Project name: 42-431

Status: done

Started: 2025-02-07 18:09:15
Settings
Chain sequence(s) A: MGSSHHHHHHSSGENLYFQGAMAIAMLVPNKTQVVPKSGGEGKVKDIFASPALVRAGGVMIAFVEGRTKNKLFPEVIDLSSSDIVAGYIKAPETWQSLVAEVTKEYWQAHTVLESANNSNHRVGVARLPTGITRGNKVFLLVGSYEERREIDDYIWKAEAWNIKVIEGEATQSTEVQPTQPINWSEPKPLFQTDSPNNKGDLKEFLGGGGSGIVMGNGTLVFPLTAKDESNKVFSLITYSTDDGQKWEIPGGVSSVACRSPRVTEWEEGTLLMVTYCEDGRKVFESRDMGKTWTEAFGTLPGVWLKSGPELPEVSLRVDALITATIEGRKVMLYTQKVRHFLEVDEPNALHLWVTDNNRTFHLGPFSVDCAENKTFANTLLYSDDALHLLQAKGDHESTAVSLARLTEELNTI
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                                          (00:05:49)
[INFO]       Auto_mut: Residue number 341 from chain A and a score of 1.698 (phenylalanine)        
                       selected for automated muatation                                            (00:05:51)
[INFO]       Auto_mut: Residue number 297 from chain A and a score of 1.336 (phenylalanine)        
                       selected for automated muatation                                            (00:05:51)
[INFO]       Auto_mut: Residue number 342 from chain A and a score of 1.271 (leucine) selected for 
                       automated muatation                                                         (00:05:51)
[INFO]       Auto_mut: Residue number 17 from chain A and a score of 1.044 (tyrosine) selected for 
                       automated muatation                                                         (00:05:51)
[INFO]       Auto_mut: Residue number 1 from chain A and a score of 0.754 omitted from automated   
                       muatation (excluded by the user).                                           (00:05:51)
[INFO]       Auto_mut: Residue number 154 from chain A and a score of 0.730 (tyrosine) selected    
                       for automated muatation                                                     (00:05:51)
[INFO]       Auto_mut: Residue number 256 from chain A and a score of 0.714 (valine) selected for  
                       automated muatation                                                         (00:05:51)
[INFO]       Auto_mut: Mutating residue number 341 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 341 from chain A (phenylalanine) into aspartic acid (00:05:51)
[INFO]       Auto_mut: Mutating residue number 297 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 297 from chain A (phenylalanine) into glutamic acid (00:05:51)
[INFO]       Auto_mut: Mutating residue number 341 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 341 from chain A (phenylalanine) into glutamic acid (00:05:51)
[INFO]       Auto_mut: Mutating residue number 341 from chain A (phenylalanine) into arginine      (00:08:40)
[INFO]       Auto_mut: Mutating residue number 297 from chain A (phenylalanine) into lysine        (00:08:43)
[INFO]       Auto_mut: Mutating residue number 341 from chain A (phenylalanine) into lysine        (00:08:48)
[INFO]       Auto_mut: Mutating residue number 297 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 297 from chain A (phenylalanine) into aspartic acid (00:11:44)
[INFO]       Auto_mut: Mutating residue number 342 from chain A (leucine) into glutamic acid       (00:11:46)
[INFO]       Auto_mut: Mutating residue number 342 from chain A (leucine) into aspartic acid       (00:11:58)
[INFO]       Auto_mut: Mutating residue number 297 from chain A (phenylalanine) into arginine      (00:14:33)
[INFO]       Auto_mut: Mutating residue number 342 from chain A (leucine) into lysine              (00:14:39)
[INFO]       Auto_mut: Mutating residue number 342 from chain A (leucine) into arginine            (00:14:48)
[INFO]       Auto_mut: Mutating residue number 17 from chain A (tyrosine) into glutamic acid       (00:17:33)
