Project name: P_S

Status: done

Started: 2023-12-15 02:51:23
Settings
Chain sequence(s) H: EVQLVESGGGLVQPGGSLRLSCAASGRTFSYNPMGWFRQAPGKGRELVAAISRTGGSTYYPDSVEGRFTISRDNAKRMVYLQMNSLRAEDTAVYYCAAAGVRAEDGRVRTLPSEYTFWGQGTQVTVSS
input PDB
Selected Chain(s) H
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 H chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:00)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:00:36)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:00:36)
[INFO]       Auto_mut: Residue number 111 from chain H and a score of 1.353 (leucine) selected for 
                       automated muatation                                                         (00:00:37)
[INFO]       Auto_mut: Residue number 11 from chain H and a score of 1.114 (leucine) selected for  
                       automated muatation                                                         (00:00:37)
[INFO]       Auto_mut: Residue number 110 from chain H and a score of 0.592 (threonine) selected   
                       for automated muatation                                                     (00:00:37)
[INFO]       Auto_mut: Residue number 5 from chain H and a score of 0.469 (valine) selected for    
                       automated muatation                                                         (00:00:37)
[INFO]       Auto_mut: Residue number 31 from chain H and a score of 0.304 (tyrosine) selected for 
                       automated muatation                                                         (00:00:37)
[INFO]       Auto_mut: Residue number 116 from chain H and a score of 0.196 (threonine) selected   
                       for automated muatation                                                     (00:00:37)
[INFO]       Auto_mut: Mutating residue number 111 from chain H (leucine) into glutamic acid       (00:00:37)
[INFO]       Auto_mut: Mutating residue number 11 from chain H (leucine) into glutamic acid        (00:00:37)
[INFO]       Auto_mut: Mutating residue number 111 from chain H (leucine) into aspartic acid       (00:00:37)
[INFO]       Auto_mut: Mutating residue number 111 from chain H (leucine) into arginine            (00:01:01)
[INFO]       Auto_mut: Mutating residue number 11 from chain H (leucine) into lysine               (00:01:02)
[INFO]       Auto_mut: Mutating residue number 111 from chain H (leucine) into lysine              (00:01:04)
[INFO]       Auto_mut: Mutating residue number 11 from chain H (leucine) into aspartic acid        (00:01:33)
[INFO]       Auto_mut: Mutating residue number 110 from chain H (threonine) into glutamic acid     (00:01:36)
[INFO]       Auto_mut: Mutating residue number 110 from chain H (threonine) into aspartic acid     (00:01:41)
[INFO]       Auto_mut: Mutating residue number 11 from chain H (leucine) into arginine             (00:01:56)
[INFO]       Auto_mut: Mutating residue number 110 from chain H (threonine) into lysine            (00:02:02)
[INFO]       Auto_mut: Mutating residue number 110 from chain H (threonine) into arginine          (00:02:08)
[INFO]       Auto_mut: Mutating residue number 5 from chain H (valine) into glutamic acid          (00:02:26)
[INFO]       Auto_mut: Mutating residue number 5 from chain H (valine) into aspartic acid          (00:02:35)
[INFO]       Auto_mut: Mutating residue number 31 from chain H (tyrosine) into glutamic acid       (00:02:36)
[INFO]       Auto_mut: Mutating residue number 5 from chain H (valine) into lysine                 (00:02:54)
[INFO]       Auto_mut: Mutating residue number 5 from chain H (valine) into arginine               (00:02:59)
[INFO]       Auto_mut: Mutating residue number 31 from chain H (tyrosine) into lysine              (00:03:08)
[INFO]       Auto_mut: Mutating residue number 31 from chain H (tyrosine) into aspartic acid       (00:03:27)
[INFO]       Auto_mut: Mutating residue number 116 from chain H (threonine) into glutamic acid     (00:03:31)
[INFO]       Auto_mut: Mutating residue number 116 from chain H (threonine) into aspartic acid     (00:03:47)
[INFO]       Auto_mut: Mutating residue number 31 from chain H (tyrosine) into arginine            (00:03:54)
[INFO]       Auto_mut: Mutating residue number 116 from chain H (threonine) into lysine            (00:03:57)
[INFO]       Auto_mut: Mutating residue number 116 from chain H (threonine) into arginine          (00:04:11)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain H (leucine) into glutamic  
                       acid: Energy difference: 0.4054 kcal/mol, Difference in average score from  
                       the base case: -0.0790                                                      (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain H (leucine) into lysine:   
