Project name: 3H3-VL-TZ-Gr

Status: done

Started: 2026-01-16 08:20:02
Settings
Chain sequence(s) H: QVQLVQSGAEVKKPGSSVKVSCKASGGSFSRLAFSWVRQAPGQGLEWMGGIIPIIGTADYAQKFQGRVTITADESTNTAYMELSSLRSEDTAVYYCARDLSSGYSDALDIWGQGSVITVSS
L: DYQLTQSPSSLSASVGDRVTITCRASALGDRYVAWYQQKPGKAPKLLIYQDTSFLYSGVPSRFSGSRRGTAFTLTISSLQPEDFATYYCQTWDRSTGVFGQGTKVEIK
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]                                                (00:00:00)
[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                                          (00:01:09)
[INFO]       Auto_mut: Residue number 59 from chain H and a score of 2.367 (isoleucine) selected   
                       for automated muatation                                                     (00:01:10)
[INFO]       Auto_mut: Residue number 62 from chain H and a score of 2.284 (isoleucine) selected   
                       for automated muatation                                                     (00:01:10)
[INFO]       Auto_mut: Residue number 66 from chain L and a score of 1.806 (phenylalanine)         
                       selected for automated muatation                                            (00:01:10)
[INFO]       Auto_mut: Residue number 15 from chain L and a score of 1.678 (valine) selected for   
                       automated muatation                                                         (00:01:10)
[INFO]       Auto_mut: Residue number 12 from chain H and a score of 1.593 (valine) selected for   
                       automated muatation                                                         (00:01:10)
[INFO]       Auto_mut: Residue number 126 from chain L and a score of 1.488 (isoleucine) selected  
                       for automated muatation                                                     (00:01:10)
[INFO]       Auto_mut: Mutating residue number 59 from chain H (isoleucine) into glutamic acid     (00:01:10)
[INFO]       Auto_mut: Mutating residue number 59 from chain H (isoleucine) into aspartic acid     (00:01:10)
[INFO]       Auto_mut: Mutating residue number 62 from chain H (isoleucine) into glutamic acid     (00:01:10)
[INFO]       Auto_mut: Mutating residue number 62 from chain H (isoleucine) into lysine            (00:01:50)
[INFO]       Auto_mut: Mutating residue number 59 from chain H (isoleucine) into lysine            (00:01:50)
[INFO]       Auto_mut: Mutating residue number 59 from chain H (isoleucine) into arginine          (00:01:57)
[INFO]       Auto_mut: Mutating residue number 62 from chain H (isoleucine) into aspartic acid     (00:02:35)
[INFO]       Auto_mut: Mutating residue number 66 from chain L (phenylalanine) into glutamic acid  
                       Mutating residue number 66 from chain L (phenylalanine) into glutamic acid  (00:02:38)
[INFO]       Auto_mut: Mutating residue number 66 from chain L (phenylalanine) into aspartic acid  
                       Mutating residue number 66 from chain L (phenylalanine) into aspartic acid  (00:02:41)
[INFO]       Auto_mut: Mutating residue number 62 from chain H (isoleucine) into arginine          (00:03:13)
[INFO]       Auto_mut: Mutating residue number 66 from chain L (phenylalanine) into arginine       (00:03:19)
[INFO]       Auto_mut: Mutating residue number 66 from chain L (phenylalanine) into lysine         (00:03:21)
[INFO]       Auto_mut: Mutating residue number 15 from chain L (valine) into glutamic acid         (00:03:53)
[INFO]       Auto_mut: Mutating residue number 15 from chain L (valine) into aspartic acid         (00:03:58)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (valine) into glutamic acid         (00:04:05)
[INFO]       Auto_mut: Mutating residue number 15 from chain L (valine) into arginine              (00:04:36)
[INFO]       Auto_mut: Mutating residue number 15 from chain L (valine) into lysine                (00:04:38)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (valine) into lysine                (00:04:45)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (valine) into aspartic acid         (00:05:19)
[INFO]       Auto_mut: Mutating residue number 126 from chain L (isoleucine) into glutamic acid    (00:05:24)
[INFO]       Auto_mut: Mutating residue number 126 from chain L (isoleucine) into aspartic acid    (00:05:31)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (valine) into arginine              (00:05:59)
[INFO]       Auto_mut: Mutating residue number 126 from chain L (isoleucine) into lysine           (00:06:06)
[INFO]       Auto_mut: Mutating residue number 126 from chain L (isoleucine) into arginine         (00:06:14)
[INFO]       Auto_mut: Effect of mutation residue number 59 from chain H (isoleucine) into         
                       glutamic acid: Energy difference: 0.2518 kcal/mol, Difference in average    
                       score from the base case: -0.0238                                           (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 59 from chain H (isoleucine) into lysine: 
                       Energy difference: -0.4424 kcal/mol, Difference in average score from the   
                       base case: -0.0233                                                          (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 59 from chain H (isoleucine) into         