[INFO]       Auto_mut: Mutating residue number 17 from chain A (tyrosine) into aspartic acid       (00:17:34)
[INFO]       Auto_mut: Mutating residue number 154 from chain A (tyrosine) into glutamic acid      (00:17:42)
[INFO]       Auto_mut: Mutating residue number 17 from chain A (tyrosine) into lysine              (00:20:21)
[INFO]       Auto_mut: Mutating residue number 17 from chain A (tyrosine) into arginine            (00:20:24)
[INFO]       Auto_mut: Mutating residue number 154 from chain A (tyrosine) into lysine             (00:20:40)
[INFO]       Auto_mut: Mutating residue number 154 from chain A (tyrosine) into aspartic acid      (00:23:14)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (valine) into glutamic acid        (00:23:16)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (valine) into aspartic acid        (00:23:46)
[INFO]       Auto_mut: Mutating residue number 154 from chain A (tyrosine) into arginine           (00:26:08)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (valine) into lysine               (00:26:14)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (valine) into arginine             (00:26:41)
[INFO]       Auto_mut: Effect of mutation residue number 341 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 0.0043 kcal/mol, Difference in average    
                       score from the base case: -0.0178                                           (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 341 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.4476 kcal/mol, Difference in average score     
                       from the base case: -0.0152                                                 (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 341 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 0.9213 kcal/mol, Difference in average    
                       score from the base case: -0.0179                                           (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 341 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.3591 kcal/mol, Difference in average score   
                       from the base case: -0.0209                                                 (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 297 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 0.1059 kcal/mol, Difference in average    
                       score from the base case: -0.0230                                           (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 297 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.1994 kcal/mol, Difference in average score     
                       from the base case: -0.0235                                                 (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 297 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 0.2549 kcal/mol, Difference in average    
                       score from the base case: -0.0247                                           (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 297 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.2637 kcal/mol, Difference in average score   
                       from the base case: -0.0268                                                 (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 342 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.2629 kcal/mol, Difference in average score from  
                       the base case: -0.0133                                                      (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 342 from chain A (leucine) into lysine:   
                       Energy difference: -0.3936 kcal/mol, Difference in average score from the   
