Project name: muSP34

Status: done

Started: 2026-04-24 06:21:13
Settings
Chain sequence(s) H: EVQLVESGGGLVQPKGSLKLSCAASGFTFNTYAMNWVRQAPGKGLEWVARIRSKYNNYATYYADSVKDRFTISRDDSQSILYLQMNNLKTEDTAMYYCVRHGNFGNSYVSWFAYWGQGTLVTVSS
L: QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNKRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNLWVFGGGTKLTVL
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                                          (00:05:14)
[INFO]       Auto_mut: Residue number 12 from chain H and a score of 1.365 (leucine) selected for  
                       automated muatation                                                         (00:05:20)
[INFO]       Auto_mut: Residue number 127 from chain L and a score of 1.263 (leucine) selected for 
                       automated muatation                                                         (00:05:20)
[INFO]       Auto_mut: Residue number 3 from chain L and a score of 1.247 (valine) selected for    
                       automated muatation                                                         (00:05:20)
[INFO]       Auto_mut: Residue number 5 from chain H and a score of 1.169 (valine) selected for    
                       automated muatation                                                         (00:05:20)
[INFO]       Auto_mut: Residue number 123 from chain H and a score of 1.099 (leucine) selected for 
                       automated muatation                                                         (00:05:20)
[INFO]       Auto_mut: Residue number 112A from chain H and a score of 0.983 (tyrosine) selected   
                       for automated muatation                                                     (00:05:20)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (leucine) into glutamic acid        (00:05:20)
[INFO]       Auto_mut: Mutating residue number 127 from chain L (leucine) into glutamic acid       (00:05:20)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (leucine) into aspartic acid        (00:05:20)
[INFO]       Auto_mut: Mutating residue number 127 from chain L (leucine) into lysine              (00:08:59)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (leucine) into arginine             (00:09:08)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (leucine) into lysine               (00:09:09)
[INFO]       Auto_mut: Mutating residue number 127 from chain L (leucine) into aspartic acid       (00:13:04)
[INFO]       Auto_mut: Mutating residue number 3 from chain L (valine) into glutamic acid          (00:13:07)
[INFO]       Auto_mut: Mutating residue number 3 from chain L (valine) into aspartic acid          (00:13:20)
[INFO]       Auto_mut: Mutating residue number 127 from chain L (leucine) into arginine            (00:16:03)
[INFO]       Auto_mut: Mutating residue number 3 from chain L (valine) into lysine                 (00:16:16)
[INFO]       Auto_mut: Mutating residue number 3 from chain L (valine) into arginine               (00:16:30)
[INFO]       Auto_mut: Mutating residue number 5 from chain H (valine) into glutamic acid          (00:18:39)
[INFO]       Auto_mut: Mutating residue number 5 from chain H (valine) into aspartic acid          (00:19:07)
[INFO]       Auto_mut: Mutating residue number 123 from chain H (leucine) into glutamic acid       (00:19:09)
[INFO]       Auto_mut: Mutating residue number 5 from chain H (valine) into lysine                 (00:21:01)
[INFO]       Auto_mut: Mutating residue number 123 from chain H (leucine) into lysine              (00:21:18)
[INFO]       Auto_mut: Mutating residue number 5 from chain H (valine) into arginine               (00:21:23)
[INFO]       Auto_mut: Mutating residue number 123 from chain H (leucine) into aspartic acid       (00:23:05)
[INFO]       Auto_mut: Mutating residue number 112A from chain H (tyrosine) into glutamic acid     (00:23:15)
[WARNING]    Auto_mut: Mutation YE112AH could have failed (this can be ignored if the main program 
                       reports the energy difference). Simulation log for that run should be       
