Project name: 2. N403-660-TSA1

Status: done

Started: 2025-02-10 17:35:42
Settings
Chain sequence(s) A: MANSVLSTWVQLDASFSESSIPTAGLVGFLSNTTSSGDTWIDGYRCMNATVTKAAKVENGFKFTGPGSRATWPVNSRWDIKQYGFVDYNFTIVAMATIHQVPSESTPLLGASLRGNKRTKLIGLSYGAGGKWETVYDGTKTVQGGTWEPGREYQVALMLQDGNKGFVYVDGVLVGNPAMLPTPEERWTEFSHFYFGGDEGDSGSDATLTDVFLYNRPLSVGELKMIKEVED
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                                          (00:02:00)
[INFO]       Auto_mut: Residue number 172 from chain A and a score of 1.958 (valine) selected for  
                       automated muatation                                                         (00:02:01)
[INFO]       Auto_mut: Residue number 10 from chain A and a score of 1.604 (valine) selected for   
                       automated muatation                                                         (00:02:01)
[INFO]       Auto_mut: Residue number 6 from chain A and a score of 1.310 (leucine) selected for   
                       automated muatation                                                         (00:02:01)
[INFO]       Auto_mut: Residue number 9 from chain A and a score of 1.118 (tryptophan) selected    
                       for automated muatation                                                     (00:02:01)
[INFO]       Auto_mut: Residue number 220 from chain A and a score of 1.109 (valine) selected for  
                       automated muatation                                                         (00:02:01)
[INFO]       Auto_mut: Residue number 173 from chain A and a score of 1.105 (leucine) selected for 
                       automated muatation                                                         (00:02:01)
[INFO]       Auto_mut: Mutating residue number 172 from chain A (valine) into glutamic acid        (00:02:01)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (valine) into glutamic acid         (00:02:01)
[INFO]       Auto_mut: Mutating residue number 172 from chain A (valine) into aspartic acid        (00:02:01)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (valine) into lysine                (00:03:18)
[INFO]       Auto_mut: Mutating residue number 172 from chain A (valine) into arginine             (00:03:23)
[INFO]       Auto_mut: Mutating residue number 172 from chain A (valine) into lysine               (00:03:27)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (valine) into aspartic acid         (00:04:44)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (leucine) into glutamic acid         (00:04:56)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (leucine) into aspartic acid         (00:05:00)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (valine) into arginine              (00:06:00)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (leucine) into arginine              (00:06:13)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (leucine) into lysine                (00:06:16)
[INFO]       Auto_mut: Mutating residue number 9 from chain A (tryptophan) into glutamic acid      (00:07:27)
[INFO]       Auto_mut: Mutating residue number 9 from chain A (tryptophan) into aspartic acid      (00:07:36)
[INFO]       Auto_mut: Mutating residue number 220 from chain A (valine) into glutamic acid        (00:07:54)
[INFO]       Auto_mut: Mutating residue number 9 from chain A (tryptophan) into arginine           (00:08:56)
[INFO]       Auto_mut: Mutating residue number 9 from chain A (tryptophan) into lysine             (00:08:58)
[INFO]       Auto_mut: Mutating residue number 220 from chain A (valine) into lysine               (00:09:19)
[INFO]       Auto_mut: Mutating residue number 220 from chain A (valine) into aspartic acid        (00:10:35)
[INFO]       Auto_mut: Mutating residue number 173 from chain A (leucine) into glutamic acid       (00:10:55)
[INFO]       Auto_mut: Mutating residue number 173 from chain A (leucine) into aspartic acid       (00:10:57)
[INFO]       Auto_mut: Mutating residue number 220 from chain A (valine) into arginine             (00:12:02)
[INFO]       Auto_mut: Mutating residue number 173 from chain A (leucine) into lysine              (00:12:11)
[INFO]       Auto_mut: Mutating residue number 173 from chain A (leucine) into arginine            (00:12:14)
[INFO]       Auto_mut: Effect of mutation residue number 172 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.1027 kcal/mol, Difference in average score from 
                       the base case: -0.0073                                                      (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 172 from chain A (valine) into lysine:    
                       Energy difference: -0.2957 kcal/mol, Difference in average score from the   
                       base case: -0.0048                                                          (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 172 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.0310 kcal/mol, Difference in average score from  
                       the base case: -0.0054                                                      (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 172 from chain A (valine) into arginine:  
