Chain sequence(s) |
A: MANSVLSTWRQLDASFSESSIPTAGLVGFLSNTTSSGDTWIDGYRSMNATVTKAAKVENGFKFTGPGSRATWPVNSRWDIKQYGFVDYNFTIVAMATIHQVPSESTPLLGASLRGNKRTKLIGLSYGAGGKWETVYDGTKTVQGGTWEPGREYQVALMLQDGNKGFVYVDGVLVGNPAMLPTPEERWTEFSHFYFGGDEGDSGSDATLTDVFLYNRPLSRGELKMIKEVED
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 (00:02:28) [INFO] Auto_mut: Residue number 172 from chain A and a score of 1.341 (valine) selected for automated muatation (00:02:29) [INFO] Auto_mut: Residue number 1 from chain A and a score of 0.823 omitted from automated muatation (excluded by the user). (00:02:29) [INFO] Auto_mut: Residue number 142 from chain A and a score of 0.804 (valine) selected for automated muatation (00:02:29) [INFO] Auto_mut: Residue number 173 from chain A and a score of 0.568 (leucine) selected for automated muatation (00:02:29) [INFO] Auto_mut: Residue number 6 from chain A and a score of 0.542 (leucine) selected for automated muatation (00:02:29) [INFO] Auto_mut: Residue number 179 from chain A and a score of 0.365 (methionine) selected for automated muatation (00:02:29) [INFO] Auto_mut: Residue number 101 from chain A and a score of 0.292 (valine) selected for automated muatation (00:02:29) [INFO] Auto_mut: Mutating residue number 172 from chain A (valine) into glutamic acid (00:02:29) [INFO] Auto_mut: Mutating residue number 142 from chain A (valine) into glutamic acid (00:02:29) [INFO] Auto_mut: Mutating residue number 172 from chain A (valine) into aspartic acid (00:02:29) [INFO] Auto_mut: Mutating residue number 142 from chain A (valine) into lysine (00:03:47) [INFO] Auto_mut: Mutating residue number 172 from chain A (valine) into arginine (00:03:54) [INFO] Auto_mut: Mutating residue number 172 from chain A (valine) into lysine (00:03:58) [INFO] Auto_mut: Mutating residue number 142 from chain A (valine) into aspartic acid (00:05:24) [INFO] Auto_mut: Mutating residue number 173 from chain A (leucine) into glutamic acid (00:05:32) [INFO] Auto_mut: Mutating residue number 173 from chain A (leucine) into aspartic acid (00:05:40) [INFO] Auto_mut: Mutating residue number 173 from chain A (leucine) into lysine (00:06:47) [INFO] Auto_mut: Mutating residue number 142 from chain A (valine) into arginine (00:06:51) [INFO] Auto_mut: Mutating residue number 173 from chain A (leucine) into arginine (00:06:58) [INFO] Auto_mut: Mutating residue number 6 from chain A (leucine) into glutamic acid (00:08:09) [INFO] Auto_mut: Mutating residue number 6 from chain A (leucine) into aspartic acid (00:08:13) [INFO] Auto_mut: Mutating residue number 179 from chain A (methionine) into glutamic acid (00:08:23) [INFO] Auto_mut: Mutating residue number 6 from chain A (leucine) into lysine (00:09:24) [INFO] Auto_mut: Mutating residue number 6 from chain A (leucine) into arginine (00:09:26) [INFO] Auto_mut: Mutating residue number 179 from chain A (methionine) into lysine (00:09:45) [INFO] Auto_mut: Mutating residue number 179 from chain A (methionine) into aspartic acid (00:10:45) [INFO] Auto_mut: Mutating residue number 101 from chain A (valine) into glutamic acid (00:11:06) [INFO] Auto_mut: Mutating residue number 101 from chain A (valine) into aspartic acid (00:11:19) [INFO] Auto_mut: Mutating residue number 179 from chain A (methionine) into arginine (00:12:07) [INFO] Auto_mut: Mutating residue number 101 from chain A (valine) into lysine (00:12:23) [INFO] Auto_mut: Mutating residue number 101 from chain A (valine) into arginine (00:12:34) [INFO] Auto_mut: Effect of mutation residue