Project name: RFA_6

Status: done

Started: 2026-04-06 02:29:03
Settings
Chain sequence(s) A: EVQLVESGGGLEQPGGSLRLSCAGSGFDLSKGAMTWVRQAPGKGLEWVSSITRSGKGTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCALTNSLTSSGIGIGSMYGWGQGTTVTVSSAS
B: DIVMTQSPLSLPVTPGEPASISSKTSTSTTDSYGNSYVGWYLQKSGQSPQLLIYRASIRAGGVPDRFSGSGSGTDFTLKISRVEAEDVGFYYVVDTKTYPIGFGQGTKLEIKRTV
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                                          (00:01:47)
[INFO]       Auto_mut: Residue number 107 from chain A and a score of 1.933 (isoleucine) selected  
                       for automated muatation                                                     (00:01:48)
[INFO]       Auto_mut: Residue number 102 from chain A and a score of 1.059 (leucine) selected for 
                       automated muatation                                                         (00:01:48)
[INFO]       Auto_mut: Residue number 3 from chain B and a score of 1.046 (valine) selected for    
                       automated muatation                                                         (00:01:48)
[INFO]       Auto_mut: Residue number 115 from chain B and a score of 0.989 (valine) selected for  
                       automated muatation                                                         (00:01:48)
[INFO]       Auto_mut: Residue number 11 from chain A and a score of 0.837 (leucine) selected for  
                       automated muatation                                                         (00:01:48)
[INFO]       Auto_mut: Residue number 33 from chain B and a score of 0.822 (tyrosine) selected for 
                       automated muatation                                                         (00:01:48)
[INFO]       Auto_mut: Mutating residue number 107 from chain A (isoleucine) into glutamic acid    (00:01:48)
[INFO]       Auto_mut: Mutating residue number 107 from chain A (isoleucine) into aspartic acid    (00:01:48)
[INFO]       Auto_mut: Mutating residue number 102 from chain A (leucine) into glutamic acid       (00:01:48)
[INFO]       Auto_mut: Mutating residue number 102 from chain A (leucine) into lysine              (00:02:40)
[INFO]       Auto_mut: Mutating residue number 107 from chain A (isoleucine) into arginine         (00:02:40)
[INFO]       Auto_mut: Mutating residue number 107 from chain A (isoleucine) into lysine           (00:02:43)
[INFO]       Auto_mut: Mutating residue number 102 from chain A (leucine) into aspartic acid       (00:03:37)
[INFO]       Auto_mut: Mutating residue number 3 from chain B (valine) into glutamic acid          (00:03:41)
[INFO]       Auto_mut: Mutating residue number 3 from chain B (valine) into aspartic acid          (00:03:53)
[INFO]       Auto_mut: Mutating residue number 102 from chain A (leucine) into arginine            (00:04:28)
[INFO]       Auto_mut: Mutating residue number 3 from chain B (valine) into lysine                 (00:04:36)
[INFO]       Auto_mut: Mutating residue number 3 from chain B (valine) into arginine               (00:04:42)
[INFO]       Auto_mut: Mutating residue number 115 from chain B (valine) into glutamic acid        (00:05:27)
[INFO]       Auto_mut: Mutating residue number 115 from chain B (valine) into aspartic acid        (00:05:35)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (leucine) into glutamic acid        (00:05:38)
[INFO]       Auto_mut: Mutating residue number 115 from chain B (valine) into lysine               (00:06:17)
[INFO]       Auto_mut: Mutating residue number 115 from chain B (valine) into arginine             (00:06:24)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (leucine) into lysine               (00:06:32)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (leucine) into aspartic acid        (00:07:09)
[INFO]       Auto_mut: Mutating residue number 33 from chain B (tyrosine) into glutamic acid       (00:07:17)
[INFO]       Auto_mut: Mutating residue number 33 from chain B (tyrosine) into aspartic acid       (00:07:30)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (leucine) into arginine             (00:07:59)
[INFO]       Auto_mut: Mutating residue number 33 from chain B (tyrosine) into lysine              (00:08:08)
[INFO]       Auto_mut: Mutating residue number 33 from chain B (tyrosine) into arginine            (00:08:20)
[INFO]       Auto_mut: Effect of mutation residue number 107 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 0.7168 kcal/mol, Difference in average    
                       score from the base case: -0.0533                                           (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 107 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.0374 kcal/mol, Difference in average score    
                       from the base case: -0.0466                                                 (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 107 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 0.9571 kcal/mol, Difference in average    
                       score from the base case: -0.0537                                           (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 107 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.0648 kcal/mol, Difference in average score   
