00:05:50)
[INFO]       Auto_mut: Mutating residue number 3 from chain H (leucine) into lysine                (00:06:30)
[INFO]       Auto_mut: Mutating residue number 3 from chain H (leucine) into arginine              (00:06:41)
[INFO]       Auto_mut: Mutating residue number 123 from chain H (leucine) into lysine              (00:06:49)
[INFO]       Auto_mut: Mutating residue number 123 from chain H (leucine) into aspartic acid       (00:07:36)
[INFO]       Auto_mut: Mutating residue number 3 from chain L (valine) into glutamic acid          (00:07:48)
[INFO]       Auto_mut: Mutating residue number 3 from chain L (valine) into aspartic acid          (00:08:05)
[INFO]       Auto_mut: Mutating residue number 123 from chain H (leucine) into arginine            (00:08:35)
[INFO]       Auto_mut: Mutating residue number 3 from chain L (valine) into lysine                 (00:08:46)
[INFO]       Auto_mut: Mutating residue number 3 from chain L (valine) into arginine               (00:08:59)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain H (valine) into glutamic     
                       acid: Energy difference: -0.2100 kcal/mol, Difference in average score from 
                       the base case: -0.0433                                                      (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain H (valine) into lysine:      
                       Energy difference: -0.2446 kcal/mol, Difference in average score from the   
                       base case: -0.0506                                                          (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain H (valine) into aspartic     
                       acid: Energy difference: -0.5763 kcal/mol, Difference in average score from 
                       the base case: -0.0431                                                      (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain H (valine) into arginine:    
                       Energy difference: -0.7587 kcal/mol, Difference in average score from the   
                       base case: -0.0454                                                          (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (valine) into glutamic    
                       acid: Energy difference: 0.2654 kcal/mol, Difference in average score from  
                       the base case: -0.0597                                                      (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (valine) into lysine:     
                       Energy difference: -0.4682 kcal/mol, Difference in average score from the   
                       base case: -0.0566                                                          (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (valine) into aspartic    
                       acid: Energy difference: 0.7888 kcal/mol, Difference in average score from  
                       the base case: -0.0609                                                      (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (valine) into arginine:   
                       Energy difference: -0.5956 kcal/mol, Difference in average score from the   
                       base case: -0.0603                                                          (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 109 from chain H (tyrosine) into glutamic 
                       acid: Energy difference: 2.2490 kcal/mol, Difference in average score from  
                       the base case: -0.0447                                                      (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 109 from chain H (tyrosine) into lysine:  
                       Energy difference: 0.1616 kcal/mol, Difference in average score from the    
                       base case: -0.0413                                                          (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 109 from chain H (tyrosine) into aspartic 
                       acid: Energy difference: 1.7417 kcal/mol, Difference in average score from  
                       the base case: -0.0492                                                      (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 109 from chain H (tyrosine) into          
                       arginine: Energy difference: -1.0338 kcal/mol, Difference in average score  
                       from the base case: -0.0426                                                 (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain H (leucine) into glutamic    
                       acid: Energy difference: 0.4671 kcal/mol, Difference in average score from  
                       the base case: -0.0643                                                      (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain H (leucine) into lysine:     
                       Energy difference: -0.8566 kcal/mol, Difference in average score from the   
                       base case: -0.0436                                                          (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain H (leucine) into aspartic    
                       acid: Energy difference: -0.2567 kcal/mol, Difference in average score from 
                       the base case: -0.0543                                                      (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain H (leucine) into arginine:   
                       Energy difference: -1.5466 kcal/mol, Difference in average score from the   
                       base case: -0.0430                                                          (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain H (leucine) into glutamic  
                       acid: Energy difference: 0.2576 kcal/mol, Difference in average score from  
                       the base case: -0.0402                                                      (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain H (leucine) into lysine:   
                       Energy difference: -0.0767 kcal/mol, Difference in average score from the   