                       base case: -0.0119                                                          (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 342 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.1922 kcal/mol, Difference in average score from  
                       the base case: -0.0155                                                      (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 342 from chain A (leucine) into arginine: 
                       Energy difference: -0.4553 kcal/mol, Difference in average score from the   
                       base case: -0.0089                                                          (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 17 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: -0.3886 kcal/mol, Difference in average score from 
                       the base case: -0.0125                                                      (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 17 from chain A (tyrosine) into lysine:   
                       Energy difference: -0.3390 kcal/mol, Difference in average score from the   
                       base case: -0.0112                                                          (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 17 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: -1.3669 kcal/mol, Difference in average score from 
                       the base case: -0.0099                                                      (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 17 from chain A (tyrosine) into arginine: 
                       Energy difference: -0.5255 kcal/mol, Difference in average score from the   
                       base case: -0.0125                                                          (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 154 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 0.0719 kcal/mol, Difference in average score from  
                       the base case: -0.0165                                                      (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 154 from chain A (tyrosine) into lysine:  
                       Energy difference: -0.1598 kcal/mol, Difference in average score from the   
                       base case: -0.0174                                                          (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 154 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: -0.2629 kcal/mol, Difference in average score from 
                       the base case: -0.0152                                                      (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 154 from chain A (tyrosine) into          
                       arginine: Energy difference: -0.1622 kcal/mol, Difference in average score  
                       from the base case: -0.0160                                                 (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.1196 kcal/mol, Difference in average score from  
                       the base case: -0.0127                                                      (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (valine) into lysine:    
                       Energy difference: 0.2028 kcal/mol, Difference in average score from the    
                       base case: -0.0108                                                          (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (valine) into aspartic   
                       acid: Energy difference: 1.0066 kcal/mol, Difference in average score from  
                       the base case: -0.0139                                                      (00:29:40)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (valine) into arginine:  
