Project name: jl3

Status: done

Started: 2025-10-27 03:29:42
Settings
Chain sequence(s) H: QVQLVQSGAEVKKPGASVKVSCKASGYTFTSHWLHWVRQATGQGLEWIGYINPDTDDTEYNQKFKDRVTLTANTSISTAYMELSSLRSEDTAVYYCARGGIYYEYAKDYWGQGTTVTVSS
L: DIVITQSPDSLAVSLGERATINCKASQSVDFGGESYMNWYQQKPGQPPKLLIYVASHLESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQSNEDPLTFGGGTKVEIK
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]                                                (00:00:00)
[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                                          (00:03:35)
[INFO]       Auto_mut: Residue number 109 from chain H and a score of 2.743 (isoleucine) selected  
                       for automated muatation                                                     (00:03:37)
[INFO]       Auto_mut: Residue number 110 from chain H and a score of 2.533 (tyrosine) selected    
                       for automated muatation                                                     (00:03:37)
[INFO]       Auto_mut: Residue number 111 from chain H and a score of 1.422 (tyrosine) selected    
                       for automated muatation                                                     (00:03:37)
[INFO]       Auto_mut: Residue number 84 from chain H and a score of 0.967 (isoleucine) selected   
                       for automated muatation                                                     (00:03:37)
[INFO]       Auto_mut: Residue number 12 from chain H and a score of 0.881 (valine) selected for   
                       automated muatation                                                         (00:03:37)
[INFO]       Auto_mut: Residue number 126 from chain L and a score of 0.879 (isoleucine) selected  
                       for automated muatation                                                     (00:03:37)
[INFO]       Auto_mut: Mutating residue number 109 from chain H (isoleucine) into glutamic acid    (00:03:37)
[INFO]       Auto_mut: Mutating residue number 110 from chain H (tyrosine) into glutamic acid      (00:03:37)
[INFO]       Auto_mut: Mutating residue number 109 from chain H (isoleucine) into aspartic acid    (00:03:37)
[INFO]       Auto_mut: Mutating residue number 109 from chain H (isoleucine) into arginine         (00:05:29)
[INFO]       Auto_mut: Mutating residue number 110 from chain H (tyrosine) into lysine             (00:05:30)
[INFO]       Auto_mut: Mutating residue number 109 from chain H (isoleucine) into lysine           (00:05:34)
[INFO]       Auto_mut: Mutating residue number 110 from chain H (tyrosine) into aspartic acid      (00:07:29)
[INFO]       Auto_mut: Mutating residue number 111 from chain H (tyrosine) into glutamic acid      (00:07:32)
[INFO]       Auto_mut: Mutating residue number 111 from chain H (tyrosine) into aspartic acid      (00:07:46)
[INFO]       Auto_mut: Mutating residue number 110 from chain H (tyrosine) into arginine           (00:09:19)
[INFO]       Auto_mut: Mutating residue number 111 from chain H (tyrosine) into lysine             (00:09:25)
[INFO]       Auto_mut: Mutating residue number 111 from chain H (tyrosine) into arginine           (00:09:42)
[INFO]       Auto_mut: Mutating residue number 84 from chain H (isoleucine) into glutamic acid     (00:11:25)
[INFO]       Auto_mut: Mutating residue number 84 from chain H (isoleucine) into aspartic acid     (00:11:34)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (valine) into glutamic acid         (00:11:45)
[INFO]       Auto_mut: Mutating residue number 84 from chain H (isoleucine) into lysine            (00:13:21)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (valine) into lysine                (00:13:35)
[INFO]       Auto_mut: Mutating residue number 84 from chain H (isoleucine) into arginine          (00:13:40)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (valine) into aspartic acid         (00:15:28)
[INFO]       Auto_mut: Mutating residue number 126 from chain L (isoleucine) into glutamic acid    (00:15:34)
[INFO]       Auto_mut: Mutating residue number 126 from chain L (isoleucine) into aspartic acid    (00:15:58)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (valine) into arginine              (00:17:17)
[INFO]       Auto_mut: Mutating residue number 126 from chain L (isoleucine) into lysine           (00:17:26)
[INFO]       Auto_mut: Mutating residue number 126 from chain L (isoleucine) into arginine         (00:17:50)
[INFO]       Auto_mut: Effect of mutation residue number 109 from chain H (isoleucine) into        
                       glutamic acid: Energy difference: 0.5134 kcal/mol, Difference in average    
                       score from the base case: -0.0418                                           (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 109 from chain H (isoleucine) into        
                       lysine: Energy difference: -0.0718 kcal/mol, Difference in average score    
                       from the base case: -0.0365                                                 (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 109 from chain H (isoleucine) into        
                       aspartic acid: Energy difference: 1.1079 kcal/mol, Difference in average    
