Project name: vpxA22P

Status: done

Started: 2024-04-19 20:45:36
Settings
Chain sequence(s) A: MSDPRERIPPGNSGEETIGEAFEWLNRTVEEINREAVNHLPRELIFQVWQRSWEYWHDEQGMSPSYVKYRYLCLIQKALFMHCKKGCRCLGEGHGAGGWRPGPPPPPPPGLAGSHTPGNSNKWKHLQENKKGRPRRGGSHTPGNSNKWKHLQENKKGRPRR
input PDB
Selected Chain(s) A
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 A 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                                          (00:02:31)
[INFO]       Auto_mut: Residue number 69 from chain A and a score of 1.021 (tyrosine) selected for 
                       automated muatation                                                         (00:02:31)
[INFO]       Auto_mut: Residue number 111 from chain A and a score of 1.015 (leucine) selected for 
                       automated muatation                                                         (00:02:31)
[INFO]       Auto_mut: Residue number 1 from chain A and a score of 0.751 (methionine) selected    
                       for automated muatation                                                     (00:02:31)
[INFO]       Auto_mut: Residue number 22 from chain A and a score of 0.726 (phenylalanine)         
                       selected for automated muatation                                            (00:02:31)
[INFO]       Auto_mut: Residue number 80 from chain A and a score of 0.659 (phenylalanine)         
                       selected for automated muatation                                            (00:02:31)
[INFO]       Auto_mut: Residue number 66 from chain A and a score of 0.607 (tyrosine) selected for 
                       automated muatation                                                         (00:02:31)
[INFO]       Auto_mut: Mutating residue number 69 from chain A (tyrosine) into glutamic acid       (00:02:31)
[INFO]       Auto_mut: Mutating residue number 69 from chain A (tyrosine) into aspartic acid       (00:02:31)
[INFO]       Auto_mut: Mutating residue number 111 from chain A (leucine) into glutamic acid       (00:02:31)
[INFO]       Auto_mut: Mutating residue number 111 from chain A (leucine) into lysine              (00:03:33)
[INFO]       Auto_mut: Mutating residue number 69 from chain A (tyrosine) into arginine            (00:03:35)
[INFO]       Auto_mut: Mutating residue number 69 from chain A (tyrosine) into lysine              (00:03:40)
[INFO]       Auto_mut: Mutating residue number 111 from chain A (leucine) into aspartic acid       (00:04:38)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into glutamic acid      (00:04:44)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into aspartic acid      (00:05:11)
[INFO]       Auto_mut: Mutating residue number 111 from chain A (leucine) into arginine            (00:05:39)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into lysine             (00:05:47)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into arginine           (00:06:13)
[INFO]       Auto_mut: Mutating residue number 22 from chain A (phenylalanine) into glutamic acid  
                       Mutating residue number 22 from chain A (phenylalanine) into glutamic acid  (00:06:43)
[INFO]       Auto_mut: Mutating residue number 22 from chain A (phenylalanine) into aspartic acid  
                       Mutating residue number 22 from chain A (phenylalanine) into aspartic acid  (00:06:51)
[INFO]       Auto_mut: Mutating residue number 80 from chain A (phenylalanine) into glutamic acid  
                       Mutating residue number 80 from chain A (phenylalanine) into glutamic acid  (00:07:16)
[INFO]       Auto_mut: Mutating residue number 22 from chain A (phenylalanine) into lysine         (00:07:49)
[INFO]       Auto_mut: Mutating residue number 22 from chain A (phenylalanine) into arginine       (00:08:06)
[INFO]       Auto_mut: Mutating residue number 80 from chain A (phenylalanine) into lysine         (00:08:25)
[INFO]       Auto_mut: Mutating residue number 80 from chain A (phenylalanine) into aspartic acid  
                       Mutating residue number 80 from chain A (phenylalanine) into aspartic acid  (00:09:05)
[INFO]       Auto_mut: Mutating residue number 66 from chain A (tyrosine) into glutamic acid       (00:09:18)
[INFO]       Auto_mut: Mutating residue number 66 from chain A (tyrosine) into aspartic acid       (00:09:46)
[INFO]       Auto_mut: Mutating residue number 80 from chain A (phenylalanine) into arginine       (00:10:17)
[INFO]       Auto_mut: Mutating residue number 66 from chain A (tyrosine) into lysine              (00:10:26)
[INFO]       Auto_mut: Mutating residue number 66 from chain A (tyrosine) into arginine            (00:10:49)
[INFO]       Auto_mut: Effect of mutation residue number 69 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 0.2151 kcal/mol, Difference in average score from  