                       Energy difference: 0.0406 kcal/mol, Difference in average score from the    
                       base case: -0.0668                                                          (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain H (leucine) into aspartic  
                       acid: Energy difference: -0.4050 kcal/mol, Difference in average score from 
                       the base case: -0.0744                                                      (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain H (leucine) into arginine: 
                       Energy difference: 0.1472 kcal/mol, Difference in average score from the    
                       base case: -0.0647                                                          (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain H (leucine) into glutamic   
                       acid: Energy difference: 0.4691 kcal/mol, Difference in average score from  
                       the base case: -0.1058                                                      (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain H (leucine) into lysine:    
                       Energy difference: -0.1600 kcal/mol, Difference in average score from the   
                       base case: -0.1011                                                          (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain H (leucine) into aspartic   
                       acid: Energy difference: 1.0541 kcal/mol, Difference in average score from  
                       the base case: -0.1057                                                      (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain H (leucine) into arginine:  
                       Energy difference: -0.4821 kcal/mol, Difference in average score from the   
                       base case: -0.1045                                                          (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 110 from chain H (threonine) into         
                       glutamic acid: Energy difference: -0.7641 kcal/mol, Difference in average   
                       score from the base case: -0.0498                                           (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 110 from chain H (threonine) into lysine: 
                       Energy difference: -1.0566 kcal/mol, Difference in average score from the   
                       base case: -0.0394                                                          (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 110 from chain H (threonine) into         
                       aspartic acid: Energy difference: 0.3359 kcal/mol, Difference in average    
                       score from the base case: -0.0510                                           (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 110 from chain H (threonine) into         
                       arginine: Energy difference: -1.0018 kcal/mol, Difference in average score  
                       from the base case: -0.0563                                                 (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain H (valine) into glutamic     
                       acid: Energy difference: 0.6229 kcal/mol, Difference in average score from  
                       the base case: -0.0722                                                      (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain H (valine) into lysine:      
                       Energy difference: -0.2551 kcal/mol, Difference in average score from the   
                       base case: -0.0610                                                          (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain H (valine) into aspartic     
                       acid: Energy difference: 1.1014 kcal/mol, Difference in average score from  
                       the base case: -0.0797                                                      (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain H (valine) into arginine:    
                       Energy difference: -0.3156 kcal/mol, Difference in average score from the   
                       base case: -0.0787                                                          (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 31 from chain H (tyrosine) into glutamic  
                       acid: Energy difference: -0.2883 kcal/mol, Difference in average score from 
                       the base case: -0.0812                                                      (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 31 from chain H (tyrosine) into lysine:   