                       available at                                                                
                       /STORAGE/DATA/lcbio/aggreskan/97a8a4633305028/YE112AH/Aggrescan.error       (00:23:17)
[INFO]       Auto_mut: Mutating residue number 112A from chain H (tyrosine) into lysine            (00:23:17)
[WARNING]    Auto_mut: Mutation YK112AH could have failed (this can be ignored if the main program 
                       reports the energy difference). Simulation log for that run should be       
                       available at                                                                
                       /STORAGE/DATA/lcbio/aggreskan/97a8a4633305028/YK112AH/Aggrescan.error       (00:23:19)
[INFO]       Auto_mut: Mutating residue number 112A from chain H (tyrosine) into aspartic acid     (00:23:19)
[WARNING]    Auto_mut: Mutation YD112AH could have failed (this can be ignored if the main program 
                       reports the energy difference). Simulation log for that run should be       
                       available at                                                                
                       /STORAGE/DATA/lcbio/aggreskan/97a8a4633305028/YD112AH/Aggrescan.error       (00:23:20)
[INFO]       Auto_mut: Mutating residue number 112A from chain H (tyrosine) into arginine          (00:23:20)
[WARNING]    Auto_mut: Mutation YR112AH could have failed (this can be ignored if the main program 
                       reports the energy difference). Simulation log for that run should be       
                       available at                                                                
                       /STORAGE/DATA/lcbio/aggreskan/97a8a4633305028/YR112AH/Aggrescan.error       (00:23:22)
[INFO]       Auto_mut: Mutating residue number 123 from chain H (leucine) into arginine            (00:24:28)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (leucine) into glutamic   
                       acid: Energy difference: 0.2060 kcal/mol, Difference in average score from  
                       the base case: -0.0562                                                      (00:26:13)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (leucine) into lysine:    
                       Energy difference: 0.0744 kcal/mol, Difference in average score from the    
                       base case: -0.0631                                                          (00:26:13)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (leucine) into aspartic   
                       acid: Energy difference: 0.5663 kcal/mol, Difference in average score from  
                       the base case: -0.0568                                                      (00:26:13)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (leucine) into arginine:  
                       Energy difference: -0.2235 kcal/mol, Difference in average score from the   
                       base case: -0.0606                                                          (00:26:13)
[INFO]       Auto_mut: Effect of mutation residue number 127 from chain L (leucine) into glutamic  
                       acid: Energy difference: 0.6039 kcal/mol, Difference in average score from  
                       the base case: -0.0559                                                      (00:26:13)
[INFO]       Auto_mut: Effect of mutation residue number 127 from chain L (leucine) into lysine:   
                       Energy difference: 0.1404 kcal/mol, Difference in average score from the    
                       base case: -0.0567                                                          (00:26:13)
[INFO]       Auto_mut: Effect of mutation residue number 127 from chain L (leucine) into aspartic  
                       acid: Energy difference: 1.1037 kcal/mol, Difference in average score from  
                       the base case: -0.0556                                                      (00:26:13)
