Chain sequence(s) |
A: SRPGLPVEYLQVPSPSMGRDIKVQFQSGGNNSPAVYLLDGLRAQDDVNGWLRNTPAFEWYYQSGLSIVMPVGGQSSFYSDWLKPACGKAGCQTYKWETFLTSELPQWLSANRAVKPTGSAAIGLSMAGSSAMILAAYHPQQFIYAGSLSALLDPSQGMGPAFIDAAMGDAGGYKAADMWGPSSDPAWERNDPTQQIPKLVANNTRLWVYCGNGTPNELGGANIPAEFLENFVRSSNLKFQDAYNAAGGHNAVFNFPPNGTHSWEYWGAQLNAMKGDLQSSLGAG
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 (00:04:02) [INFO] Auto_mut: Residue number 228 from chain A and a score of 1.966 (phenylalanine) selected for automated muatation (00:04:04) [INFO] Auto_mut: Residue number 224 from chain A and a score of 1.754 (isoleucine) selected for automated muatation (00:04:04) [INFO] Auto_mut: Residue number 256 from chain A and a score of 1.555 (phenylalanine) selected for automated muatation (00:04:04) [INFO] Auto_mut: Residue number 229 from chain A and a score of 1.290 (leucine) selected for automated muatation (00:04:04) [INFO] Auto_mut: Residue number 254 from chain A and a score of 1.258 (phenylalanine) selected for automated muatation (00:04:04) [INFO] Auto_mut: Residue number 253 from chain A and a score of 1.024 (valine) selected for automated muatation (00:04:04) [INFO] Auto_mut: Mutating residue number 224 from chain A (isoleucine) into glutamic acid (00:04:04) [INFO] Auto_mut: Mutating residue number 228 from chain A (phenylalanine) into glutamic acid Mutating residue number 228 from chain A (phenylalanine) into glutamic acid (00:04:04) [INFO] Auto_mut: Mutating residue number 228 from chain A (phenylalanine) into aspartic acid Mutating residue number 228 from chain A (phenylalanine) into aspartic acid (00:04:04) [INFO] Auto_mut: Mutating residue number 224 from chain A (isoleucine) into lysine (00:05:17) [INFO] Auto_mut: Mutating residue number 228 from chain A (phenylalanine) into arginine (00:05:18) [INFO] Auto_mut: Mutating residue number 228 from chain A (phenylalanine) into lysine (00:05:22) [INFO] Auto_mut: Mutating residue number 224 from chain A (isoleucine) into aspartic acid (00:06:36) [INFO] Auto_mut: Mutating residue number 256 from chain A (phenylalanine) into glutamic acid Mutating residue number 256 from chain A (phenylalanine) into glutamic acid (00:06:51) [INFO] Auto_mut: Mutating residue number 256 from chain A (phenylalanine) into aspartic acid Mutating residue number 256 from chain A (phenylalanine) into aspartic acid (00:06:59) [INFO] Auto_mut: Mutating residue number 224 from chain A (isoleucine) into arginine (00:07:50) [INFO] Auto_mut: Mutating residue number 256 from chain A (phenylalanine) into lysine (00:08:02) [INFO] Auto_mut: Mutating residue number 256 from chain A (phenylalanine) into arginine (00:08:12) [INFO] Auto_mut: Mutating residue number 229 from chain A (leucine) into glutamic acid (00:09:07) [INFO] Auto_mut: Mutating residue number 229 from chain A (leucine) into aspartic acid (00:09:14) [INFO] Auto_mut: Mutating residue number 254 from chain A (phenylalanine) into glutamic acid Mutating residue number 254 from chain A (phenylalanine) into glutamic acid (00:09:24) [INFO] Auto_mut: Mutating residue number 229 from chain A (leucine) into lysine (00:10:27) [INFO] Auto_mut: Mutating residue number 229 from chain A (leucine) into arginine (00:10:29) [INFO] Auto_mut: Mutating residue number 254 from chain A (phenylalanine) into lysine (00:10:39) [INFO] Auto_mut: Mutating residue number 254 from chain A (phenylalanine) into aspartic acid Mutating residue number 254 from chain A (phenylalanine) into aspartic acid (00:11:53) [INFO] Auto_mut: Mutating residue number 253 from chain A (valine) into glutamic acid (00:12:00) [INFO] Auto_mut: Mutating residue number 253 from chain A (valine) into aspartic acid (00:12:13) [INFO] Auto_mut: Mutating residue number 254 from chain A (phenylalanine) into arginine (00:13:08) [INFO] Auto_mut: Mutating residue number 253 from chain A (valine) into lysine (00:13:21) [INFO] Auto_mut: Mutating residue number 253 from chain A (valine) into arginine (00:13:31) [INFO] Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into glutamic acid: Energy difference: 0.4036 kcal/mol, Difference in average score from the base case: -0.0478 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into lysine: Energy difference: -0.2129 kcal/mol, Difference in average score from the base case: -0.0476 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into aspartic acid: Energy difference: 0.9083 kcal/mol, Difference in average score from the base case: -0.0470 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into arginine: Energy difference: 0.2567 kcal/mol, Difference in average score from the base case: -0.0500 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into glutamic acid: Energy difference: -1.0575 kcal/mol, Difference in average score from the base case: -0.0353 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into lysine: Energy difference: -0.3605 kcal/mol, Difference in average score from the base case: -0.0354 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into aspartic acid: Energy difference: -0.0423 kcal/mol, Difference in average score from the base case: -0.0371 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into arginine: Energy difference: -0.4732 kcal/mol, Difference in average score from the base case: -0.0451 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into glutamic acid: Energy difference: -0.7155 kcal/mol, Difference in average score from the base case: -0.0172 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into lysine: Energy difference: -0.2570 kcal/mol, Difference in average score from the base case: -0.0298 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into aspartic acid: Energy difference: 0.0314 kcal/mol, Difference in average score from the base case: -0.0144 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into arginine: Energy difference: 0.2469 kcal/mol, Difference in average score from the base case: -0.0337 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 229 from chain A (leucine) into glutamic acid: Energy difference: 1.0984 kcal/mol, Difference in average score from the base case: -0.0060 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 229 from chain A (leucine) into lysine: Energy difference: 0.4858 kcal/mol, Difference in average score from the base case: -0.0120 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 229 from chain A (leucine) into aspartic acid: Energy