Project name: L426-660 TSA-1

Status: done

Started: 2025-02-10 17:15:39
Settings
Chain sequence(s) A: MALVGFLSNTTSSGDTWIDGYRCMNATVTKAAKVENGFKFTGPGSRATWPVNSRWDIKQYGFVDYNFTIVAMATIHQVPSESTPLLGASLRGNKRTKLIGLSYGAGGKWETVYDGTKTVQGGTWEPGREYQVALMLQDGNKGFVYVDGVLVGNPAMLPTPEERWTEFSHFYFGGDEGDSGSDATLTDVFLYNRPLSVGELKMIKEVED
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]                                                (00:00:00)
[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 A 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                                          (00:02:07)
[INFO]       Auto_mut: Residue number 149 from chain A and a score of 1.842 (valine) selected for  
                       automated muatation                                                         (00:02:08)
[INFO]       Auto_mut: Residue number 1 from chain A and a score of 1.165 omitted from automated   
                       muatation (excluded by the user).                                           (00:02:08)
[INFO]       Auto_mut: Residue number 150 from chain A and a score of 1.086 (leucine) selected for 
                       automated muatation                                                         (00:02:08)
[INFO]       Auto_mut: Residue number 145 from chain A and a score of 0.965 (tyrosine) selected    
                       for automated muatation                                                     (00:02:08)
[INFO]       Auto_mut: Residue number 3 from chain A and a score of 0.890 (leucine) selected for   
                       automated muatation                                                         (00:02:08)
[INFO]       Auto_mut: Residue number 4 from chain A and a score of 0.832 (valine) selected for    
                       automated muatation                                                         (00:02:08)
[INFO]       Auto_mut: Residue number 197 from chain A and a score of 0.754 (valine) selected for  
                       automated muatation                                                         (00:02:08)
[INFO]       Auto_mut: Mutating residue number 149 from chain A (valine) into glutamic acid        (00:02:08)
[INFO]       Auto_mut: Mutating residue number 149 from chain A (valine) into aspartic acid        (00:02:08)
[INFO]       Auto_mut: Mutating residue number 150 from chain A (leucine) into glutamic acid       (00:02:08)
[INFO]       Auto_mut: Mutating residue number 150 from chain A (leucine) into lysine              (00:03:11)
[INFO]       Auto_mut: Mutating residue number 149 from chain A (valine) into arginine             (00:03:16)
[INFO]       Auto_mut: Mutating residue number 149 from chain A (valine) into lysine               (00:03:17)
[INFO]       Auto_mut: Mutating residue number 150 from chain A (leucine) into aspartic acid       (00:04:18)
[INFO]       Auto_mut: Mutating residue number 145 from chain A (tyrosine) into glutamic acid      (00:04:33)
[INFO]       Auto_mut: Mutating residue number 145 from chain A (tyrosine) into aspartic acid      (00:04:37)
[INFO]       Auto_mut: Mutating residue number 150 from chain A (leucine) into arginine            (00:05:21)
[INFO]       Auto_mut: Mutating residue number 145 from chain A (tyrosine) into lysine             (00:05:37)
[INFO]       Auto_mut: Mutating residue number 145 from chain A (tyrosine) into arginine           (00:05:43)
[INFO]       Auto_mut: Mutating residue number 3 from chain A (leucine) into glutamic acid         (00:06:24)
[INFO]       Auto_mut: Mutating residue number 3 from chain A (leucine) into aspartic acid         (00:06:43)
[INFO]       Auto_mut: Mutating residue number 4 from chain A (valine) into glutamic acid          (00:06:47)
[INFO]       Auto_mut: Mutating residue number 3 from chain A (leucine) into lysine                (00:07:43)
[INFO]       Auto_mut: Mutating residue number 3 from chain A (leucine) into arginine              (00:07:59)
[INFO]       Auto_mut: Mutating residue number 4 from chain A (valine) into lysine                 (00:08:00)
[INFO]       Auto_mut: Mutating residue number 4 from chain A (valine) into aspartic acid          (00:09:16)
[INFO]       Auto_mut: Mutating residue number 197 from chain A (valine) into glutamic acid        (00:09:20)
[INFO]       Auto_mut: Mutating residue number 197 from chain A (valine) into aspartic acid        (00:09:21)
[INFO]       Auto_mut: Mutating residue number 4 from chain A (valine) into arginine               (00:10:26)
[INFO]       Auto_mut: Mutating residue number 197 from chain A (valine) into lysine               (00:10:30)
[INFO]       Auto_mut: Mutating residue number 197 from chain A (valine) into arginine             (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 149 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.1326 kcal/mol, Difference in average score from 
                       the base case: -0.0655                                                      (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 149 from chain A (valine) into lysine:    
                       Energy difference: -0.2441 kcal/mol, Difference in average score from the   