                       Energy difference: -0.7516 kcal/mol, Difference in average score from the   
                       base case: 0.0050                                                           (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (valine) into glutamic    
                       acid: Energy difference: -0.1823 kcal/mol, Difference in average score from 
                       the base case: -0.0228                                                      (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (valine) into lysine:     
                       Energy difference: -0.4788 kcal/mol, Difference in average score from the   
                       base case: -0.0395                                                          (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (valine) into aspartic    
                       acid: Energy difference: 0.2533 kcal/mol, Difference in average score from  
                       the base case: -0.0275                                                      (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (valine) into arginine:   
                       Energy difference: -0.6509 kcal/mol, Difference in average score from the   
                       base case: -0.0355                                                          (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (leucine) into glutamic    
                       acid: Energy difference: 0.6571 kcal/mol, Difference in average score from  
                       the base case: -0.0123                                                      (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (leucine) into lysine:     
                       Energy difference: 0.5519 kcal/mol, Difference in average score from the    
                       base case: -0.0250                                                          (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (leucine) into aspartic    
                       acid: Energy difference: 1.0184 kcal/mol, Difference in average score from  
                       the base case: -0.0160                                                      (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (leucine) into arginine:   
                       Energy difference: 0.5435 kcal/mol, Difference in average score from the    
                       base case: -0.0228                                                          (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 9 from chain A (tryptophan) into glutamic 
                       acid: Energy difference: 2.4793 kcal/mol, Difference in average score from  
                       the base case: 0.0349                                                       (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 9 from chain A (tryptophan) into lysine:  
                       Energy difference: 1.4598 kcal/mol, Difference in average score from the    
                       base case: 0.0185                                                           (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 9 from chain A (tryptophan) into aspartic 
                       acid: Energy difference: 3.8617 kcal/mol, Difference in average score from  
                       the base case: 0.0284                                                       (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 9 from chain A (tryptophan) into          
                       arginine: Energy difference: 1.5221 kcal/mol, Difference in average score   
                       from the base case: 0.0269                                                  (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 220 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.6522 kcal/mol, Difference in average score from 
                       the base case: -0.0132                                                      (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 220 from chain A (valine) into lysine:    
                       Energy difference: -0.8286 kcal/mol, Difference in average score from the   
                       base case: -0.0095                                                          (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 220 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.3304 kcal/mol, Difference in average score from  
                       the base case: -0.0057                                                      (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 220 from chain A (valine) into arginine:  
                       Energy difference: -1.0910 kcal/mol, Difference in average score from the   
                       base case: -0.0119                                                          (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 173 from chain A (leucine) into glutamic  
                       acid: Energy difference: 2.2094 kcal/mol, Difference in average score from  
                       the base case: 0.0048                                                       (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 173 from chain A (leucine) into lysine:   