difference: 1.6356 kcal/mol, Difference in average score from the base case: -0.0112 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 229 from chain A (leucine) into arginine: Energy difference: -0.1036 kcal/mol, Difference in average score from the base case: -0.0094 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into glutamic acid: Energy difference: 1.0803 kcal/mol, Difference in average score from the base case: -0.0229 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into lysine: Energy difference: 4.2039 kcal/mol, Difference in average score from the base case: 0.0007 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into aspartic acid: Energy difference: 2.4943 kcal/mol, Difference in average score from the base case: -0.0125 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into arginine: Energy difference: -0.2871 kcal/mol, Difference in average score from the base case: -0.0245 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 253 from chain A (valine) into glutamic acid: Energy difference: -0.1702 kcal/mol, Difference in average score from the base case: -0.0302 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 253 from chain A (valine) into lysine: Energy difference: -0.7770 kcal/mol, Difference in average score from the base case: -0.0131 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 253 from chain A (valine) into aspartic acid: Energy difference: -0.1387 kcal/mol, Difference in average score from the base case: -0.0291 (00:15:17) [INFO] Auto_mut: Effect of mutation residue number 253 from chain A (valine) into arginine: Energy difference: -0.2698 kcal/mol, Difference in average score from the base case: -0.0212 (00:15:17) [INFO] Main: Simulation completed successfully. (00:15:24) |
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 | |
2 | S | A | -1.0745 | |
3 | R | A | -1.7225 | |
4 | P | A | -1.1667 | |
5 | G | A | -0.9022 | |
6 | L | A | -0.4426 | |
7 | P | A | -0.1044 | |
8 | V | A | 0.2152 | |
9 | E | A | -0.1971 | |
10 | Y | A | 0.1255 | |
11 | L | A | 0.0000 | |
12 | Q | A | -1.3610 | |
13 | V | A | 0.0000 | |
14 | P | A | -1.2938 | |
15 | S | A | 0.0000 | |
16 | P | A | -0.9410 | |
17 | S | A | -0.7043 | |
18 | M | A | 0.0000 | |
19 | G | A | -1.3357 | |
20 | R | A | -1.8551 | |
21 | D | A | -2.1562 | |
22 | I | A | 0.0000 | |
23 | K | A | -1.4762 | |
24 | V | A | 0.0000 | |
25 | Q | A | 0.0000 | |
26 | F | A | 0.0000 | |
27 | Q | A | 0.0000 | |
28 | S | A | -0.8034 | |
29 | G | A | -1.1322 | |
30 | G | A | -1.5881 | |
31 | N | A | -2.3559 | |
32 | N | A | -2.5034 | |
33 | S | A | 0.0000 | |
34 | P | A | 0.0000 | |
35 | A | A | 0.0000 | |
36 | V | A | 0.0000 | |
37 | Y | A | 0.0000 | |
38 | L | A | 0.0000 | |
39 | L | A | 0.0000 | |
40 | D | A | 0.0000 | |
41 | G | A | -0.6257 | |
42 | L | A | -1.1267 | |
43 | R | A | -2.5560 | |
44 | A | A | 0.0000 | |
45 | Q | A | -2.6007 | |
46 | D | A | -3.2525 | |
47 | D | A | -2.6720 | |
48 | V | A | -1.4783 | |
49 | N | A | 0.0000 | |
50 | G | A | 0.0000 | |
51 | W | A | 0.0000 | |
52 | L | A | -0.7184 | |
53 | R | A | -1.6627 | |
54 | N | A | -0.9204 | |
55 | T | A | 0.0000 | |
56 | P | A | -0.7917 | |
57 | A | A | 0.0000 | |
