Project name: H_L11E_L_L9E_V111R

Status: done

Started: 2026-03-15 03:24:10
Settings
Chain sequence(s) A: EVQLVESGGGEEQPGGSLRLSCAGSGFDLSKGAMTWVRQAPGKGLEWVSSITRSGKGTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCALTNSLTSSGIGIGSMYGWGQGTTVTVSSAS
B: DIVMTQSPESLPVTPGEPASISSKTSDSYGNSYVGWYLQKSGQSPQLLIYRASIRAGGVPDRFSGSGSGTDFTLKISRVEAEDVGFYYVVDTKTYPIGFGQGTKLEIKRTR
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]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with all chain(s) selected           (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:03:16)
[INFO]       Auto_mut: Residue number 3 from chain B and a score of 1.047 (valine) selected for    
                       automated muatation                                                         (00:03:18)
[INFO]       Auto_mut: Residue number 107 from chain A and a score of 0.970 (isoleucine) selected  
                       for automated muatation                                                     (00:03:18)
[INFO]       Auto_mut: Residue number 29 from chain B and a score of 0.785 (tyrosine) selected for 
                       automated muatation                                                         (00:03:18)
[INFO]       Auto_mut: Residue number 113 from chain A and a score of 0.476 (tyrosine) selected    
                       for automated muatation                                                     (00:03:18)
[INFO]       Auto_mut: Residue number 108 from chain A and a score of 0.459 (glycine) selected for 
                       automated muatation                                                         (00:03:18)
[INFO]       Auto_mut: Residue number 59 from chain A and a score of 0.304 (tyrosine) selected for 
                       automated muatation                                                         (00:03:18)
[INFO]       Auto_mut: Mutating residue number 3 from chain B (valine) into glutamic acid          (00:03:18)
[INFO]       Auto_mut: Mutating residue number 3 from chain B (valine) into aspartic acid          (00:03:18)
[INFO]       Auto_mut: Mutating residue number 107 from chain A (isoleucine) into glutamic acid    (00:03:18)
[INFO]       Auto_mut: Mutating residue number 3 from chain B (valine) into arginine               (00:04:59)
[INFO]       Auto_mut: Mutating residue number 3 from chain B (valine) into lysine                 (00:05:04)
[INFO]       Auto_mut: Mutating residue number 107 from chain A (isoleucine) into lysine           (00:05:12)
[INFO]       Auto_mut: Mutating residue number 107 from chain A (isoleucine) into aspartic acid    (00:06:52)
[INFO]       Auto_mut: Mutating residue number 29 from chain B (tyrosine) into glutamic acid       (00:07:13)
[INFO]       Auto_mut: Mutating residue number 29 from chain B (tyrosine) into aspartic acid       (00:07:29)
[INFO]       Auto_mut: Mutating residue number 107 from chain A (isoleucine) into arginine         (00:08:42)
[INFO]       Auto_mut: Mutating residue number 29 from chain B (tyrosine) into lysine              (00:09:10)
[INFO]       Auto_mut: Mutating residue number 29 from chain B (tyrosine) into arginine            (00:09:20)
[INFO]       Auto_mut: Mutating residue number 113 from chain A (tyrosine) into glutamic acid      (00:10:31)
[INFO]       Auto_mut: Mutating residue number 113 from chain A (tyrosine) into aspartic acid      (00:11:09)
[INFO]       Auto_mut: Mutating residue number 108 from chain A (glycine) into glutamic acid       (00:11:14)
[INFO]       Auto_mut: Mutating residue number 113 from chain A (tyrosine) into lysine             (00:12:13)
[INFO]       Auto_mut: Mutating residue number 113 from chain A (tyrosine) into arginine           (00:12:51)
[INFO]       Auto_mut: Mutating residue number 108 from chain A (glycine) into lysine              (00:13:28)
[INFO]       Auto_mut: Mutating residue number 108 from chain A (glycine) into aspartic acid       (00:13:54)
[INFO]       Auto_mut: Mutating residue number 59 from chain A (tyrosine) into glutamic acid       (00:14:36)
[INFO]       Auto_mut: Mutating residue number 108 from chain A (glycine) into arginine            (00:15:50)
[INFO]       Auto_mut: Mutating residue number 59 from chain A (tyrosine) into lysine              (00:16:21)
[INFO]       Auto_mut: Mutating residue number 59 from chain A (tyrosine) into aspartic acid       (00:17:35)
[INFO]       Auto_mut: Mutating residue number 59 from chain A (tyrosine) into arginine            (00:19:18)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain B (valine) into glutamic     
                       acid: Energy difference: 0.1034 kcal/mol, Difference in average score from  
                       the base case: -0.0377                                                      (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain B (valine) into lysine:      
                       Energy difference: -0.1878 kcal/mol, Difference in average score from the   
                       base case: -0.0306                                                          (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain B (valine) into aspartic     
                       acid: Energy difference: 0.5316 kcal/mol, Difference in average score from  