                       from the base case: -0.0547                                                 (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 102 from chain A (leucine) into glutamic  
                       acid: Energy difference: -0.3953 kcal/mol, Difference in average score from 
                       the base case: -0.0487                                                      (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 102 from chain A (leucine) into lysine:   
                       Energy difference: -0.0550 kcal/mol, Difference in average score from the   
                       base case: -0.0480                                                          (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 102 from chain A (leucine) into aspartic  
                       acid: Energy difference: -0.3744 kcal/mol, Difference in average score from 
                       the base case: -0.0544                                                      (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 102 from chain A (leucine) into arginine: 
                       Energy difference: -0.3807 kcal/mol, Difference in average score from the   
                       base case: -0.0484                                                          (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain B (valine) into glutamic     
                       acid: Energy difference: -0.2381 kcal/mol, Difference in average score from 
                       the base case: -0.0397                                                      (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain B (valine) into lysine:      
                       Energy difference: -0.2182 kcal/mol, Difference in average score from the   
                       base case: -0.0399                                                          (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain B (valine) into aspartic     
                       acid: Energy difference: 0.0796 kcal/mol, Difference in average score from  
                       the base case: -0.0409                                                      (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain B (valine) into arginine:    
                       Energy difference: -0.4023 kcal/mol, Difference in average score from the   
                       base case: -0.0403                                                          (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 115 from chain B (valine) into glutamic   
                       acid: Energy difference: -0.1807 kcal/mol, Difference in average score from 
                       the base case: -0.0276                                                      (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 115 from chain B (valine) into lysine:    
                       Energy difference: -0.1632 kcal/mol, Difference in average score from the   
                       base case: -0.0266                                                          (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 115 from chain B (valine) into aspartic   
                       acid: Energy difference: -0.1781 kcal/mol, Difference in average score from 
                       the base case: -0.0273                                                      (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 115 from chain B (valine) into arginine:  
                       Energy difference: -0.2316 kcal/mol, Difference in average score from the   
                       base case: -0.0238                                                          (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (leucine) into glutamic   
                       acid: Energy difference: 0.5546 kcal/mol, Difference in average score from  
                       the base case: -0.0541                                                      (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (leucine) into lysine:    
                       Energy difference: -0.1008 kcal/mol, Difference in average score from the   
                       base case: -0.0517                                                          (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (leucine) into aspartic   
                       acid: Energy difference: 0.7539 kcal/mol, Difference in average score from  
                       the base case: -0.0537                                                      (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (leucine) into arginine:  
                       Energy difference: -0.2831 kcal/mol, Difference in average score from the   
                       base case: -0.0544                                                          (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 33 from chain B (tyrosine) into glutamic  
                       acid: Energy difference: 0.5521 kcal/mol, Difference in average score from  
                       the base case: -0.0357                                                      (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 33 from chain B (tyrosine) into lysine:   