[INFO]       Auto_mut: Effect of mutation residue number 127 from chain L (leucine) into arginine: 
                       Energy difference: 0.0073 kcal/mol, Difference in average score from the    
                       base case: -0.0562                                                          (00:26:13)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain L (valine) into glutamic     
                       acid: Energy difference: 0.0895 kcal/mol, Difference in average score from  
                       the base case: -0.0586                                                      (00:26:13)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain L (valine) into lysine:      
                       Energy difference: -0.3072 kcal/mol, Difference in average score from the   
                       base case: -0.0567                                                          (00:26:13)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain L (valine) into aspartic     
                       acid: Energy difference: 0.2917 kcal/mol, Difference in average score from  
                       the base case: -0.0586                                                      (00:26:13)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain L (valine) into arginine:    
                       Energy difference: -0.2237 kcal/mol, Difference in average score from the   
                       base case: -0.0610                                                          (00:26:13)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain H (valine) into glutamic     
                       acid: Energy difference: 0.2455 kcal/mol, Difference in average score from  
                       the base case: -0.0540                                                      (00:26:13)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain H (valine) into lysine:      
                       Energy difference: -0.6329 kcal/mol, Difference in average score from the   
                       base case: -0.0543                                                          (00:26:13)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain H (valine) into aspartic     
                       acid: Energy difference: 0.4866 kcal/mol, Difference in average score from  
                       the base case: -0.0619                                                      (00:26:13)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain H (valine) into arginine:    
                       Energy difference: -1.3457 kcal/mol, Difference in average score from the   
                       base case: -0.0400                                                          (00:26:13)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain H (leucine) into glutamic  
                       acid: Energy difference: 0.3771 kcal/mol, Difference in average score from  
                       the base case: -0.0600                                                      (00:26:13)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain H (leucine) into lysine:   
                       Energy difference: -0.1971 kcal/mol, Difference in average score from the   
                       base case: -0.0566                                                          (00:26:13)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain H (leucine) into aspartic  
                       acid: Energy difference: 1.1936 kcal/mol, Difference in average score from  
                       the base case: -0.0520                                                      (00:26:13)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain H (leucine) into arginine: 
                       Energy difference: -0.7424 kcal/mol, Difference in average score from the   
                       base case: -0.0588                                                          (00:26:14)
[INFO]       Main:     Simulation completed successfully.                                          (00:26:20)
Show buried residues
Minimal score value
-3.1392
Maximal score value
1.3646