                       Energy difference: 0.7784 kcal/mol, Difference in average score from the    
                       base case: 0.0155                                                           (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 173 from chain A (leucine) into aspartic  
                       acid: Energy difference: 2.4289 kcal/mol, Difference in average score from  
                       the base case: 0.0076                                                       (00:13:30)
[INFO]       Auto_mut: Effect of mutation residue number 173 from chain A (leucine) into arginine: 
                       Energy difference: 0.5185 kcal/mol, Difference in average score from the    
                       base case: 0.0080                                                           (00:13:30)
[INFO]       Main:     Simulation completed successfully.                                          (00:13:35)
Show buried residues
Minimal score value
-3.8636
Maximal score value
1.9577
Average score
-0.7328
Total score value
-169.2667
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 0.8202
2 A A 0.2707
3 N A -0.5656
4 S A 0.0690
5 V A 0.5869
6 L A 1.3100
7 S A 0.6440
8 T A 0.3092
9 W A 1.1177
10 V A 1.6044
11 Q A -0.1063
12 L A -0.0371
13 D A -0.3653
14 A A -0.6221
15 S A -0.8948
16 F A 0.0000
17 S A -1.4539
18 E A -2.1003
19 S A -1.5383
20 S A -0.9396
21 I A 0.0000
22 P A -0.4132
23 T A -0.1974
24 A A -0.2357
25 G A -0.4062
26 L A 0.0000
27 V A -0.0795
28 G A 0.0000
29 F A 0.0000
30 L A 0.0000
31 S A -1.4148
32 N A -2.1317
33 T A -1.7428
34 T A -0.9919
35 S A -0.9580
36 S A -1.0418
37 G A -1.7898
38 D A -2.1041
39 T A -1.2596
40 W A 0.0000
41 I A -0.8392
42 D A 0.0000
43 G A -0.5895
44 Y A 0.0000
45 R A -1.0279
46 C A -0.4191
47 M A -0.4076
48 N A -0.6921
49 A A 0.0000
50 T A -0.6038
51 V A 0.0000
52 T A -1.3873
53 K A -2.3798
54 A A -1.8398
55 A A -1.5643
56 K A -2.8780
57 V A -2.0438
58 E A -2.8524
59 N A -2.4873
60 G A 0.0000
61 F A 0.0000
62 K A -1.6997
63 F A 0.0000
64 T A -1.1438
65 G A -1.2002
66 P A -1.8904
67 G A -1.9924
68 S A 0.0000
69 R A -1.3830
70 A A 0.0000
71 T A -0.4716
72 W A 0.0000
73 P A -0.3420
74 V A 0.0000
75 N A -1.3696
76 S A -1.5762
77 R A -1.9363
78 W A -0.4623
79 D A -1.2941
80 I A 0.1145
81 K A -1.6135
82 Q A -0.9408
83 Y A 0.0000
84 G A -0.3692
85 F A 0.0549
86 V A 0.0000
87 D A -0.0984
88 Y A 0.0299
89 N A -0.7750
90 F A 0.0000
91 T A 0.0000
92 I A 0.0000
93 V A 0.0000
94 A A 0.0000
95 M A -0.6378
96 A A 0.0000
97 T A -2.0753
98 I A 0.0000
99 H A -1.8142
100 Q A -1.0882
101 V A 0.3023
102 P A -0.4585
103 S A -0.9203
104 E A -1.8124
105 S A -1.0745
106 T A 0.0000
107 P A 0.0000
108 L A 0.0000
109 L A 0.0000
110 G A 0.0000
111 A A 0.0000
112 S A 0.0000
113 L A 0.0000
114 R A -2.7353
115 G A -2.6328
116 N A -3.0619
117 K A -3.5747
118 R A -3.8636
119 T A -2.4945
120 K A -1.7875
121 L A 0.0000
122 I A 0.0000
123 G A 0.0000
124 L A 0.0000
125 S A 0.0000
126 Y A 0.0000
127 G A 0.0000
128 A A -0.5473
129 G A -0.6260
130 G A -0.9127
131 K A -1.3825
132 W A 0.0000
133 E A -0.3462
134 T A 0.0000
135 V A 0.0000
136 Y A -0.9455
137 D A -1.6943
138 G A -1.7718
139 T A -1.4251
140 K A -1.5577
141 T A -0.1172
142 V A 0.7559
143 Q A -0.3647
144 G A -0.7484
145 G A -0.6135
146 T A -1.2868
147 W A 0.0000
148 E A -2.8136
149 P A -2.2511
150 G A -2.6415
151 R A -3.5620
152 E A -3.2715
153 Y A 0.0000
154 Q A 0.0000
155 V A 0.0000
156 A A 0.0000
157 L A 0.0000
158 M A 0.0000
159 L A 0.0000
160 Q A -1.2120
161 D A -1.9459
162 G A 0.0000
163 N A -0.8672
164 K A -0.7976
165 G A 0.0000
166 F A -0.0569
167 V A 0.0000
168 Y A 0.0000
169 V A 0.0000
170 D A -0.0979
171 G A 0.0000
172 V A 1.9577
173 L A 1.1050
174 V A 0.0000
175 G A -0.5161
176 N A -1.2439
177 P A -0.5006
178 A A -0.2039
179 M A 0.4240
180 L A 0.0000
181 P A -1.0475
182 T A -1.3451
183 P A -1.4143
184 E A -2.4598
185 E A -2.4971
186 R A -1.4652
187 W A -0.3466
188 T A -0.9104
189 E A -0.8264
190 F A 0.0000
191 S A -1.3012
192 H A -0.6833
193 F A 0.0000
194 Y A 0.0000
195 F A 0.0000
196 G A 0.0000
197 G A 0.0000
198 D A -1.8919
199 E A -2.9516
200 G A -2.4920
201 D A -2.6903
202 S A -2.1332
203 G A -1.8497
204 S A 0.0000
205 D A -1.0843
206 A A 0.0000
207 T A -0.9324
208 L A 0.0000
209 T A -0.9861
210 D A -1.0234
211 V A 0.0000
212 F A 0.0000
213 L A 0.0000
214 Y A 0.0000
215 N A -0.7642
216 R A -1.0463
217 P A -0.6450
218 L A 0.0000
219 S A 0.0287
220 V A 1.1094
221 G A -0.1900
222 E A -0.4204
223 L A 0.0000
224 K A -1.0354
225 M A -0.8413
226 I A 0.0000
227 K A -2.4715
228 E A -2.7317
229 V A -1.5418
230 E A -2.9397
231 D A -2.6089
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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
VR10A -0.6509 -0.0355 View CSV PDB
VK10A -0.4788 -0.0395 View CSV PDB
VR220A -1.091 -0.0119 View CSV PDB
VE220A -0.6522 -0.0132 View CSV PDB
VE172A -0.1027 -0.0073 View CSV PDB
VK172A -0.2957 -0.0048 View CSV PDB
LK6A 0.5519 -0.025 View CSV PDB
LR6A 0.5435 -0.0228 View CSV PDB
LR173A 0.5185 0.008 View CSV PDB
LE173A 2.2094 0.0048 View CSV PDB
WK9A 1.4598 0.0185 View CSV PDB
WR9A 1.5221 0.0269 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018