                       Energy difference: 0.2539 kcal/mol, Difference in average score from the    
                       base case: -0.0329                                                          (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 33 from chain B (tyrosine) into aspartic  
                       acid: Energy difference: 0.5107 kcal/mol, Difference in average score from  
                       the base case: -0.0361                                                      (00:09:15)
[INFO]       Auto_mut: Effect of mutation residue number 33 from chain B (tyrosine) into arginine: 
                       Energy difference: -0.0638 kcal/mol, Difference in average score from the   
                       base case: -0.0343                                                          (00:09:15)
[INFO]       Main:     Simulation completed successfully.                                          (00:09:21)
Show buried residues
Minimal score value
-3.4087
Maximal score value
1.933
Average score
-0.6478
Total score value
-156.7675
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 -1.5468
2 V A -0.2925
3 Q A -0.6704
4 L A 0.0000
5 V A 0.4312
6 E A 0.0000
7 S A -0.5610
8 G A -1.0798
9 G A -0.5013
10 G A 0.0667
11 L A 0.8367
12 E A -0.8142
13 Q A -1.7467
14 P A -1.9155
15 G A -1.6958
16 G A -1.3249
17 S A -1.7201
18 L A -1.2834
19 R A -2.3761
20 L A 0.0000
21 S A -0.5486
22 C A 0.0000
23 A A -0.2408
24 G A -0.5003
25 S A -0.6121
26 G A -0.8816
27 F A -0.6962
28 D A -1.5968
29 L A 0.0000
30 S A -2.0943
31 K A -2.2031
32 G A -1.3074
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 -0.8414
40 A A -1.2436
41 P A -1.0038
42 G A -1.4567
43 K A -2.3359
44 G A -1.4274
45 L A 0.0000
46 E A -1.0455
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 0.0000
53 R A -1.8181
54 S A -1.5478
55 G A -1.6192
56 K A -2.1012
57 G A -1.1674
58 T A -0.3884
59 Y A -0.1023
60 Y A -0.8029
61 A A 0.0000
62 D A -2.6727
63 S A -1.7533
64 V A 0.0000
65 K A -2.6036
66 G A -1.8683
67 R A -1.9859
68 F A 0.0000
69 T A -1.0558
70 I A 0.0000
71 S A -0.5184
72 R A -1.1719
73 D A -1.6560
74 N A -2.4062
75 S A -1.7888
76 K A -2.4675
77 N A -1.9891
78 T A 0.0000
79 L A 0.0000
80 Y A -0.6996
81 L A 0.0000
82 Q A -1.7807
83 M A 0.0000
84 N A -2.2453
85 S A -1.6312
86 L A 0.0000
87 R A -2.8912
88 A A -1.9919
89 E A -2.3739
90 D A 0.0000
91 T A -0.7962
92 A A 0.0000
93 V A 0.1081
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 -0.6858
101 S A 0.0000
102 L A 1.0590
103 T A 0.4498
104 S A -0.2935
105 S A 0.3244
106 G A 0.0000
107 I A 1.9330
108 G A 0.7191
109 I A 0.0000
110 G A -0.1920
111 S A 0.0000
112 M A 0.0000
113 Y A 0.2273
114 G A -0.1125
115 W A 0.0000
116 G A 0.0000
117 Q A -1.3697
118 G A 0.0000
119 T A -0.2294
120 T A -0.0192
121 V A 0.0000
122 T A -0.2606
123 V A 0.0000
124 S A -0.9092
125 S A -0.8456
126 A A -0.2860
127 S A -0.3234
1 D B -1.3486
2 I B 0.2009
3 V B 1.0457
4 M B 0.0000
5 T B -0.2077
6 Q B 0.0000
7 S B -0.2130
8 P B 0.1731
9 L B 0.7852
10 S B -0.0123
11 L B -0.2544
12 P B -1.2498
13 V B 0.0000
14 T B -1.9216
15 P B -2.1519
16 G B -2.0465
17 E B -2.7460
18 P B -2.3856
19 A B 0.0000
20 S B -0.9027
21 I B 0.0000
22 S B -0.9338
23 S B 0.0000
24 K B -1.6153
25 T B 0.0000
26 S B -0.3680
27 T B -0.3893
28 S B -0.6256
29 T B 0.0000
30 T B -0.5335
31 D B -0.0740
32 S B 0.0956
33 Y B 0.8215
34 G B -0.2731
35 N B -0.5847
36 S B 0.0000
37 Y B -0.3551
38 V B 0.0000
39 G B 0.0000
40 W B 0.0000
41 Y B 0.0000
42 L B 0.0000
43 Q B 0.0000
44 K B -1.3987
45 S B -0.9065
46 G B -1.4634
47 Q B -2.1130
48 S B -1.4673
49 P B 0.0000
50 Q B -1.1182
51 L B 0.0000
52 L B 0.0000
53 I B 0.0000
54 Y B -0.2226
55 R B -1.1959
56 A B 0.0000
57 S B -0.5404
58 I B -0.0665
59 R B -1.3266
60 A B -0.7536
61 G B -0.8621
62 G B -1.1095
63 V B 0.0000
64 P B -1.4507
65 D B -2.4884
66 R B -2.2319
67 F B 0.0000
68 S B -1.4065
69 G B -0.9523
70 S B -1.0383
71 G B -1.2944
72 S B -1.1595
73 G B -0.9885
74 T B -1.3192
75 D B -2.1073
76 F B 0.0000
77 T B -1.2061
78 L B 0.0000
79 K B -2.1465
80 I B 0.0000
81 S B -2.4828
82 R B -3.4087
83 V B 0.0000
84 E B -2.2852
85 A B -1.2667
86 E B -1.9852
87 D B 0.0000
88 V B -0.4999
89 G B 0.0000
90 F B 0.2517
91 Y B 0.0000
92 Y B 0.0000
93 V B 0.0000
94 V B 0.0000
95 D B 0.0000
96 T B 0.0000
97 K B 0.1555
98 T B 0.6112
99 Y B 0.2914
100 P B -0.5620
101 I B 0.0000
102 G B 0.0000
103 F B 0.1408
104 G B 0.0000
105 Q B -0.7620
106 G B 0.0000
107 T B 0.0000
108 K B -0.5277
109 L B 0.0000
110 E B -1.4706
111 I B -1.7103
112 K B -2.3338
113 R B -2.1904
114 T B -0.4869
115 V B 0.9889
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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
LD102A -0.3744 -0.0544 View CSV PDB
LE102A -0.3953 -0.0487 View CSV PDB
LR11A -0.2831 -0.0544 View CSV PDB
VR3B -0.4023 -0.0403 View CSV PDB
LK11A -0.1008 -0.0517 View CSV PDB
VE3B -0.2381 -0.0397 View CSV PDB
IK107A -0.0374 -0.0466 View CSV PDB
YR33B -0.0638 -0.0343 View CSV PDB
VE115B -0.1807 -0.0276 View CSV PDB
VD115B -0.1781 -0.0273 View CSV PDB
IR107A 0.0648 -0.0547 View CSV PDB
YK33B 0.2539 -0.0329 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018