                       the base case: -0.0343                                                      (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 69 from chain A (tyrosine) into lysine:   
                       Energy difference: 0.1887 kcal/mol, Difference in average score from the    
                       base case: -0.0274                                                          (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 69 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 1.4716 kcal/mol, Difference in average score from  
                       the base case: -0.0244                                                      (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 69 from chain A (tyrosine) into arginine: 
                       Energy difference: 0.8602 kcal/mol, Difference in average score from the    
                       base case: -0.0477                                                          (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.0136 kcal/mol, Difference in average score from  
                       the base case: -0.0560                                                      (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain A (leucine) into lysine:   
                       Energy difference: -0.0513 kcal/mol, Difference in average score from the   
                       base case: -0.0512                                                          (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.4075 kcal/mol, Difference in average score from  
                       the base case: -0.0553                                                      (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain A (leucine) into arginine: 
                       Energy difference: -0.2283 kcal/mol, Difference in average score from the   
                       base case: -0.0564                                                          (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into glutamic 
                       acid: Energy difference: 0.3792 kcal/mol, Difference in average score from  
                       the base case: -0.0302                                                      (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into lysine:  
                       Energy difference: 0.1035 kcal/mol, Difference in average score from the    
                       base case: -0.0237                                                          (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into aspartic 
                       acid: Energy difference: 0.3909 kcal/mol, Difference in average score from  
                       the base case: -0.0272                                                      (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into          
                       arginine: Energy difference: -0.3372 kcal/mol, Difference in average score  
                       from the base case: -0.0269                                                 (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 22 from chain A (phenylalanine) into      
                       glutamic acid: Energy difference: 0.6367 kcal/mol, Difference in average    
                       score from the base case: -0.0657                                           (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 22 from chain A (phenylalanine) into      
                       lysine: Energy difference: 0.9841 kcal/mol, Difference in average score     
                       from the base case: -0.0700                                                 (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 22 from chain A (phenylalanine) into      
                       aspartic acid: Energy difference: 1.1520 kcal/mol, Difference in average    
                       score from the base case: -0.0607                                           (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 22 from chain A (phenylalanine) into      
                       arginine: Energy difference: 1.3201 kcal/mol, Difference in average score   
                       from the base case: -0.1014                                                 (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 80 from chain A (phenylalanine) into      
                       glutamic acid: Energy difference: 0.4594 kcal/mol, Difference in average    
                       score from the base case: -0.0745                                           (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 80 from chain A (phenylalanine) into      
                       lysine: Energy difference: 0.4328 kcal/mol, Difference in average score     
                       from the base case: -0.0710                                                 (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 80 from chain A (phenylalanine) into      
                       aspartic acid: Energy difference: 0.9889 kcal/mol, Difference in average    