                       the base case: -0.0379                                                      (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain B (valine) into arginine:    
                       Energy difference: -0.4054 kcal/mol, Difference in average score from the   
                       base case: -0.0374                                                          (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 107 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 0.4399 kcal/mol, Difference in average    
                       score from the base case: -0.0273                                           (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 107 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.1347 kcal/mol, Difference in average score    
                       from the base case: -0.0253                                                 (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 107 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 0.6664 kcal/mol, Difference in average    
                       score from the base case: -0.0357                                           (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 107 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.5912 kcal/mol, Difference in average score  
                       from the base case: -0.0336                                                 (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 29 from chain B (tyrosine) into glutamic  
                       acid: Energy difference: 0.3072 kcal/mol, Difference in average score from  
                       the base case: -0.0234                                                      (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 29 from chain B (tyrosine) into lysine:   
                       Energy difference: 0.1070 kcal/mol, Difference in average score from the    
                       base case: -0.0261                                                          (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 29 from chain B (tyrosine) into aspartic  
                       acid: Energy difference: 0.4129 kcal/mol, Difference in average score from  
                       the base case: -0.0236                                                      (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 29 from chain B (tyrosine) into arginine: 
                       Energy difference: 0.0150 kcal/mol, Difference in average score from the    
                       base case: -0.0251                                                          (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 113 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 0.8700 kcal/mol, Difference in average score from  
                       the base case: -0.0278                                                      (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 113 from chain A (tyrosine) into lysine:  
                       Energy difference: 0.6966 kcal/mol, Difference in average score from the    
                       base case: -0.0244                                                          (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 113 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 1.4872 kcal/mol, Difference in average score from  
                       the base case: -0.0308                                                      (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 113 from chain A (tyrosine) into          
                       arginine: Energy difference: 0.5416 kcal/mol, Difference in average score   
                       from the base case: -0.0247                                                 (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 108 from chain A (glycine) into glutamic  
                       acid: Energy difference: 31.2240 kcal/mol, Difference in average score from 
                       the base case: 0.0067                                                       (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 108 from chain A (glycine) into lysine:   
                       Energy difference: 27.0797 kcal/mol, Difference in average score from the   
                       base case: 0.0034                                                           (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 108 from chain A (glycine) into aspartic  
                       acid: Energy difference: 27.8222 kcal/mol, Difference in average score from 
                       the base case: 0.0098                                                       (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 108 from chain A (glycine) into arginine: 
                       Energy difference: 29.7328 kcal/mol, Difference in average score from the   
                       base case: 0.0011                                                           (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 59 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 2.6464 kcal/mol, Difference in average score from  
                       the base case: -0.0108                                                      (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 59 from chain A (tyrosine) into lysine:   