Average score
-0.4564
Total score value
-106.7987
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 H -1.9147
2 V H -0.8633
3 Q H -0.7423
4 L H 0.0000
5 V H 1.1685
6 E H 0.3178
7 S H -0.2429
8 G H -0.6620
9 G H 0.0541
11 G H 0.7050
12 L H 1.3646
13 V H -0.1898
14 Q H -1.7171
15 P H -2.3972
16 K H -3.1392
17 G H -2.0926
18 S H -1.6852
19 L H -0.8165
20 K H -1.4093
21 L H 0.0000
22 S H -0.1539
23 C H 0.0000
24 A H 0.2866
25 A H 0.0000
26 S H -0.5744
27 G H -0.9895
28 F H -0.3307
29 T H -0.2722
30 F H 0.0000
35 N H -0.9520
36 T H -0.5056
37 Y H -0.3321
38 A H -0.7310
39 M H 0.0000
40 N H 0.0000
41 W H 0.0000
42 V H 0.0000
43 R H 0.0000
44 Q H 0.0000
45 A H -1.0441
46 P H -0.8780
47 G H -1.4371
48 K H -2.2543
49 G H -1.3786
50 L H 0.0000
51 E H -0.8764
52 W H 0.0000
53 V H 0.0000
54 A H 0.0000
55 R H -0.3391
56 I H 0.0000
57 R H -1.1388
58 S H 0.0000
59 K H -1.8034
60 Y H -0.1721
61 N H -1.0953
62 N H -1.6355
63 Y H -1.0126
64 A H -0.6594
65 T H -0.3496
66 Y H -0.3824
67 Y H -0.9781
68 A H 0.0000
69 D H -2.5517
70 S H -1.8094
71 V H 0.0000
72 K H -2.5849
74 D H -2.9068
75 R H -2.2789
76 F H 0.0000
77 T H -0.9296
78 I H 0.0000
79 S H -0.3282
80 R H -0.8505
81 D H -1.1455
82 D H -1.4102
83 S H -1.1538
84 Q H -1.5396
85 S H -0.8863
86 I H -0.2042
87 L H 0.0000
88 Y H -0.2937
89 L H 0.0000
90 Q H -1.0118
91 M H 0.0000
92 N H -2.3086
93 N H -3.0841
94 L H 0.0000
95 K H -2.9859
96 T H -2.0135
97 E H -2.3302
98 D H 0.0000
99 T H -0.4924
100 A H 0.0000
101 M H 0.4015
102 Y H 0.0000
103 Y H 0.0000
104 C H 0.0000
105 V H 0.0000
106 R H 0.0000
107 H H 0.0000
108 G H 0.1618
109 N H -0.2324
110 F H 0.5066
111 G H -0.5466
111A N H -1.0989
112B S H -0.0414
112A Y H 0.9834
112 V H 0.4033
113 S H 0.3760
114 W H 0.0000
115 F H 0.0000
116 A H 0.0000
117 Y H 0.4287
118 W H 0.0000
119 G H 0.0650
120 Q H -0.8495
121 G H -0.0077
122 T H 0.2875
123 L H 1.0994
124 V H 0.0000
125 T H 0.2176
126 V H 0.0000
127 S H -0.6575
128 S H -0.6640
1 Q L -0.9479
2 A L 0.2479
3 V L 1.2466
4 V L 0.0000
5 T L -0.3309
6 Q L -0.9514
7 E L -1.0062
8 S L -0.6461
9 A L -0.2952
11 L L 0.0119
12 T L 0.2004
13 T L 0.0000
14 S L -0.2505
15 P L -0.9167
16 G L -1.4282
17 E L -1.7863
18 T L -0.9423
19 V L -0.2660
20 T L 0.1452
21 L L 0.0000
22 T L 0.0000
23 C L 0.0000
24 R L -1.0469
25 S L 0.0000
26 S L -0.0906
27 T L -0.2422
28 G L -0.7142
29 A L -0.6296
30 V L 0.0000
31 T L -0.2209
35 T L -0.1771
36 S L -0.1712
37 N L 0.0057
38 Y L 0.2182
39 A L 0.0000
40 N L 0.0000
41 W L 0.0000
42 V L 0.0000
43 Q L 0.0629
44 E L 0.0000
45 K L -0.6103
46 P L -0.9731
47 D L -1.8915
48 H L -0.9882
49 L L 0.3002
50 F L 0.0000
51 T L 0.3381
52 G L 0.0000
53 L L 0.0000
54 I L 0.0000
55 G L 0.0000
56 G L 0.0000
57 T L 0.0000
65 N L -1.9797
66 K L -1.9826
67 R L -1.7426
68 A L 0.0000
69 P L -0.7518
70 G L -0.6302
71 V L -0.3779
72 P L -0.3683
74 A L -0.3075
75 R L -0.3967
76 F L 0.0000
77 S L -0.9254
78 G L 0.0000
79 S L -0.3575
80 L L 0.3555
83 I L 0.7591
84 G L -0.2724
85 D L -0.9146
86 K L -0.7020
87 A L 0.0000
88 A L 0.0000
89 L L 0.0000
90 T L -0.1152
91 I L 0.0000
92 T L -0.6682
93 G L -1.0706
94 A L 0.0000
95 Q L -1.4992
96 T L -1.1260
97 E L -2.1302
98 D L 0.0000
99 E L -1.2066
100 A L 0.0000
101 I L 0.1120
102 Y L 0.0000
103 F L 0.0000
104 C L 0.0000
105 A L 0.0000
106 L L 0.0000
107 W L 0.0131
108 Y L -0.3305
109 S L -0.7113
114 N L -1.1638
115 L L -0.6456
116 W L 0.0000
117 V L 0.2926
118 F L 0.0000
119 G L 0.0000
120 G L -0.8174
121 G L -0.6784
122 T L 0.0000
123 K L -0.5616
124 L L 0.0000
125 T L 0.1049
126 V L 0.0000
127 L L 1.2630
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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
VR5H -1.3457 -0.04 View CSV PDB
LR123H -0.7424 -0.0588 View CSV PDB
VK5H -0.6329 -0.0543 View CSV PDB
VK3L -0.3072 -0.0567 View CSV PDB
VR3L -0.2237 -0.061 View CSV PDB
LR12H -0.2235 -0.0606 View CSV PDB
LK123H -0.1971 -0.0566 View CSV PDB
LR127L 0.0073 -0.0562 View CSV PDB
LK12H 0.0744 -0.0631 View CSV PDB
LK127L 0.1404 -0.0567 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018