                       aspartic acid: Energy difference: 0.7801 kcal/mol, Difference in average    
                       score from the base case: -0.0225                                           (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 59 from chain H (isoleucine) into         
                       arginine: Energy difference: -0.1699 kcal/mol, Difference in average score  
                       from the base case: -0.0207                                                 (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 62 from chain H (isoleucine) into         
                       glutamic acid: Energy difference: 0.6428 kcal/mol, Difference in average    
                       score from the base case: -0.0265                                           (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 62 from chain H (isoleucine) into lysine: 
                       Energy difference: -0.0139 kcal/mol, Difference in average score from the   
                       base case: -0.0260                                                          (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 62 from chain H (isoleucine) into         
                       aspartic acid: Energy difference: 1.1049 kcal/mol, Difference in average    
                       score from the base case: -0.0262                                           (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 62 from chain H (isoleucine) into         
                       arginine: Energy difference: -0.0068 kcal/mol, Difference in average score  
                       from the base case: -0.0247                                                 (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 66 from chain L (phenylalanine) into      
                       glutamic acid: Energy difference: -0.0251 kcal/mol, Difference in average   
                       score from the base case: -0.0193                                           (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 66 from chain L (phenylalanine) into      
                       lysine: Energy difference: -0.3375 kcal/mol, Difference in average score    
                       from the base case: -0.0208                                                 (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 66 from chain L (phenylalanine) into      
                       aspartic acid: Energy difference: -0.7533 kcal/mol, Difference in average   
                       score from the base case: -0.0159                                           (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 66 from chain L (phenylalanine) into      
                       arginine: Energy difference: -0.5177 kcal/mol, Difference in average score  
                       from the base case: -0.0260                                                 (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 15 from chain L (valine) into glutamic    
                       acid: Energy difference: 0.4162 kcal/mol, Difference in average score from  
                       the base case: -0.0285                                                      (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 15 from chain L (valine) into lysine:     
                       Energy difference: -0.3353 kcal/mol, Difference in average score from the   
                       base case: -0.0251                                                          (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 15 from chain L (valine) into aspartic    
                       acid: Energy difference: 0.9057 kcal/mol, Difference in average score from  
                       the base case: -0.0254                                                      (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 15 from chain L (valine) into arginine:   
                       Energy difference: -0.5316 kcal/mol, Difference in average score from the   
                       base case: -0.0237                                                          (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (valine) into glutamic    
                       acid: Energy difference: 0.5173 kcal/mol, Difference in average score from  
                       the base case: -0.0277                                                      (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (valine) into lysine:     
                       Energy difference: 0.1568 kcal/mol, Difference in average score from the    
                       base case: -0.0267                                                          (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (valine) into aspartic    
                       acid: Energy difference: 0.5875 kcal/mol, Difference in average score from  
                       the base case: -0.0279                                                      (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (valine) into arginine:   
                       Energy difference: -0.0019 kcal/mol, Difference in average score from the   
                       base case: -0.0246                                                          (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 126 from chain L (isoleucine) into        