                       Energy difference: 1.8777 kcal/mol, Difference in average score from the    
                       base case: -0.0107                                                          (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 59 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 2.8669 kcal/mol, Difference in average score from  
                       the base case: -0.0080                                                      (00:21:03)
[INFO]       Auto_mut: Effect of mutation residue number 59 from chain A (tyrosine) into arginine: 
                       Energy difference: 1.9195 kcal/mol, Difference in average score from the    
                       base case: -0.0213                                                          (00:21:03)
[INFO]       Main:     Simulation completed successfully.                                          (00:21:10)
Show buried residues
Minimal score value
-3.3653
Maximal score value
1.0474
Average score
-0.7895
Total score value
-187.9081
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 E A -1.3114
2 V A 0.1395
3 Q A -0.5439
4 L A 0.0000
5 V A 0.2375
6 E A 0.0000
7 S A -0.5774
8 G A -1.1835
9 G A -1.1613
10 G A -1.5078
11 E A -2.5314
12 E A -2.3501
13 Q A -2.3844
14 P A -2.0844
15 G A -1.5063
16 G A -1.4806
17 S A -1.5245
18 L A -1.4431
19 R A -2.0411
20 L A 0.0000
21 S A -0.4714
22 C A 0.0000
23 A A -0.3259
24 G A -0.4484
25 S A -0.5719
26 G A -0.7839
27 F A -0.7474
28 D A -1.7971
29 L A 0.0000
30 S A -2.1771
31 K A -2.5422
32 G A 0.0000
33 A A 0.0000
34 M A 0.0000
35 T A 0.0000
36 W A 0.0000
37 V A 0.0000
38 R A 0.0000
39 Q A -0.8549
40 A A -1.2512
41 P A -1.0219
42 G A -1.4743
43 K A -2.3358
44 G A -1.4139
45 L A 0.0000
46 E A -1.0687
47 W A 0.0000
48 V A 0.0000
49 S A 0.0000
50 S A 0.0000
51 I A 0.0000
52 T A -1.4753
53 R A -2.2778
54 S A -1.8260
55 G A -1.7083
56 K A -2.1207
57 G A -1.1797
58 T A -0.3910
59 Y A 0.3040
60 Y A -0.6106
61 A A 0.0000
62 D A -2.3857
63 S A -1.7225
64 V A 0.0000
65 K A -2.4469
66 G A -1.6645
67 R A 0.0000
68 F A 0.0000
69 T A -0.7237
70 I A 0.0000
71 S A -0.6754
72 R A -1.3277
73 D A -1.5870
74 N A -2.2119
75 S A -1.6969
76 K A -2.4097
77 N A -1.9783
78 T A 0.0000
79 L A 0.0000
80 Y A -0.5534
81 L A 0.0000
82 Q A -1.2047
83 M A 0.0000
84 N A -1.4020
85 S A -1.2201
86 L A 0.0000
87 R A -2.3887
88 A A -1.8280
89 E A -2.2340
90 D A 0.0000
91 T A -1.1502
92 A A 0.0000
93 V A 0.0533
94 Y A 0.0000
95 Y A 0.0000
96 C A 0.0000
97 A A 0.0000
98 L A 0.0000
99 T A 0.0000
100 N A -0.9807
101 S A -0.8018
102 L A -0.0451
103 T A -0.1254
104 S A -0.0990
105 S A -0.1001
106 G A 0.2847
107 I A 0.9695
108 G A 0.4588
109 I A 0.0000
110 G A 0.0000
111 S A 0.0000
112 M A 0.0000
113 Y A 0.4761
114 G A 0.2196
115 W A -0.3987
116 G A 0.0000
117 Q A -1.4167
118 G A -0.6251
119 T A -0.2949
120 T A -0.5408
121 V A 0.0000
122 T A -1.5276
123 V A 0.0000
124 S A -1.6067
125 S A -1.1765
126 A A -0.6511
127 S A -0.6943
1 D B -1.2505
2 I B 0.0853
3 V B 1.0474
4 M B 0.0000
5 T B -0.6646
6 Q B 0.0000
7 S B -1.2181
8 P B -1.3270
9 E B -2.1698
10 S B -1.2888
11 L B -0.7091
12 P B -0.9494
13 V B 0.0000
14 T B -1.7517
15 P B -1.8934
16 G B -2.0626
17 E B -2.7243
18 P B -2.3087
19 A B 0.0000
20 S B -0.7852
21 I B 0.0000
22 S B -1.1201
23 S B 0.0000
24 K B -1.9379
25 T B 0.0000
26 S B -0.2378
27 D B 0.0000
28 S B 0.1537
29 Y B 0.7852
30 G B -0.3467
31 N B -1.4094
32 S B -1.1451
33 Y B -0.8312
34 V B 0.0000
35 G B 0.0000
36 W B 0.0000
37 Y B 0.0000
38 L B 0.0000
39 Q B -0.9583
40 K B -1.6574
41 S B -1.0395
42 G B -1.5527
43 Q B -2.2096
44 S B -1.5443
45 P B 0.0000
46 Q B -1.0523
47 L B 0.0000
48 L B 0.0000
49 I B 0.0000
50 Y B -0.4167
51 R B -1.8056
52 A B -1.1367
53 S B -0.6446
54 I B -0.1069
55 R B -1.1454
56 A B -0.7640
57 G B -0.6276
58 G B -0.9782
59 V B -1.0099
60 P B -1.2673
61 D B -2.3318
62 R B -2.1214
63 F B 0.0000
64 S B -1.1607
65 G B -0.8990
66 S B -1.1216
67 G B -1.5917
68 S B -1.7027
69 G B -1.4307
70 T B -1.7328
71 D B -2.6731
72 F B 0.0000
73 T B -1.2736
74 L B 0.0000
75 K B -1.8363
76 I B 0.0000
77 S B -2.3484
78 R B -3.3653
79 V B 0.0000
80 E B -2.4086
81 A B -1.2099
82 E B -2.0970
83 D B 0.0000
84 V B -0.4191
85 G B 0.0000
86 F B 0.0195
87 Y B 0.0000
88 Y B 0.0000
89 V B 0.0000
90 V B 0.0000
91 D B 0.0000
92 T B 0.0000
93 K B -0.3274
94 T B 0.1264
95 Y B -0.0102
96 P B -0.2645
97 I B 0.0000
98 G B -0.0154
99 F B 0.0857
100 G B 0.0000
101 Q B -1.3630
102 G B 0.0000
103 T B 0.0000
104 K B -1.0477
105 L B 0.0000
106 E B -0.9568
107 I B -1.0964
108 K B -2.4394
109 R B -2.9770
110 T B -2.1509
111 R B -2.5311
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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
IR107A -0.5912 -0.0336 View CSV PDB
VR3B -0.4054 -0.0374 View CSV PDB
VK3B -0.1878 -0.0306 View CSV PDB
IK107A -0.1347 -0.0253 View CSV PDB
YR29B 0.015 -0.0251 View CSV PDB
YK29B 0.107 -0.0261 View CSV PDB
YR113A 0.5416 -0.0247 View CSV PDB
YK113A 0.6966 -0.0244 View CSV PDB
YR59A 1.9195 -0.0213 View CSV PDB
YK59A 1.8777 -0.0107 View CSV PDB
GR108A 29.7328 0.0011 View CSV PDB
GK108A 27.0797 0.0034 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018