                       base case: -0.0628                                                          (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 149 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.2107 kcal/mol, Difference in average score from  
                       the base case: -0.0636                                                      (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 149 from chain A (valine) into arginine:  
                       Energy difference: -0.8906 kcal/mol, Difference in average score from the   
                       base case: -0.0562                                                          (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 150 from chain A (leucine) into glutamic  
                       acid: Energy difference: 2.0103 kcal/mol, Difference in average score from  
                       the base case: -0.0362                                                      (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 150 from chain A (leucine) into lysine:   
                       Energy difference: 0.8017 kcal/mol, Difference in average score from the    
                       base case: -0.0369                                                          (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 150 from chain A (leucine) into aspartic  
                       acid: Energy difference: 2.2496 kcal/mol, Difference in average score from  
                       the base case: -0.0494                                                      (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 150 from chain A (leucine) into arginine: 
                       Energy difference: 0.6659 kcal/mol, Difference in average score from the    
                       base case: -0.0434                                                          (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 145 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 4.3983 kcal/mol, Difference in average score from  
                       the base case: -0.0025                                                      (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 145 from chain A (tyrosine) into lysine:  
                       Energy difference: 1.9314 kcal/mol, Difference in average score from the    
                       base case: -0.0090                                                          (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 145 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 5.1807 kcal/mol, Difference in average score from  
                       the base case: -0.0037                                                      (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 145 from chain A (tyrosine) into          
                       arginine: Energy difference: 1.7790 kcal/mol, Difference in average score   
                       from the base case: -0.0248                                                 (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain A (leucine) into glutamic    
                       acid: Energy difference: 1.8134 kcal/mol, Difference in average score from  
                       the base case: -0.0317                                                      (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain A (leucine) into lysine:     
                       Energy difference: 0.6145 kcal/mol, Difference in average score from the    
                       base case: -0.0312                                                          (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain A (leucine) into aspartic    
                       acid: Energy difference: 1.5048 kcal/mol, Difference in average score from  
                       the base case: -0.0261                                                      (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain A (leucine) into arginine:   
                       Energy difference: -1.1998 kcal/mol, Difference in average score from the   
                       base case: -0.0309                                                          (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 4 from chain A (valine) into glutamic     
                       acid: Energy difference: 1.2370 kcal/mol, Difference in average score from  
                       the base case: -0.0301                                                      (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 4 from chain A (valine) into lysine:      
                       Energy difference: 0.8099 kcal/mol, Difference in average score from the    
                       base case: -0.0317                                                          (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 4 from chain A (valine) into aspartic     
                       acid: Energy difference: 1.8503 kcal/mol, Difference in average score from  
                       the base case: -0.0343                                                      (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 4 from chain A (valine) into arginine:    
                       Energy difference: 1.0238 kcal/mol, Difference in average score from the    