                       base case: -0.0395                                                          (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain H (leucine) into aspartic  
                       acid: Energy difference: 0.6122 kcal/mol, Difference in average score from  
                       the base case: -0.0422                                                      (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain H (leucine) into arginine: 
                       Energy difference: -0.4760 kcal/mol, Difference in average score from the   
                       base case: -0.0470                                                          (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain L (valine) into glutamic     
                       acid: Energy difference: -2.3222 kcal/mol, Difference in average score from 
                       the base case: -0.0450                                                      (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain L (valine) into lysine:      
                       Energy difference: -0.0295 kcal/mol, Difference in average score from the   
                       base case: -0.0494                                                          (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain L (valine) into aspartic     
                       acid: Energy difference: -1.0925 kcal/mol, Difference in average score from 
                       the base case: -0.0508                                                      (00:09:56)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain L (valine) into arginine:    
                       Energy difference: 0.2631 kcal/mol, Difference in average score from the    
                       base case: -0.0515                                                          (00:09:56)
[INFO]       Main:     Simulation completed successfully.                                          (00:10:01)
Show buried residues
Minimal score value
-3.0646
Maximal score value
1.66
Average score
-0.5069
Total score value
-115.5783
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 V H 1.6600
2 K H 0.7711
3 L H 0.9814
4 L H 0.0000
5 E H -0.7721
6 Q H 0.0000
7 S H -0.7961
8 G H -0.6232
9 A H 0.3394
11 E H 0.2855
12 V H 1.1069
13 K H -0.8094
14 K H -2.0393
15 P H -1.7265
16 G H -1.2720
17 A H -1.0887
18 S H -0.9709
19 V H 0.0000
20 K H -1.8009
21 V H 0.0000
22 S H -0.7422
23 C H 0.0000
24 K H -0.8231
25 A H 0.0000
26 S H 0.0659
27 G H 0.3173
28 Y H 0.2895
29 S H -0.3332
30 F H 0.0000
35 T H -0.3636
36 S H -0.0566
37 Y H 0.3006
38 G H 0.0000
39 L H 0.0000
40 H H 0.0000
41 W H 0.0000
42 V H 0.0000
43 R H 0.0000
44 Q H -0.6758
45 A H -1.0899
46 P H -1.1519
47 G H -1.3730
48 Q H -2.0732
49 R H -1.8249
50 L H 0.0000
51 E H -0.9921
52 W H 0.0000
53 M H 0.0000
54 G H 0.0000
55 W H 0.0000
56 I H 0.0000
57 S H 0.0000
58 A H 0.0000
59 G H -0.5918
62 T H -0.6598
63 G H -1.0246
64 N H -1.5814
65 T H -0.9526
66 K H -1.0516
67 Y H -0.9843
68 S H 0.0000
69 Q H -2.8732
70 K H -2.8638
71 F H 0.0000
72 R H -3.0646
74 G H -1.8714
75 R H -1.4037
76 V H 0.0000
77 T H -0.7448
78 F H 0.0000
79 T H -0.7190
80 R H -1.0491
81 D H -1.1213
82 T H -0.7298
83 S H -0.4906
84 A H -0.4503
85 T H -0.5893
86 T H 0.0000
87 A H 0.0000
88 Y H -0.5507
89 M H 0.0000
90 G H -0.9024
91 L H 0.0000
92 S H -0.8616
93 S H -0.9273
94 L H 0.0000
95 R H -2.0164
96 P H -1.8181
97 E H -2.2036
98 D H 0.0000
99 T H -0.5219
100 A H 0.0000
101 V H 0.3560
102 Y H 0.0000
103 Y H 0.0000
104 C H 0.0000
105 A H 0.0000
106 R H 0.0000
107 D H 0.0000
108 P H 0.4653
109 Y H 0.9838
110 G H 0.1742
111 G H -0.3568
112A G H 0.0000
112 K H -0.8634
113 S H 0.0000
114 E H 0.0000
115 F H 0.0000
116 D H 0.0000
117 Y H 0.2463
118 W H -0.2366
119 G H 0.0000
120 Q H -1.5127
121 G H -0.7878
122 T H 0.0000
123 L H 0.9720
124 V H 0.0000
125 T H 0.1173
126 V H 0.0000
127 S H -1.0408
128 S H -1.0911
1 E L -1.5002
2 L L -0.2586
3 V L 0.7297
4 M L 0.0000
5 T L -0.5508
6 Q L 0.0000
7 S L -0.8124
8 P L -0.6227
9 S L -0.5328
10 S L -0.6319
11 L L -0.5081
12 S L -0.8632
13 A L 0.0000
14 S L -0.8151
15 V L 0.0769
16 G L -0.8066
17 D L -1.7534
18 R L -2.4197
19 V L 0.0000
20 N L -1.6680
21 I L 0.0000
22 A L -0.9702
23 C L 0.0000
24 R L -2.3098
25 A L 0.0000
26 S L -0.9835
27 Q L -1.7877
28 G L -1.6182
29 I L 0.0000
36 S L -0.9814
37 S L -0.8428
38 A L 0.0000
39 L L 0.0000
40 A L 0.0000
41 W L 0.0000
42 Y L 0.0000
43 Q L -0.2489
44 Q L 0.0000
45 K L -1.1576
46 P L -0.9934
47 G L -1.5910
48 K L -2.4152
49 A L -1.4226
50 P L 0.0000
51 R L -0.8030
52 L L 0.0000
53 L L 0.0000
54 I L 0.0000
55 Y L -0.2662
56 D L -0.9766
57 A L 0.0000
65 S L -0.7991
66 N L -0.8001
67 L L -0.0459
68 E L 0.0000
69 S L -0.4096
70 G L -0.5364
71 V L 0.0000
72 P L -0.3845
74 S L -0.4265
75 R L -0.7769
76 F L 0.0000
77 S L -0.5643
78 G L -0.6166
79 S L -0.8003
80 G L -1.1136
83 S L -1.1848
84 G L -1.2715
85 T L -1.7468
86 D L -2.0507
87 F L 0.0000
88 T L -0.9342
89 L L 0.0000
90 T L -1.0436
91 I L 0.0000
92 S L -1.3981
93 S L -1.2665
94 L L 0.0000
95 Q L -0.8524
96 P L -1.0862
97 E L -1.6534
98 D L 0.0000
99 F L -0.0931
100 A L 0.0000
101 I L 0.0477
102 Y L 0.0000
103 Y L 0.0000
104 C L 0.0000
105 Q L 0.0000
106 Q L 0.0000
107 F L 0.0000
108 N L -0.6780
109 S L -0.4804
114 Y L -0.0100
115 P L -0.6125
116 L L 0.0000
117 T L -0.0138
118 F L 0.0000
119 G L 0.0000
120 G L -0.6494
121 G L -0.7236
122 T L 0.0000
123 K L -0.6028
124 V L 0.0000
125 E L -0.9894
126 I L -0.7464
127 K L -1.4853
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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
VE3L -2.3222 -0.045 View CSV PDB
LR3H -1.5466 -0.043 View CSV PDB
VD3L -1.0925 -0.0508 View CSV PDB
VR12H -0.5956 -0.0603 View CSV PDB
YR109H -1.0338 -0.0426 View CSV PDB
LK3H -0.8566 -0.0436 View CSV PDB
VR1H -0.7587 -0.0454 View CSV PDB
VK12H -0.4682 -0.0566 View CSV PDB
VD1H -0.5763 -0.0431 View CSV PDB
LR123H -0.476 -0.047 View CSV PDB
LK123H -0.0767 -0.0395 View CSV PDB
YK109H 0.1616 -0.0413 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018