number 172 from chain A (valine) into glutamic acid: Energy difference: -0.2180 kcal/mol, Difference in average score from the base case: -0.0322 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 172 from chain A (valine) into lysine: Energy difference: -0.2570 kcal/mol, Difference in average score from the base case: -0.0295 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 172 from chain A (valine) into aspartic acid: Energy difference: -0.0814 kcal/mol, Difference in average score from the base case: -0.0307 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 172 from chain A (valine) into arginine: Energy difference: -0.4774 kcal/mol, Difference in average score from the base case: -0.0147 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 142 from chain A (valine) into glutamic acid: Energy difference: 0.1682 kcal/mol, Difference in average score from the base case: -0.0579 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 142 from chain A (valine) into lysine: Energy difference: -0.7366 kcal/mol, Difference in average score from the base case: -0.0389 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 142 from chain A (valine) into aspartic acid: Energy difference: -0.2169 kcal/mol, Difference in average score from the base case: -0.0510 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 142 from chain A (valine) into arginine: Energy difference: -1.0218 kcal/mol, Difference in average score from the base case: -0.0424 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 173 from chain A (leucine) into glutamic acid: Energy difference: 2.3680 kcal/mol, Difference in average score from the base case: 0.0008 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 173 from chain A (leucine) into lysine: Energy difference: 1.9284 kcal/mol, Difference in average score from the base case: -0.0024 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 173 from chain A (leucine) into aspartic acid: Energy difference: 2.4167 kcal/mol, Difference in average score from the base case: 0.0026 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 173 from chain A (leucine) into arginine: Energy difference: 1.4215 kcal/mol, Difference in average score from the base case: -0.0034 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 6 from chain A (leucine) into glutamic acid: Energy difference: 0.9070 kcal/mol, Difference in average score from the base case: -0.0492 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 6 from chain A (leucine) into lysine: Energy difference: 0.5195 kcal/mol, Difference in average score from the base case: -0.0362 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 6 from chain A (leucine) into aspartic acid: Energy difference: 1.4568 kcal/mol, Difference in average score from the base case: -0.0395 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 6 from chain A (leucine) into arginine: Energy difference: 0.8319 kcal/mol, Difference in average score from the base case: -0.0425 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 179 from chain A (methionine) into glutamic acid: Energy difference: 0.4878 kcal/mol, Difference in average score from the base case: -0.0276 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 179 from chain A (methionine) into lysine: Energy difference: -0.3030 kcal/mol, Difference in average score from the base case: -0.0305 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 179 from chain A (methionine) into aspartic acid: Energy difference: 0.5700 kcal/mol, Difference