58 | F | A | 0.0000 | |
59 | E | A | -0.5721 | |
60 | W | A | -0.2426 | |
61 | Y | A | 0.0000 | |
62 | Y | A | -0.0631 | |
63 | Q | A | -1.0871 | |
64 | S | A | 0.0000 | |
65 | G | A | -1.0223 | |
66 | L | A | 0.0000 | |
67 | S | A | 0.0000 | |
68 | I | A | 0.0000 | |
69 | V | A | 0.0000 | |
70 | M | A | 0.0000 | |
71 | P | A | 0.0000 | |
72 | V | A | 0.0000 | |
73 | G | A | -1.8182 | |
74 | G | A | -1.1636 | |
75 | Q | A | -1.5748 | |
76 | S | A | 0.0000 | |
77 | S | A | 0.0000 | |
78 | F | A | 0.0000 | |
79 | Y | A | 0.0000 | |
80 | S | A | 0.0000 | |
81 | D | A | -0.6702 | |
82 | W | A | 0.0000 | |
83 | L | A | -0.0129 | |
84 | K | A | -1.6839 | |
85 | P | A | -1.1031 | |
86 | A | A | 0.0000 | |
87 | C | A | -0.5562 | |
88 | G | A | -1.1018 | |
89 | K | A | -1.8151 | |
90 | A | A | -0.7907 | |
91 | G | A | -0.4600 | |
92 | C | A | 0.1530 | |
93 | Q | A | -0.7057 | |
94 | T | A | -0.7485 | |
95 | Y | A | 0.0000 | |
96 | K | A | -0.8389 | |
97 | W | A | 0.0000 | |
98 | E | A | 0.0000 | |
99 | T | A | -0.4272 | |
100 | F | A | 0.0000 | |
101 | L | A | 0.0000 | |
102 | T | A | -0.3985 | |
103 | S | A | -0.6529 | |
104 | E | A | -0.8115 | |
105 | L | A | 0.0000 | |
106 | P | A | 0.0000 | |
107 | Q | A | -1.4866 | |
108 | W | A | -0.6050 | |
109 | L | A | 0.0000 | |
110 | S | A | -1.3891 | |
111 | A | A | -0.7797 | |
112 | N | A | -1.0332 | |
113 | R | A | -1.5640 | |
114 | A | A | -1.7449 | |
115 | V | A | 0.0000 | |
116 | K | A | -2.2056 | |
117 | P | A | -1.3576 | |
118 | T | A | -1.0182 | |
119 | G | A | -0.6438 | |
120 | S | A | 0.0000 | |
121 | A | A | 0.0000 | |
122 | A | A | 0.0000 | |
123 | I | A | 0.0000 | |
124 | G | A | 0.0000 | |
125 | L | A | 0.3293 | |
126 | S | A | -0.0100 | |
127 | M | A | -0.0481 | |
128 | A | A | 0.0000 | |
129 | G | A | 0.0000 | |
130 | S | A | 0.0000 | |
131 | S | A | 0.0000 | |
132 | A | A | 0.0000 | |
133 | M | A | 0.0000 | |
134 | I | A | 0.0000 | |
135 | L | A | 0.0000 | |
136 | A | A | 0.0000 | |
137 | A | A | 0.0000 | |
138 | Y | A | -0.1425 | |
139 | H | A | -0.5334 | |
140 | P | A | -0.9924 | |
141 | Q | A | -1.3928 | |
142 | Q | A | -0.9945 | |
143 | F | A | 0.0000 | |
144 | I | A | -0.4548 | |
145 | Y | A | 0.0000 | |
146 | A | A | 0.0000 | |
147 | G | A | 0.0000 | |
148 | S | A | 0.0000 | |
149 | L | A | 0.0000 | |
150 | S | A | 0.0000 | |
151 | A | A | 0.0000 | |
152 | L | A | 0.3022 | |
153 | L | A | 0.0000 | |
154 | D | A | -1.1167 | |
155 | P | A | 0.0000 | |
156 | S | A | -1.3093 | |
157 | Q | A | -1.5470 | |
158 | G | A | -0.5483 | |
159 | M | A | 0.5337 | |
160 | G | A | -0.0025 | |
161 | P | A | 0.0000 | |
162 | A | A | 0.1016 | |
163 | F | A | 0.5890 | |
164 | I | A | 0.0000 | |
165 | D | A | -1.3211 | |
166 | A | A | -0.9473 | |
167 | A | A | -1.1506 | |
168 | M | A | 0.0000 | |
169 | G | A | -1.8895 | |
170 | D | A | -2.5640 | |
171 | A | A | 0.0000 | |
172 | G | A | -1.7354 | |
173 | G | A | -1.7696 | |
174 | Y | A | 0.0000 | |
175 | K | A | -2.4087 | |
176 | A | A | 0.0000 | |
177 | A | A | -1.1361 | |
178 | D | A | -1.2084 | |
179 | M | A | 0.0000 | |
180 | W | A | 0.0000 | |
181 | G | A | 0.0000 | |
182 | P | A | -0.8312 | |
183 | S | A | -0.9689 | |
184 | S | A | -0.8587 | |