                       base case: -0.0421                                                          (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 197 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.6272 kcal/mol, Difference in average score from 
                       the base case: -0.0536                                                      (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 197 from chain A (valine) into lysine:    
                       Energy difference: -0.7026 kcal/mol, Difference in average score from the   
                       base case: -0.0524                                                          (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 197 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.5902 kcal/mol, Difference in average score from 
                       the base case: -0.0540                                                      (00:12:00)
[INFO]       Auto_mut: Effect of mutation residue number 197 from chain A (valine) into arginine:  
                       Energy difference: -0.9532 kcal/mol, Difference in average score from the   
                       base case: -0.0628                                                          (00:12:00)
[INFO]       Main:     Simulation completed successfully.                                          (00:12:04)
Show buried residues
Minimal score value
-3.5389
Maximal score value
1.8422
Average score
-0.7079
Total score value
-147.2397
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 1.1646
2 A A 0.3935
3 L A 0.8904
4 V A 0.8318
5 G A 0.0000
6 F A 0.5277
7 L A 0.0000
8 S A -0.9400
9 N A -1.8060
10 T A -1.6228
11 T A -1.0067
12 S A -0.9547
13 S A -1.0886
14 G A -1.6736
15 D A -2.4658
16 T A -1.4880
17 W A 0.0000
18 I A -0.8525
19 D A 0.0000
20 G A -0.2389
21 Y A 0.3429
22 R A -1.2535
23 C A -0.1869
24 M A -0.5146
25 N A -1.1698
26 A A 0.0000
27 T A -0.7854
28 V A 0.0000
29 T A -1.4390
30 K A -2.3521
31 A A -1.7713
32 A A -1.3906
33 K A -2.3488
34 V A -1.5251
35 E A -2.3931
36 N A -1.7755
37 G A 0.0000
38 F A 0.0000
39 K A -1.6016
40 F A 0.0000
41 T A -1.1238
42 G A 0.0000
43 P A -1.7655
44 G A -1.7668
45 S A 0.0000
46 R A -1.1348
47 A A 0.0000
48 T A -0.2978
49 W A 0.0000
50 P A -0.2515
51 V A 0.0000
52 N A 0.0000
53 S A -1.3353
54 R A -1.7402
55 W A -0.3842
56 D A -1.2014
57 I A -0.0376
58 K A -1.7164
59 Q A -1.2787
60 Y A 0.0000
61 G A -0.5778
62 F A -0.1204
63 V A 0.0000
64 D A 0.0000
65 Y A -0.2037
66 N A -1.0147
67 F A 0.0000
68 T A 0.0000
69 I A 0.0000
70 V A 0.0000
71 A A 0.0000
72 M A -0.4851
73 A A 0.0000
74 T A 0.0000
75 I A 0.0000
76 H A -1.6255
77 Q A -0.9334
78 V A 0.4785
79 P A -0.4418
80 S A -0.9210
81 E A -1.9901
82 S A -1.0519
83 T A 0.0000
84 P A 0.0000
85 L A 0.0000
86 L A 0.0000
87 G A 0.0000
88 A A 0.0000
89 S A 0.0000
90 L A 0.0000
91 R A -2.3777
92 G A -2.5563
93 N A -3.0019
94 K A -3.5389
95 R A -3.5240
96 T A -2.5003
97 K A -1.8622
98 L A 0.0000
99 I A 0.0000
100 G A 0.0000
101 L A 0.0000
102 S A 0.0000
103 Y A 0.0000
104 G A 0.0000
105 A A -0.5461
106 G A -0.5981
107 G A -0.5891
108 K A -1.1693
109 W A 0.0000
110 E A -0.3789
111 T A 0.0000
112 V A 0.0000
113 Y A -1.0145
114 D A -1.7722
115 G A -1.8516
116 T A -1.5146
117 K A -1.7053
118 T A -0.1972
119 V A 0.7348
120 Q A -0.3962
121 G A -0.8270
122 G A -0.6289
123 T A -1.0420
124 W A 0.0000
125 E A -1.5951
126 P A -1.6401
127 G A -2.2727
128 R A -3.0615
129 E A -2.8843
130 Y A 0.0000
131 Q A 0.0000
132 V A 0.0000
133 A A 0.0000
134 L A 0.0000
135 M A 0.0000
136 L A 0.0000
137 Q A -1.5621
138 D A -2.1529
139 G A 0.0000
140 N A -0.9753
141 K A -1.0710
142 G A 0.0000
143 F A -0.0879
144 V A 0.0000
145 Y A 0.9645
146 V A 0.0000
147 D A -0.2938
148 G A 0.0000
149 V A 1.8422
150 L A 1.0861
151 V A 0.0000
152 G A -0.4887
153 N A -1.2409
154 P A -0.5462
155 A A -0.2582
156 M A 0.3447
157 L A 0.0000
158 P A -1.0643
159 T A -1.3526
160 P A -1.4881
161 E A -2.5059
162 E A -2.4909
163 R A -1.5204
164 W A -0.4017
165 T A -0.7905
166 E A -1.0438
167 F A 0.0000
168 S A -1.1493
169 H A -0.6015
170 F A 0.0000
171 Y A 0.0000
172 F A 0.0000
173 G A 0.0000
174 G A 0.0000
175 D A -1.7417
176 E A -2.5799
177 G A -2.3045
178 D A -2.7268
179 S A -2.0647
180 G A -1.6054
181 S A 0.0000
182 D A -1.1045
183 A A 0.0000
184 T A -0.8490
185 L A 0.0000
186 T A 0.0000
187 D A -0.8094
188 V A 0.0000
189 F A 0.5864
190 L A 0.0000
191 Y A 0.0503
192 N A -0.6375
193 R A -1.3051
194 P A -0.8821
195 L A 0.0000
196 S A -0.1635
197 V A 0.7545
198 G A -0.4224
199 E A -0.5860
200 L A 0.0000
201 K A -1.0883
202 M A -0.6565
203 I A 0.0000
204 K A -2.1342
205 E A -2.3918
206 V A -0.6686
207 E A -2.4952
208 D A -2.8392
Download PDB file
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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
VR197A -0.9532 -0.0628 View CSV PDB
VR149A -0.8906 -0.0562 View CSV PDB
VK197A -0.7026 -0.0524 View CSV PDB
LR3A -1.1998 -0.0309 View CSV PDB
VK149A -0.2441 -0.0628 View CSV PDB
LR150A 0.6659 -0.0434 View CSV PDB
LK3A 0.6145 -0.0312 View CSV PDB
LK150A 0.8017 -0.0369 View CSV PDB
VR4A 1.0238 -0.0421 View CSV PDB
VK4A 0.8099 -0.0317 View CSV PDB
YR145A 1.779 -0.0248 View CSV PDB
YK145A 1.9314 -0.009 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018