in average score from the base case: -0.0316 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 179 from chain A (methionine) into arginine: Energy difference: -1.8457 kcal/mol, Difference in average score from the base case: -0.0257 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 101 from chain A (valine) into glutamic acid: Energy difference: -0.1345 kcal/mol, Difference in average score from the base case: -0.0517 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 101 from chain A (valine) into lysine: Energy difference: -0.7912 kcal/mol, Difference in average score from the base case: -0.0495 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 101 from chain A (valine) into aspartic acid: Energy difference: 0.7341 kcal/mol, Difference in average score from the base case: -0.0514 (00:13:54) [INFO] Auto_mut: Effect of mutation residue number 101 from chain A (valine) into arginine: Energy difference: -0.3919 kcal/mol, Difference in average score from the base case: -0.0540 (00:13:54) [INFO] Main: Simulation completed successfully. (00:13:59) |
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 | |
1 | M | A | 0.8234 | |
2 | A | A | 0.2822 | |
3 | N | A | -0.5537 | |
4 | S | A | -0.0834 | |
5 | V | A | 0.0481 | |
6 | L | A | 0.5419 | |
7 | S | A | -0.5565 | |
8 | T | A | -0.8010 | |
9 | W | A | -0.5627 | |
10 | R | A | -1.8943 | |
11 | Q | A | -1.7574 | |
12 | L | A | -0.9953 | |
13 | D | A | -1.2926 | |
14 | A | A | -1.4675 | |
15 | S | A | -1.3244 | |
16 | F | A | 0.0000 | |
17 | S | A | -1.3697 | |
18 | E | A | -1.9772 | |
19 | S | A | -1.4201 | |
20 | S | A | -1.1093 | |
21 | I | A | 0.0000 | |
22 | P | A | -0.3857 | |
23 | T | A | -0.2784 | |
24 | A | A | -0.1692 | |
25 | G | A | -0.3598 | |
26 | L | A | 0.0000 | |
27 | V | A | -0.0474 | |
28 | G | A | 0.0000 | |
29 | F | A | 0.0000 | |
30 | L | A | 0.0000 | |
31 | S | A | -1.4275 | |
32 | N | A | -2.1698 | |
33 | T | A | 0.0000 | |
34 | T | A | -0.9447 | |
35 | S | A | -0.9307 | |
36 | S | A | -0.9875 | |
37 | G | A | -1.7080 | |
38 | D | A | -1.9343 | |
39 | T | A | -1.2767 | |
40 | W | A | 0.0000 | |
41 | I | A | -1.0594 | |
42 | D | A | 0.0000 | |
43 | G | A | -0.8032 | |
44 | Y | A | 0.0000 | |
45 | R | A | -1.7818 | |
46 | S | A | -1.0839 | |
47 | M | A | -0.8708 | |
48 | N | A | -1.2183 | |
49 | A | A | 0.0000 | |
50 | T | A | -0.7022 | |
51 | V | A | 0.0000 | |
52 | T | A | -1.3893 | |
53 | K | A | -2.3805 | |
54 | A | A | -1.8557 | |
55 | A | A | -1.5503 | |
56 | K | A | -2.8776 | |
57 | V | A | -2.0810 | |
58 | E | A | -2.8940 | |
59 | N | A | -2.5536 | |
60 | G | A | 0.0000 | |
61 | F | A | 0.0000 | |
62 | K | A | -1.7492 | |
63 | F | A | 0.0000 | |
64 | T | A | -1.1616 | |
65 | G | A | -1.2049 | |
66 | P | A | -1.8716 | |
67 | G | A | -1.9492 | |
68 | S | A | 0.0000 | |
69 | R | A | -1.5513 | |
70 | A | A | 0.0000 | |
71 | T | A | -0.4114 | |
72 | W | A | 0.0000 | |
73 | P | A | -0.4001 | |
74 | V | A | 0.0000 | |
75 | N | A | 0.0000 | |
76 | S | A | -1.6359 | |
77 | R | A | -1.9161 | |
78 | W | A | -0.4198 | |
79 | D | A | -1.3257 | |
80 | I | A | 0.0426 | |
81 | K | A | -1.7171 | |
82 | Q | A | -1.3047 | |
83 | Y | A | 0.0000 | |
84 | G | A | -0.4922 | |
85 | F | A | 0.0897 | |
86 | V | A | 0.0000 | |
87 | D | A | 0.0000 | |
88 | Y | A | 0.0432 | |
89 | N | A | -0.7486 | |
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 | -0.5461 | |
96 | A | A | 0.0000 | |
97 | T | A | -1.7459 | |
98 | I | A | 0.0000 | |
99 | H | A | -1.6222 | |
100 | Q | A | -1.0769 | |