185 | D | A | -1.1664 | |
186 | P | A | -1.1224 | |
187 | A | A | -0.8265 | |
188 | W | A | 0.0000 | |
189 | E | A | -1.9583 | |
190 | R | A | -1.3933 | |
191 | N | A | 0.0000 | |
192 | D | A | 0.0000 | |
193 | P | A | 0.0000 | |
194 | T | A | -1.2399 | |
195 | Q | A | -1.5817 | |
196 | Q | A | 0.0000 | |
197 | I | A | 0.0000 | |
198 | P | A | -1.0715 | |
199 | K | A | -1.4578 | |
200 | L | A | 0.0000 | |
201 | V | A | -1.3338 | |
202 | A | A | -0.9476 | |
203 | N | A | -1.5192 | |
204 | N | A | -1.7361 | |
205 | T | A | 0.0000 | |
206 | R | A | -1.3548 | |
207 | L | A | 0.0000 | |
208 | W | A | 0.0000 | |
209 | V | A | 0.0000 | |
210 | Y | A | 0.7809 | |
211 | C | A | 0.0000 | |
212 | G | A | 0.0000 | |
213 | N | A | -0.4147 | |
214 | G | A | 0.0000 | |
215 | T | A | -0.7246 | |
216 | P | A | -1.5086 | |
217 | N | A | -2.1238 | |
218 | E | A | -2.1770 | |
219 | L | A | -0.7481 | |
220 | G | A | -0.8866 | |
221 | G | A | -0.5591 | |
222 | A | A | -0.6577 | |
223 | N | A | -0.0225 | |
224 | I | A | 1.7537 | |
225 | P | A | 0.8377 | |
226 | A | A | 0.0000 | |
227 | E | A | 0.4141 | |
228 | F | A | 1.9662 | |
229 | L | A | 1.2895 | |
230 | E | A | 0.0000 | |
231 | N | A | -0.4971 | |
232 | F | A | 0.8437 | |
233 | V | A | 0.0000 | |
234 | R | A | -0.4761 | |
235 | S | A | -0.7821 | |
236 | S | A | -0.9263 | |
237 | N | A | 0.0000 | |
238 | L | A | -0.7846 | |
239 | K | A | -2.4859 | |
240 | F | A | 0.0000 | |
241 | Q | A | -1.6053 | |
242 | D | A | -2.7734 | |
243 | A | A | -1.8784 | |
244 | Y | A | 0.0000 | |
245 | N | A | -2.4044 | |
246 | A | A | -1.2843 | |
247 | A | A | -0.9331 | |
248 | G | A | -1.1355 | |
249 | G | A | -1.7786 | |
250 | H | A | -1.6655 | |
251 | N | A | -1.3038 | |
252 | A | A | -0.3291 | |
253 | V | A | 1.0241 | |
254 | F | A | 1.2575 | |
255 | N | A | 1.0137 | |
256 | F | A | 1.5554 | |
257 | P | A | 0.4157 | |
258 | P | A | -0.3333 | |
259 | N | A | -0.7772 | |
260 | G | A | 0.0000 | |
261 | T | A | 0.0000 | |
262 | H | A | 0.0473 | |
263 | S | A | 0.0613 | |
264 | W | A | 0.5285 | |
265 | E | A | 0.1447 | |
266 | Y | A | 0.0000 | |
267 | W | A | 0.0000 | |
268 | G | A | 0.0000 | |
269 | A | A | -0.0226 | |
270 | Q | A | 0.0000 | |
271 | L | A | 0.0000 | |
272 | N | A | -0.6976 | |
273 | A | A | -0.7223 | |
274 | M | A | 0.0000 | |
275 | K | A | -1.4388 | |
276 | G | A | -1.7334 | |
277 | D | A | -2.2278 | |
278 | L | A | 0.0000 | |
279 | Q | A | -1.4463 | |
280 | S | A | -1.2996 | |
281 | S | A | -0.9809 | |
282 | L | A | -0.6214 | |
283 | G | A | -0.8692 | |
284 | A | A | -1.0222 | |
285 | G | A | -0.8989 |
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 |
|||
IE224A | -1.0575 | -0.0353 | View | CSV | PDB |
IR224A | -0.4732 | -0.0451 | View | CSV | PDB |
FK228A | -0.2129 | -0.0476 | View | CSV | PDB |
FK256A | -0.257 | -0.0298 | View | CSV | PDB |
FE256A | -0.7155 | -0.0172 | View | CSV | PDB |
VE253A | -0.1702 | -0.0302 | View | CSV | PDB |
FR254A | -0.2871 | -0.0245 | View | CSV | PDB |
VD253A | -0.1387 | -0.0291 | View | CSV | PDB |
LR229A | -0.1036 | -0.0094 | View | CSV | PDB |
FR228A | 0.2567 | -0.05 | View | CSV | PDB |
LK229A | 0.4858 | -0.012 | View | CSV | PDB |
FE254A | 1.0803 | -0.0229 | View | CSV | PDB |