                       Energy difference: -0.0330 kcal/mol, Difference in average score from the   
                       base case: -0.0813                                                          (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 31 from chain H (tyrosine) into aspartic  
                       acid: Energy difference: -0.0318 kcal/mol, Difference in average score from 
                       the base case: -0.0694                                                      (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 31 from chain H (tyrosine) into arginine: 
                       Energy difference: -0.0483 kcal/mol, Difference in average score from the   
                       base case: -0.0748                                                          (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 116 from chain H (threonine) into         
                       glutamic acid: Energy difference: -0.8874 kcal/mol, Difference in average   
                       score from the base case: -0.0476                                           (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 116 from chain H (threonine) into lysine: 
                       Energy difference: -1.3231 kcal/mol, Difference in average score from the   
                       base case: -0.0468                                                          (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 116 from chain H (threonine) into         
                       aspartic acid: Energy difference: -0.6486 kcal/mol, Difference in average   
                       score from the base case: -0.0481                                           (00:04:38)
[INFO]       Auto_mut: Effect of mutation residue number 116 from chain H (threonine) into         
                       arginine: Energy difference: -1.2408 kcal/mol, Difference in average score  
                       from the base case: -0.0490                                                 (00:04:38)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:42)
Show buried residues
Minimal score value
-2.7432
Maximal score value
1.3534
Average score
-0.7305
Total score value
-93.5053
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 -2.7046
2 V H 0.0000
3 Q H -1.7410
4 L H 0.0000
5 V H 0.4694
6 E H 0.0000
7 S H -0.6686
8 G H -1.1033
9 G H -0.6826
10 G H 0.0311
11 L H 1.1143
12 V H -0.0203
13 Q H -1.3893
14 P H -1.8364
15 G H -1.4359
16 G H -1.0076
17 S H -1.2119
18 L H -0.8152
19 R H -2.0441
20 L H 0.0000
21 S H -0.4078
22 C H 0.0000
23 A H -0.3230
24 A H 0.0000
25 S H -1.5065
26 G H -2.3370
27 R H -2.7432
28 T H -1.7276
29 F H 0.0000
30 S H -0.6500
31 Y H 0.3037
32 N H 0.0000
33 P H 0.0000
34 M H 0.0000
35 G H 0.0000
36 W H 0.0000
37 F H 0.0000
38 R H 0.0000
39 Q H -1.6128
40 A H -1.6197
41 P H -1.0575
42 G H -1.5408
43 K H -2.6925
44 G H -2.2907
45 R H -2.2556
46 E H -1.7015
47 L H -0.3128
48 V H 0.0000
49 A H 0.0000
50 A H 0.0000
51 I H 0.0000
52 S H 0.0000
53 R H -0.9698
54 T H -0.6783
55 G H -0.8028
56 G H -0.9047
57 S H -0.6993
58 T H -0.1919
59 Y H 0.1305
60 Y H -0.6476
61 P H -1.2697
62 D H -2.4718
63 S H -1.6858
64 V H 0.0000
65 E H -2.6396
66 G H -1.7676
67 R H -1.5896
68 F H 0.0000
69 T H -0.7483
70 I H 0.0000
71 S H -0.3537
72 R H -0.8095
73 D H -1.2029
74 N H -1.2369
75 A H -1.1815
76 K H -2.2991
77 R H -1.7839
78 M H -0.8165
79 V H 0.0000
80 Y H -0.3542
81 L H 0.0000
82 Q H -1.0683
83 M H 0.0000
84 N H -1.3525
85 S H -1.2749
86 L H 0.0000
87 R H -2.3255
88 A H -1.7178
89 E H -2.2300
90 D H 0.0000
91 T H -0.7555
92 A H 0.0000
93 V H -0.2943
94 Y H 0.0000
95 Y H -0.2567
96 C H 0.0000
97 A H 0.0000
98 A H 0.0000
99 A H 0.0000
100 G H -0.6797
101 V H -0.4329
102 R H -1.9644
103 A H -1.7111
104 E H -2.5519
105 D H -2.1477
106 G H -1.8052
107 R H -2.2500
108 V H -0.5601
109 R H 0.0000
110 T H 0.5919
111 L H 1.3534
112 P H 0.1315
113 S H 0.1932
114 E H 0.0657
115 Y H 0.0000
116 T H 0.1962
117 F H -0.0283
118 W H 0.1657
119 G H -0.2867
120 Q H -0.9756
121 G H -0.4851
122 T H -0.5813
123 Q H -0.6202
124 V H 0.0000
125 T H -0.1591
126 V H 0.0000
127 S H -0.6878
128 S H -0.5045
Download PDB file
View in 3Dmol
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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
LR11H -0.4821 -0.1045 View CSV PDB
TK116H -1.3231 -0.0468 View CSV PDB
TR116H -1.2408 -0.049 View CSV PDB
TR110H -1.0018 -0.0563 View CSV PDB
LD111H -0.405 -0.0744 View CSV PDB
LK11H -0.16 -0.1011 View CSV PDB
VR5H -0.3156 -0.0787 View CSV PDB
YE31H -0.2883 -0.0812 View CSV PDB
TE110H -0.7641 -0.0498 View CSV PDB
VK5H -0.2551 -0.061 View CSV PDB
YK31H -0.033 -0.0813 View CSV PDB
LK111H 0.0406 -0.0668 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018