                       score from the base case: -0.0744                                           (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 80 from chain A (phenylalanine) into      
                       arginine: Energy difference: 0.7731 kcal/mol, Difference in average score   
                       from the base case: -0.0780                                                 (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 66 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 0.3627 kcal/mol, Difference in average score from  
                       the base case: -0.0124                                                      (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 66 from chain A (tyrosine) into lysine:   
                       Energy difference: 0.8206 kcal/mol, Difference in average score from the    
                       base case: -0.0283                                                          (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 66 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: -0.4804 kcal/mol, Difference in average score from 
                       the base case: -0.0267                                                      (00:11:58)
[INFO]       Auto_mut: Effect of mutation residue number 66 from chain A (tyrosine) into arginine: 
                       Energy difference: 1.2453 kcal/mol, Difference in average score from the    
                       base case: -0.0575                                                          (00:11:58)
[INFO]       Main:     Simulation completed successfully.                                          (00:12:03)
Show buried residues
Minimal score value
-4.5601
Maximal score value
1.0206
Average score
-1.6355
Total score value
-263.3085
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 M A 0.7509
2 S A -1.0142
3 D A -2.1782
4 P A -2.2855
5 R A -3.3732
6 E A -3.3775
7 R A -2.6919
8 I A -0.3065
9 P A -0.8864
10 P A -0.7951
11 G A -1.2775
12 N A -1.5284
13 S A -1.1473
14 G A -2.0076
15 E A -2.5905
16 E A -2.9588
17 T A -1.7282
18 I A 0.0758
19 G A -1.0268
20 E A -1.9141
21 A A -0.3351
22 F A 0.7259
23 E A -1.4360
24 W A -0.5827
25 L A 0.0000
26 N A -1.9315
27 R A -2.9119
28 T A -2.0005
29 V A 0.0000
30 E A -3.6298
31 E A -3.8831
32 I A -2.5374
33 N A -2.6872
34 R A -3.3205
35 E A -2.5681
36 A A 0.0000
37 V A -1.3551
38 N A -1.2246
39 H A -0.8585
40 L A -0.5873
41 P A -1.0698
42 R A -1.8682
43 E A -2.2145
44 L A -0.8932
45 I A 0.0000
46 F A -1.3283
47 Q A -2.1212
48 V A -1.0966
49 W A 0.0000
50 Q A -1.8793
51 R A -2.6796
52 S A 0.0000
53 W A 0.0000
54 E A -2.7370
55 Y A -1.6081
56 W A -1.5099
57 H A -2.0358
58 D A -3.1497
59 E A -2.9860
60 Q A -2.3021
61 G A -1.8402
62 M A -0.7641
63 S A -0.3620
64 P A -0.1921
65 S A 0.2486
66 Y A 0.6073
67 V A 0.0000
68 K A 0.3054
69 Y A 1.0206
70 R A 0.1401
71 Y A 0.0000
72 L A -0.1072
73 C A -0.1781
74 L A -0.0062
75 I A 0.0000
76 Q A -1.1350
77 K A -1.1665
78 A A -0.3458
79 L A 0.0000
80 F A 0.6588
81 M A -0.3748
82 H A -0.8695
83 C A -0.6756
84 K A -1.7516
85 K A -2.4101
86 G A -1.9340
87 C A -1.0293
88 R A -1.9997
89 C A -0.9137
90 L A 0.0696
91 G A -1.2696
92 E A -2.3124
93 G A -1.8681
94 H A -1.6960
95 G A -1.1437
96 A A -0.9417
97 G A -1.1587
98 G A -1.2290
99 W A -0.4260
100 R A -1.6938
101 P A -1.1357
102 G A -0.8568
103 P A -0.8516
104 P A -0.8737
105 P A -0.6839
106 P A -0.7085
107 P A -0.4480
108 P A -0.3294
109 P A -0.3011
110 G A -0.0002
111 L A 1.0153
112 A A 0.1907
113 G A -0.4088
114 S A -0.7149
115 H A -1.3389
116 T A -1.0349
117 P A -1.3034
118 G A -1.7563
119 N A -2.4666
120 S A -2.1632
121 N A -3.1461
122 K A -3.4231
123 W A -2.6047
124 K A -3.6528
125 H A -3.5560
126 L A -2.8553
127 Q A -2.9188
128 E A -3.9878
129 N A -3.9874
130 K A -3.6907
131 K A -3.7894
132 G A -3.3245
133 R A -3.7679
134 P A -3.0366
135 R A -3.7137
136 R A -3.4264
137 G A -2.3231
138 G A -1.7657
139 S A -1.2455
140 H A -1.4106
141 T A -0.8790
142 P A -1.0455
143 G A -1.5258
144 N A -2.2698
145 S A -1.9284
146 N A -2.7075
147 K A -2.6114
148 W A -1.9190
149 K A -3.2463
150 H A -3.2652
151 L A -2.2271
152 Q A -3.4551
153 E A -4.5601
154 N A -4.4596
155 K A -4.5339
156 K A -4.3434
157 G A -3.7263
158 R A -3.8797
159 P A -2.8799
160 R A -3.3843
161 R A -3.0574
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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
LR111A -0.2283 -0.0564 View CSV PDB
LK111A -0.0513 -0.0512 View CSV PDB
YD66A -0.4804 -0.0267 View CSV PDB
MR1A -0.3372 -0.0269 View CSV PDB
MK1A 0.1035 -0.0237 View CSV PDB
FK80A 0.4328 -0.071 View CSV PDB
FE80A 0.4594 -0.0745 View CSV PDB
YE69A 0.2151 -0.0343 View CSV PDB
YK69A 0.1887 -0.0274 View CSV PDB
FE22A 0.6367 -0.0657 View CSV PDB
FR22A 1.3201 -0.1014 View CSV PDB
YR66A 1.2453 -0.0575 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018