                       score from the base case: -0.0417                                           (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 109 from chain H (isoleucine) into        
                       arginine: Energy difference: -0.0495 kcal/mol, Difference in average score  
                       from the base case: -0.0383                                                 (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 110 from chain H (tyrosine) into glutamic 
                       acid: Energy difference: 0.2210 kcal/mol, Difference in average score from  
                       the base case: -0.0257                                                      (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 110 from chain H (tyrosine) into lysine:  
                       Energy difference: -0.1610 kcal/mol, Difference in average score from the   
                       base case: -0.0248                                                          (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 110 from chain H (tyrosine) into aspartic 
                       acid: Energy difference: 0.2838 kcal/mol, Difference in average score from  
                       the base case: -0.0250                                                      (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 110 from chain H (tyrosine) into          
                       arginine: Energy difference: -0.1245 kcal/mol, Difference in average score  
                       from the base case: -0.0191                                                 (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain H (tyrosine) into glutamic 
                       acid: Energy difference: 1.5985 kcal/mol, Difference in average score from  
                       the base case: -0.0015                                                      (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain H (tyrosine) into lysine:  
                       Energy difference: 0.6079 kcal/mol, Difference in average score from the    
                       base case: 0.0138                                                           (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain H (tyrosine) into aspartic 
                       acid: Energy difference: 1.6556 kcal/mol, Difference in average score from  
                       the base case: 0.0047                                                       (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain H (tyrosine) into          
                       arginine: Energy difference: 0.7776 kcal/mol, Difference in average score   
                       from the base case: 0.0120                                                  (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 84 from chain H (isoleucine) into         
                       glutamic acid: Energy difference: -1.6897 kcal/mol, Difference in average   
                       score from the base case: -0.0240                                           (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 84 from chain H (isoleucine) into lysine: 
                       Energy difference: -0.5702 kcal/mol, Difference in average score from the   
                       base case: -0.0278                                                          (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 84 from chain H (isoleucine) into         
                       aspartic acid: Energy difference: -0.4887 kcal/mol, Difference in average   
                       score from the base case: -0.0328                                           (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 84 from chain H (isoleucine) into         
                       arginine: Energy difference: -0.1236 kcal/mol, Difference in average score  
                       from the base case: -0.0345                                                 (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (valine) into glutamic    
                       acid: Energy difference: 0.6598 kcal/mol, Difference in average score from  
                       the base case: -0.0440                                                      (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (valine) into lysine:     
                       Energy difference: 0.0672 kcal/mol, Difference in average score from the    
                       base case: -0.0406                                                          (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (valine) into aspartic    
                       acid: Energy difference: 0.7003 kcal/mol, Difference in average score from  
                       the base case: -0.0444                                                      (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (valine) into arginine:   
                       Energy difference: -0.0222 kcal/mol, Difference in average score from the   
                       base case: -0.0453                                                          (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 126 from chain L (isoleucine) into        
                       glutamic acid: Energy difference: 2.2214 kcal/mol, Difference in average    