                       glutamic acid: Energy difference: 0.0176 kcal/mol, Difference in average    
                       score from the base case: -0.0278                                           (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 126 from chain L (isoleucine) into        
                       lysine: Energy difference: -0.5126 kcal/mol, Difference in average score    
                       from the base case: -0.0303                                                 (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 126 from chain L (isoleucine) into        
                       aspartic acid: Energy difference: 0.7671 kcal/mol, Difference in average    
                       score from the base case: -0.0318                                           (00:07:06)
[INFO]       Auto_mut: Effect of mutation residue number 126 from chain L (isoleucine) into        
                       arginine: Energy difference: -0.8314 kcal/mol, Difference in average score  
                       from the base case: -0.0292                                                 (00:07:06)
[INFO]       Main:     Simulation completed successfully.                                          (00:07:11)
Show buried residues
Minimal score value
-2.0379
Maximal score value
2.367
Average score
-0.2139
Total score value
-48.9799
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 -1.1662
2 V H -0.2624
3 Q H -0.9212
4 L H 0.0000
5 V H 1.4244
6 Q H 0.0000
7 S H -0.1543
8 G H -0.4683
9 A H 0.0087
11 E H -0.3490
12 V H 1.5926
13 K H -0.2895
14 K H -1.7979
15 P H -0.6271
16 G H -0.5519
17 S H -0.1827
18 S H -0.1089
19 V H 0.0000
20 K H -1.7480
21 V H 0.0000
22 S H -0.0146
23 C H 0.0000
24 K H -0.9584
25 A H 0.0000
26 S H -0.2083
27 G H -0.5549
28 G H -0.5590
29 S H -0.1280
30 F H 0.0000
35 S H -0.4078
36 R H -1.8582
37 L H 0.0000
38 A H 0.0373
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 -0.1286
45 A H -0.0562
46 P H -0.3365
47 G H -0.7252
48 Q H -1.3094
49 G H -0.3724
50 L H 0.0000
51 E H -0.4435
52 W H 0.0000
53 M H 0.0000
54 G H 0.0000
55 G H -0.0491
56 I H 0.0000
57 I H 0.2265
58 P H 0.0000
59 I H 2.3670
62 I H 2.2843
63 G H -0.1185
64 T H -0.1310
65 A H -0.0809
66 D H -0.4251
67 Y H 0.1353
68 A H -0.1692
69 Q H -1.6133
70 K H -1.9118
71 F H 0.0000
72 Q H -1.2922
74 G H -0.7476
75 R H -0.5729
76 V H 0.0000
77 T H -0.0999
78 I H 0.0000
79 T H -0.0259
80 A H -0.0554
81 D H -0.6604
82 E H -1.9516
83 S H -0.5520
84 T H -0.1530
85 N H -0.5091
86 T H 0.0000
87 A H 0.0000
88 Y H 0.2538
89 M H 0.0000
90 E H -0.5833
91 L H 0.0000
92 S H -0.1363
93 S H -0.2693
94 L H 0.0000
95 R H -1.8826
96 S H -0.8704
97 E H -1.8577
98 D H 0.0000
99 T H -0.0182
100 A H 0.0000
101 V H 0.5959
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 L H 0.1364
109 S H -0.1258
110 S H -0.2718
111 G H -0.0487
112A Y H 1.2685
112 S H 0.1414
113 D H -0.3589
114 A H 0.0000
115 L H 0.0000
116 D H 0.0000
117 I H 0.2002
118 W H 0.0000
119 G H 0.0000
120 Q H -1.2087
121 G H -0.2722
122 S H 0.0000
123 V H 1.4301
124 I H 0.0000
125 T H 0.1698
126 V H 0.0000
127 S H -0.1517
128 S H -0.2335
1 D L -1.7894
2 Y L 0.0000
3 Q L -1.0630
4 L L 0.0000
5 T L -0.1862
6 Q L 0.0000
7 S L -0.0838
8 P L -0.1706
9 S L -0.2723
10 S L -0.3450
11 L L 0.3127
12 S L -0.2538
13 A L 0.0000
14 S L 0.0664
15 V L 1.6782
16 G L -0.3038
17 D L -1.2097
18 R L -2.0040
19 V L 0.0000
20 T L -0.0312
21 I L 0.0000
22 T L -0.0184
23 C L 0.0000
24 R L -1.4230
25 A L -0.2921
26 S L -0.2086
27 A L 0.2604
28 L L 1.3823
29 G L 0.0000
36 D L -1.3574
37 R L -1.4751
38 Y L 1.0293
39 V L 0.0000
40 A L 0.0000
41 W L 0.0000
42 Y L 0.0000
43 Q L -0.1316
44 Q L 0.0000
45 K L -0.6118
46 P L -0.4409
47 G L -0.8148
48 K L -1.7804
49 A L -0.3003
50 P L 0.0000
51 K L -0.7011
52 L L 0.0000
53 L L 0.0000
54 I L 0.0000
55 Y L 0.1710
56 Q L -0.2795
57 D L -0.3198
64 T L -0.1161
65 S L 0.0941
66 F L 1.8062
67 L L 1.0157
68 Y L 0.2692
69 S L -0.2637
70 G L -0.5050
71 V L 0.0000
72 P L -0.1602
74 S L -0.2785
75 R L -0.2975
76 F L 0.0000
77 S L -0.1513
78 G L -0.1153
79 S L -0.1659
80 R L -0.9462
83 R L -2.0379
84 G L -0.8075
85 T L -0.1071
86 A L -0.1808
87 F L 0.0000
88 T L -0.0094
89 L L 0.0000
90 T L -0.0129
91 I L 0.0000
92 S L -0.4168
93 S L -0.2213
94 L L 0.0000
95 Q L -0.4589
96 P L -0.6276
97 E L -1.7200
98 D L 0.0000
99 F L 0.2199
100 A L 0.0000
101 T L -0.1896
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 0.2098
108 D L -0.5745
109 R L -1.9338
114 S L -0.5391
115 T L -0.0506
116 G L 0.0000
117 V L 0.2360
118 F L 0.0000
119 G L 0.0000
120 Q L -1.1983
121 G L 0.0000
122 T L 0.0000
123 K L -1.2113
124 V L 0.0000
125 E L -0.8833
126 I L 1.4882
127 K L -1.3471
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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
IR126L -0.8314 -0.0292 View CSV PDB
IK126L -0.5126 -0.0303 View CSV PDB
FR66L -0.5177 -0.026 View CSV PDB
VR15L -0.5316 -0.0237 View CSV PDB
IK59H -0.4424 -0.0233 View CSV PDB
VK15L -0.3353 -0.0251 View CSV PDB
FD66L -0.7533 -0.0159 View CSV PDB
IR59H -0.1699 -0.0207 View CSV PDB
IK62H -0.0139 -0.026 View CSV PDB
IR62H -0.0068 -0.0247 View CSV PDB
VR12H -0.0019 -0.0246 View CSV PDB
VK12H 0.1568 -0.0267 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018