                       Energy difference: 0.2733 kcal/mol, Difference in average score from the    
                       base case: -0.0121                                                          (00:29:40)
[INFO]       Main:     Simulation completed successfully.                                          (00:29:49)
Show buried residues
Minimal score value
-3.8643
Maximal score value
1.6982
Average score
-0.8244
Total score value
-340.481
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 0.7541
2 G A -0.2054
3 S A -0.6561
4 S A -1.1454
5 H A -2.0373
6 H A -2.3943
7 H A -2.6099
8 H A -2.5759
9 H A -2.3933
10 H A -2.0269
11 S A -1.5422
12 S A -1.5092
13 G A -1.8394
14 E A -2.3035
15 N A -1.3546
16 L A 0.3150
17 Y A 1.0444
18 F A 0.5419
19 Q A -0.9962
20 G A -1.0786
21 A A 0.0000
22 M A 0.6283
23 A A 0.0000
24 I A 0.0000
25 A A -0.2850
26 M A 0.0000
27 L A 0.0000
28 V A -0.3606
29 P A -1.2385
30 N A -2.1828
31 K A -2.4326
32 T A 0.0000
33 Q A -2.0485
34 V A 0.0000
35 V A -1.4183
36 P A -1.7521
37 K A -1.5911
38 S A -1.3631
39 G A -1.5248
40 G A -2.0220
41 E A -2.7637
42 G A -2.3222
43 K A -2.5526
44 V A -1.2079
45 K A 0.0000
46 D A -1.4085
47 I A 0.0000
48 F A 0.0000
49 A A -0.1124
50 S A -0.0439
51 P A 0.0000
52 A A 0.0000
53 L A 0.0000
54 V A 0.0000
55 R A -1.0122
56 A A 0.0000
57 G A -1.4496
58 G A -1.2468
59 V A 0.0000
60 M A 0.0000
61 I A 0.0000
62 A A 0.0000
63 F A 0.0000
64 V A 0.0000
65 E A 0.0000
66 G A 0.0000
67 R A -0.7649
68 T A -0.9874
69 K A -1.3520
70 N A -1.5633
71 K A -1.8268
72 L A -0.5962
73 F A -0.6969
74 P A -1.0030
75 E A -1.3401
76 V A 0.2520
77 I A 0.4194
78 D A -1.4211
79 L A 0.0000
80 S A 0.0000
81 S A 0.0000
82 S A 0.0000
83 D A -0.7138
84 I A 0.0000
85 V A 0.0000
86 A A 0.0000
87 G A 0.0000
88 Y A 0.0000
89 I A 0.0000
90 K A -1.2403
91 A A -1.0654
92 P A 0.0000
93 E A -2.3873
94 T A -1.3603
95 W A 0.0000
96 Q A -1.4391
97 S A -1.1715
98 L A 0.0000
99 V A -0.2992
100 A A -0.5908
101 E A -0.9106
102 V A 0.0000
103 T A -0.9570
104 K A -1.6535
105 E A -1.7769
106 Y A -0.1698
107 W A -0.6028
108 Q A -0.8659
109 A A 0.0000
110 H A 0.0000
111 T A 0.0000
112 V A 0.0000
113 L A 0.0000
114 E A -1.2623
115 S A -1.1133
116 A A -1.2468
117 N A -2.4149
118 N A -2.5980
119 S A -2.2283
120 N A -2.3427
121 H A -1.8526
122 R A -2.6243
123 V A 0.0000
124 G A 0.0000
125 V A 0.0000
126 A A 0.0000
127 R A -0.6878
128 L A -0.1427
129 P A 0.0000
130 T A 0.0000
131 G A 0.0000
132 I A 0.0000
133 T A -1.1514
134 R A -1.9258
135 G A -1.7774
136 N A -2.1482
137 K A -2.7357
138 V A 0.0000
139 F A 0.0000
140 L A 0.0000
141 L A 0.0000
142 V A 0.0000
143 G A 0.0000
144 S A -0.6597
145 Y A 0.0000
146 E A -1.3764
147 E A -1.6789
148 R A -1.7022
149 R A -1.0816
150 E A -0.7546
151 I A 0.6732
152 D A -1.3888
153 D A -1.3149
154 Y A 0.7298
155 I A 0.4335
156 W A -0.3519
157 K A -1.4131
158 A A -1.0412
159 E A -0.9798
160 A A -0.5946
161 W A -0.7531
162 N A -1.2885
163 I A 0.0000
164 K A -0.9612
165 V A 0.0000
166 I A 0.0000
167 E A -1.6265
168 G A 0.0000
169 E A -2.5804
170 A A 0.0000
171 T A -1.7348
172 Q A -1.7617
173 S A -1.2950
174 T A -1.0257
175 E A -1.6361
176 V A 0.2883
177 Q A -1.1033
178 P A -1.2436
179 T A -0.6617
180 Q A -0.9975
181 P A 0.0000
182 I A 0.0000
183 N A -1.8825
184 W A -1.6262
185 S A -1.6158
186 E A -2.1046
187 P A -1.3587
188 K A -1.4137
189 P A -1.1275
190 L A 0.0000
191 F A -1.5329
192 Q A -2.1979
193 T A -1.6505
194 D A -2.4868
195 S A -2.2841
196 P A -2.5054
197 N A -3.6027
198 N A -3.2178
199 K A -3.3690
200 G A -3.1405
201 D A -3.8643
202 L A -2.8793
203 K A -3.0770
204 E A -1.7310
205 F A 0.0000
206 L A -0.4070
207 G A 0.0000
208 G A 0.0000