                       score from the base case: -0.0485                                           (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 126 from chain L (isoleucine) into        
                       lysine: Energy difference: 1.6328 kcal/mol, Difference in average score     
                       from the base case: -0.0483                                                 (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 126 from chain L (isoleucine) into        
                       aspartic acid: Energy difference: 2.4569 kcal/mol, Difference in average    
                       score from the base case: -0.0476                                           (00:19:42)
[INFO]       Auto_mut: Effect of mutation residue number 126 from chain L (isoleucine) into        
                       arginine: Energy difference: 0.9962 kcal/mol, Difference in average score   
                       from the base case: -0.0530                                                 (00:19:42)
[INFO]       Main:     Simulation completed successfully.                                          (00:19:48)
Show buried residues
Minimal score value
-3.4385
Maximal score value
2.7426
Average score
-0.6275
Total score value
-143.6919
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 D L -2.2818
2 I L 0.0000
3 V L 0.8407
4 I L 0.0000
5 T L -0.4516
6 Q L 0.0000
7 S L -1.2465
8 P L -1.4392
9 D L -2.2660
10 S L -1.4432
11 L L -0.5019
12 A L 0.3412
13 V L -0.1432
14 S L -0.0248
15 L L 0.6050
16 G L -0.9684
17 E L -2.2890
18 R L -2.6787
19 A L 0.0000
20 T L -0.8446
21 I L 0.0000
22 N L -1.6359
23 C L 0.0000
24 K L -1.7858
25 A L -0.8790
26 S L -0.9703
27 Q L -1.6868
28 S L -1.1434
29 V L 0.0000
30 D L -0.6963
31 F L 0.6107
34 G L -0.3691
35 G L -1.0585
36 E L -1.6042
37 S L -0.8078
38 Y L -0.2892
39 M L 0.0000
40 N L 0.0000
41 W L 0.0000
42 Y L 0.0000
43 Q L 0.0000
44 Q L 0.0000
45 K L -1.4334
46 P L -0.9863
47 G L -1.3237
48 Q L -2.0700
49 P L -1.3367
50 P L 0.0000
51 K L -1.5030
52 L L 0.0000
53 L L 0.0000
54 I L 0.0000
55 Y L 0.2190
56 V L -0.1426
57 A L 0.0000
65 S L -0.5601
66 H L -0.3307
67 L L -0.1970
68 E L -0.5960
69 S L -0.5442
70 G L -0.8184
71 V L 0.0000
72 P L -1.1672
74 D L -1.9367
75 R L -1.4865
76 F L 0.0000
77 S L -0.6371
78 G L -0.3129
79 S L -0.9050
80 G L -1.2818
83 S L -1.4552
84 G L -1.2842
85 T L -1.8049
86 D L -2.5190
87 F L 0.0000
88 T L -1.0781
89 L L 0.0000
90 T L -0.6636
91 I L 0.0000
92 S L -1.6849
93 S L -1.5242
94 L L 0.0000
95 Q L -1.0066
96 A L -0.5481
97 E L -1.8245
98 D L 0.0000
99 V L -0.3934
100 A L 0.0000
101 V L -0.4595
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 S L 0.0000
108 N L -1.1757
109 E L -2.4457
114 D L -2.7413
115 P L 0.0000
116 L L 0.0000
117 T L -0.4210
118 F L 0.0000
119 G L 0.0000
120 G L -0.9829
121 G L -1.0788
122 T L 0.0000
123 K L -1.2569
124 V L 0.0000
125 E L -0.2814
126 I L 0.8795
1 Q H -1.5475
2 V H -0.8519
3 Q H -1.2887
4 L H 0.0000
5 V H 0.4372
6 Q H 0.0000
7 S H -0.5615
8 G H -0.5996
9 A H -0.1063
11 E H -0.1350
12 V H 0.8814
13 K H -0.7802
14 K H -1.9957
15 P H -1.6221
16 G H -1.4554
17 A H -1.1776
18 S H -1.4005
19 V H 0.0000
20 K H -2.1631
21 V H 0.0000
22 S H -0.5754
23 C H 0.0000
24 K H -0.4903
25 A H 0.0000
26 S H -0.6709
27 G H -1.0560
28 Y H -0.4553
29 T H -0.1343
30 F H 0.0000
35 T H -0.7613
36 S H -0.1894
37 H H 0.0000
38 W H -0.0210
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 -0.7095
45 A H -0.9509
46 T H -0.7988
47 G H -1.1231
48 Q H -1.6467
49 G H -0.9814
50 L H 0.0000
51 E H -0.6306
52 W H 0.0000
53 I H 0.0000
54 G H 0.0000
55 Y H -0.5444
56 I H 0.0000
57 N H -1.9518
58 P H 0.0000
59 D H -2.7903
62 T H -2.5108
63 D H -3.4385
64 D H -3.1803
65 T H -1.6918
66 E H -1.6901
67 Y H -1.5694
68 N H -2.3226
69 Q H -3.0151
70 K H -2.9355
71 F H 0.0000
72 K H -3.1512
74 D H -2.8916
75 R H -1.9084
76 V H 0.0000
77 T H -1.1629
78 L H 0.0000
79 T H -0.8456
80 A H -1.0334
81 N H -0.7154
82 T H -0.4899
83 S H 0.3089
84 I H 0.9668
85 S H 0.1236
86 T H 0.0000
87 A H 0.0000
88 Y H -0.6708
89 M H 0.0000
90 E H -1.6419
91 L H 0.0000
92 S H -1.2566
93 S H -1.1467
94 L H 0.0000
95 R H -2.2761
96 S H -1.8790
97 E H -2.1756
98 D H 0.0000
99 T H -0.6937
100 A H 0.0000
101 V H 0.1195
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 G H 0.0000
108 G H 0.0000
109 I H 2.7426
110 Y H 2.5333
111 Y H 1.4220
112 E H 0.6357
113 Y H -0.0303
114 A H 0.0000
115 K H 0.0000
116 D H -0.1627
117 Y H -0.1206
118 W H -0.2264
119 G H 0.0000
120 Q H -1.1804
121 G H -0.5920
122 T H 0.0000
123 T H 0.1169
124 V H 0.0000
125 T H -0.2157
126 V H 0.0000
127 S H -0.7840
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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
IE84H -1.6897 -0.024 View CSV PDB
ID84H -0.4887 -0.0328 View CSV PDB
VR12H -0.0222 -0.0453 View CSV PDB
IR109H -0.0495 -0.0383 View CSV PDB
IK109H -0.0718 -0.0365 View CSV PDB
YK110H -0.161 -0.0248 View CSV PDB
YR110H -0.1245 -0.0191 View CSV PDB
VK12H 0.0672 -0.0406 View CSV PDB
IR126L 0.9962 -0.053 View CSV PDB
IK126L 1.6328 -0.0483 View CSV PDB
YE111H 1.5985 -0.0015 View CSV PDB
YD111H 1.6556 0.0047 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018