101 | V | A | 0.2922 | |
102 | P | A | -0.4658 | |
103 | S | A | -0.9263 | |
104 | E | A | -1.8329 | |
105 | S | A | -1.1023 | |
106 | T | A | 0.0000 | |
107 | P | A | -0.5159 | |
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 | -3.2340 | |
115 | G | A | -2.8472 | |
116 | N | A | -3.1144 | |
117 | K | A | -3.6286 | |
118 | R | A | -3.9441 | |
119 | T | A | -2.6191 | |
120 | K | A | -1.9096 | |
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 | -0.5532 | |
129 | G | A | -0.5853 | |
130 | G | A | -0.8558 | |
131 | K | A | -1.2758 | |
132 | W | A | 0.0000 | |
133 | E | A | 0.0000 | |
134 | T | A | 0.0000 | |
135 | V | A | 0.0000 | |
136 | Y | A | -1.0445 | |
137 | D | A | -1.8316 | |
138 | G | A | -1.8669 | |
139 | T | A | -1.5095 | |
140 | K | A | -1.6704 | |
141 | T | A | -0.1338 | |
142 | V | A | 0.8042 | |
143 | Q | A | -0.3153 | |
144 | G | A | -0.7219 | |
145 | G | A | -0.5878 | |
146 | T | A | -1.2831 | |
147 | W | A | 0.0000 | |
148 | E | A | -2.5374 | |
149 | P | A | -1.9279 | |
150 | G | A | -2.1117 | |
151 | R | A | -2.5056 | |
152 | E | A | -2.7178 | |
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 | -1.3582 | |
161 | D | A | -1.9807 | |
162 | G | A | 0.0000 | |
163 | N | A | -0.8955 | |
164 | K | A | -0.9150 | |
165 | G | A | 0.0000 | |
166 | F | A | 0.0000 | |
167 | V | A | 0.0000 | |
168 | Y | A | 0.0000 | |
169 | V | A | 0.0000 | |
170 | D | A | -0.3899 | |
171 | G | A | 0.0000 | |
172 | V | A | 1.3412 | |
173 | L | A | 0.5679 | |
174 | V | A | 0.0000 | |
175 | G | A | -0.5380 | |
176 | N | A | -1.2974 | |
177 | P | A | -0.5876 | |
178 | A | A | -0.2648 | |
179 | M | A | 0.3654 | |
180 | L | A | 0.0000 | |
181 | P | A | -1.0693 | |
182 | T | A | -1.4336 | |
183 | P | A | -1.5325 | |
184 | E | A | -2.5481 | |
185 | E | A | -2.4964 | |
186 | R | A | -1.6283 | |
187 | W | A | -0.5503 | |
188 | T | A | -1.3339 | |
189 | E | A | -1.5727 | |
190 | F | A | 0.0000 | |
191 | S | A | 0.0000 | |
192 | H | A | -0.7793 | |
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 | -1.9831 | |
199 | E | A | -2.9603 | |
200 | G | A | -2.4891 | |
201 | D | A | -2.6497 | |
202 | S | A | -2.1252 | |
203 | G | A | -1.8766 | |
204 | S | A | 0.0000 | |
205 | D | A | -1.1120 | |
206 | A | A | 0.0000 | |
207 | T | A | -0.9340 | |
208 | L | A | 0.0000 | |
209 | T | A | -0.9884 | |
210 | D | A | -1.0018 | |
211 | V | A | 0.0000 | |
212 | F | A | 0.0000 | |
213 | L | A | 0.0000 | |
214 | Y | A | 0.0000 | |
215 | N | A | -0.6606 | |
216 | R | A | -0.9685 | |
217 | P | A | -1.0030 | |
218 | L | A | 0.0000 | |
219 | S | A | -1.5219 | |
220 | R | A | -2.0624 | |
221 | G | A | -1.7757 | |
222 | E | A | -1.4965 | |
223 | L | A | 0.0000 | |
224 | K | A | -1.8836 | |
225 | M | A | -1.3705 | |
226 | I | A | 0.0000 | |
227 | K | A | -2.7830 | |
228 | E | A | -3.0470 | |
229 | V | A | -2.0274 | |
230 | E | A | -3.0681 | |
231 | D | A | -3.0477 |
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 |
|||
VR142A | -1.0218 | -0.0424 | View | CSV | PDB |
VK101A | -0.7912 | -0.0495 | View | CSV | PDB |
MR179A | -1.8457 | -0.0257 | View | CSV | PDB |
VR101A | -0.3919 | -0.054 | View | CSV | PDB |
VK142A | -0.7366 | -0.0389 | View | CSV | PDB |
MK179A | -0.303 | -0.0305 | View | CSV | PDB |
VE172A | -0.218 | -0.0322 | View | CSV | PDB |
VK172A | -0.257 | -0.0295 | View | CSV | PDB |
LK6A | 0.5195 | -0.0362 | View | CSV | PDB |
LE6A | 0.907 | -0.0492 | View | CSV | PDB |
LR173A | 1.4215 | -0.0034 | View | CSV | PDB |
LK173A | 1.9284 | -0.0024 | View | CSV | PDB |