209 G A 0.0000
210 G A 0.0000
211 S A 0.1341
212 G A 0.0000
213 I A 0.4025
214 V A 0.2947
215 M A 0.0000
216 G A -1.6049
217 N A -1.7552
218 G A -1.0728
219 T A 0.0000
220 L A 0.0000
221 V A 0.0000
222 F A 0.0000
223 P A 0.0000
224 L A 0.0000
225 T A -0.2334
226 A A 0.0000
227 K A -2.2681
228 D A -3.1823
229 E A -3.6086
230 S A -2.5392
231 N A -2.9913
232 K A -2.1217
233 V A -0.7978
234 F A 0.1815
235 S A 0.0000
236 L A 0.0000
237 I A 0.0000
238 T A 0.0000
239 Y A -0.5834
240 S A 0.0000
241 T A -1.4517
242 D A -1.6753
243 D A -2.2325
244 G A 0.0000
245 Q A -2.4856
246 K A -3.0208
247 W A -2.0330
248 E A -2.0459
249 I A -0.9992
250 P A 0.0000
251 G A -1.7509
252 G A 0.0000
253 V A 0.5076
254 S A 0.0000
255 S A 0.0879
256 V A 0.7135
257 A A -0.6471
258 C A 0.0000
259 R A -0.7804
260 S A -0.4315
261 P A 0.0000
262 R A -0.2263
263 V A 0.0000
264 T A 0.0000
265 E A -0.9577
266 W A -1.5718
267 E A -3.1604
268 E A -3.3477
269 G A -2.4800
270 T A 0.0000
271 L A 0.0000
272 L A 0.0000
273 M A 0.0000
274 V A 0.0000
275 T A 0.0000
276 Y A 0.0000
277 C A 0.0000
278 E A -3.0371
279 D A -3.2276
280 G A 0.0000
281 R A 0.0000
282 K A -0.9377
283 V A 0.0000
284 F A 0.0000
285 E A -0.8443
286 S A 0.0000
287 R A -2.9219
288 D A -2.0057
289 M A -1.1414
290 G A 0.0000
291 K A -2.1075
292 T A -1.3121
293 W A -0.9126
294 T A -0.5451
295 E A -0.7094
296 A A 0.1364
297 F A 1.3361
298 G A 0.0981
299 T A -0.2233
300 L A 0.0000
301 P A -0.4617
302 G A -0.0398
303 V A 0.0000
304 W A 0.0198
305 L A -0.8829
306 K A -2.3282
307 S A -2.3186
308 G A -1.7768
309 P A -1.2236
310 E A -2.0763
311 L A -1.2638
312 P A -0.8541
313 E A -1.0316
314 V A 0.3333
315 S A 0.0000
316 L A 0.0000
317 R A -0.2679
318 V A 0.0000
319 D A 0.0000
320 A A 0.0000
321 L A 0.0000
322 I A 0.2744
323 T A -0.0610
324 A A 0.0000
325 T A -1.7711
326 I A -2.0062
327 E A -2.7908
328 G A -2.4293
329 R A -3.0711
330 K A -2.4739
331 V A 0.0000
332 M A 0.0000
333 L A 0.0000
334 Y A 0.0000
335 T A 0.0000
336 Q A 0.0000
337 K A 0.0000
338 V A 0.1262
339 R A -0.2923
340 H A -0.1475
341 F A 1.6982
342 L A 1.2714
343 E A -0.8490
344 V A 0.3334
345 D A -1.8000
346 E A -1.6953
347 P A -1.0748
348 N A -0.5112
349 A A -0.1076
350 L A 0.0000
351 H A 0.0000
352 L A 0.0000
353 W A 0.1527
354 V A 0.0000
355 T A 0.0000
356 D A -1.8293
357 N A -1.9789
358 N A -2.5809
359 R A -2.4814
360 T A -1.0515
361 F A 0.3575
362 H A -0.1146
363 L A -0.2382
364 G A -0.5706
365 P A -0.2751
366 F A 0.0000
367 S A 0.0000
368 V A 0.6301
369 D A 0.0000
370 C A -0.8032
371 A A -1.1143
372 E A -2.5495
373 N A -2.0148
374 K A -1.4928
375 T A 0.0000
376 F A -0.1272
377 A A 0.0916
378 N A 0.0000
379 T A 0.0000
380 L A 0.0000
381 L A 0.0378
382 Y A -0.4639
383 S A -1.3832
384 D A -2.8864
385 D A -2.7728
386 A A -1.5730
387 L A 0.0000
388 H A 0.0000
389 L A 0.0000
390 L A 0.0000
391 Q A 0.0000
392 A A 0.0000
393 K A -1.0650
394 G A 0.0000
395 D A -2.7961
396 H A -2.6813
397 E A -2.7245
398 S A -2.1354
399 T A 0.0000
400 A A -0.2503
401 V A 0.0000
402 S A 0.1099
403 L A 0.0000
404 A A 0.0000
405 R A -0.5231
406 L A 0.0000
407 T A -1.4571
408 E A -2.4564
409 E A 0.0000
410 L A -1.0875
411 N A -1.6829
412 T A -0.8180
413 I A -0.2243
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
YD17A -1.3669 -0.0099 View CSV PDB
YR17A -0.5255 -0.0125 View CSV PDB
YD154A -0.2629 -0.0152 View CSV PDB
YK154A -0.1598 -0.0174 View CSV PDB
LK342A -0.3936 -0.0119 View CSV PDB
LR342A -0.4553 -0.0089 View CSV PDB
FE341A 0.0043 -0.0178 View CSV PDB
FE297A 0.1059 -0.023 View CSV PDB
FK297A 0.1994 -0.0235 View CSV PDB
VE256A 0.1196 -0.0127 View CSV PDB
FR341A 0.3591 -0.0209 View CSV PDB
VK256A 0.2028 -0.0108 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018