Project name: E2-Indian

Status: done

Started: 2024-07-19 10:13:37
Settings
Chain sequence(s) B: NFNVYKATRPYLAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDDSHDWTKLRYMDNHMPADAERAGLFVRTSAPCTITGTMGHFILARCPKGETLTAGFTDSRKISHSCTHPFHHDPPVIGREKFHSRPQHGKELPCSTYVQSTAATTEEIEVHMPPDTPDRTLMSQQSGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSPLVPRNAELGDRKGKIHIPFPLANATCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNMGEEPNYQEEWVMHKKEVVLTVPTEGLEVTWGNNEPYKYWPQLSTNGTAHGHPHEIILYYYELYPTMTVVVVSVATFILLSMVGMAAGMCICARRRCITPYELTPGATVPFLLSLVCCVRTAKA
input PDB
Selected Chain(s) B
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 B 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                                          (00:05:00)
[INFO]       Auto_mut: Residue number 376 from chain B and a score of 4.902 (phenylalanine)        
                       selected for automated muatation                                            (00:05:02)
[INFO]       Auto_mut: Residue number 377 from chain B and a score of 4.857 (isoleucine) selected  
                       for automated muatation                                                     (00:05:02)
[INFO]       Auto_mut: Residue number 378 from chain B and a score of 4.570 (leucine) selected for 
                       automated muatation                                                         (00:05:02)
[INFO]       Auto_mut: Residue number 373 from chain B and a score of 4.380 (valine) selected for  
                       automated muatation                                                         (00:05:02)
[INFO]       Auto_mut: Residue number 379 from chain B and a score of 4.357 (leucine) selected for 
                       automated muatation                                                         (00:05:02)
[INFO]       Auto_mut: Residue number 370 from chain B and a score of 4.318 (valine) selected for  
                       automated muatation                                                         (00:05:02)
[INFO]       Auto_mut: Mutating residue number 377 from chain B (isoleucine) into glutamic acid    (00:05:02)
[INFO]       Auto_mut: Mutating residue number 376 from chain B (phenylalanine) into aspartic acid 
                       Mutating residue number 376 from chain B (phenylalanine) into aspartic acid (00:05:02)
[INFO]       Auto_mut: Mutating residue number 376 from chain B (phenylalanine) into glutamic acid 
                       Mutating residue number 376 from chain B (phenylalanine) into glutamic acid (00:05:02)
[INFO]       Auto_mut: Mutating residue number 377 from chain B (isoleucine) into lysine           (00:07:04)
[INFO]       Auto_mut: Mutating residue number 376 from chain B (phenylalanine) into arginine      (00:07:04)
[INFO]       Auto_mut: Mutating residue number 376 from chain B (phenylalanine) into lysine        (00:07:08)
[INFO]       Auto_mut: Mutating residue number 377 from chain B (isoleucine) into aspartic acid    (00:09:13)
[INFO]       Auto_mut: Mutating residue number 378 from chain B (leucine) into glutamic acid       (00:09:16)
[INFO]       Auto_mut: Mutating residue number 378 from chain B (leucine) into aspartic acid       (00:09:20)
[INFO]       Auto_mut: Mutating residue number 377 from chain B (isoleucine) into arginine         (00:11:13)
[INFO]       Auto_mut: Mutating residue number 378 from chain B (leucine) into lysine              (00:11:19)
[INFO]       Auto_mut: Mutating residue number 378 from chain B (leucine) into arginine            (00:11:30)
[INFO]       Auto_mut: Mutating residue number 373 from chain B (valine) into glutamic acid        (00:13:19)
[INFO]       Auto_mut: Mutating residue number 373 from chain B (valine) into aspartic acid        (00:13:25)
[INFO]       Auto_mut: Mutating residue number 379 from chain B (leucine) into glutamic acid       (00:13:43)
[INFO]       Auto_mut: Mutating residue number 373 from chain B (valine) into lysine               (00:15:22)
[INFO]       Auto_mut: Mutating residue number 373 from chain B (valine) into arginine             (00:15:26)
[INFO]       Auto_mut: Mutating residue number 379 from chain B (leucine) into lysine              (00:15:48)
[INFO]       Auto_mut: Mutating residue number 379 from chain B (leucine) into aspartic acid       (00:17:32)
[INFO]       Auto_mut: Mutating residue number 370 from chain B (valine) into glutamic acid        (00:17:37)
[INFO]       Auto_mut: Mutating residue number 370 from chain B (valine) into aspartic acid        (00:17:54)
[INFO]       Auto_mut: Mutating residue number 379 from chain B (leucine) into arginine            (00:19:33)
[INFO]       Auto_mut: Mutating residue number 370 from chain B (valine) into lysine               (00:19:38)
[INFO]       Auto_mut: Mutating residue number 370 from chain B (valine) into arginine             (00:19:54)
[INFO]       Auto_mut: Effect of mutation residue number 376 from chain B (phenylalanine) into     
                       glutamic acid: Energy difference: 0.3865 kcal/mol, Difference in average    
                       score from the base case: -0.0419                                           (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 376 from chain B (phenylalanine) into     
                       lysine: Energy difference: 0.3252 kcal/mol, Difference in average score     
                       from the base case: -0.0443                                                 (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 376 from chain B (phenylalanine) into     
                       aspartic acid: Energy difference: 0.8973 kcal/mol, Difference in average    
                       score from the base case: -0.0416                                           (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 376 from chain B (phenylalanine) into     
                       arginine: Energy difference: 0.1404 kcal/mol, Difference in average score   
                       from the base case: -0.0433                                                 (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 377 from chain B (isoleucine) into        
                       glutamic acid: Energy difference: 0.2826 kcal/mol, Difference in average    
                       score from the base case: -0.0479                                           (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 377 from chain B (isoleucine) into        
                       lysine: Energy difference: 0.1165 kcal/mol, Difference in average score     
                       from the base case: -0.0481                                                 (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 377 from chain B (isoleucine) into        
                       aspartic acid: Energy difference: 0.7173 kcal/mol, Difference in average    
                       score from the base case: -0.0445                                           (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 377 from chain B (isoleucine) into        
                       arginine: Energy difference: -0.1081 kcal/mol, Difference in average score  
                       from the base case: -0.0415                                                 (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 378 from chain B (leucine) into glutamic  
                       acid: Energy difference: 0.5166 kcal/mol, Difference in average score from  
                       the base case: -0.0403                                                      (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 378 from chain B (leucine) into lysine:   
                       Energy difference: 0.0652 kcal/mol, Difference in average score from the    
                       base case: -0.0384                                                          (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 378 from chain B (leucine) into aspartic  
                       acid: Energy difference: 1.0536 kcal/mol, Difference in average score from  
                       the base case: -0.0393                                                      (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 378 from chain B (leucine) into arginine: 
                       Energy difference: 0.0229 kcal/mol, Difference in average score from the    
                       base case: -0.0403                                                          (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 373 from chain B (valine) into glutamic   
                       acid: Energy difference: -0.2066 kcal/mol, Difference in average score from 
                       the base case: -0.0378                                                      (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 373 from chain B (valine) into lysine:    
                       Energy difference: -0.3770 kcal/mol, Difference in average score from the   
                       base case: -0.0342                                                          (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 373 from chain B (valine) into aspartic   
                       acid: Energy difference: 0.4339 kcal/mol, Difference in average score from  
                       the base case: -0.0356                                                      (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 373 from chain B (valine) into arginine:  
                       Energy difference: -0.0021 kcal/mol, Difference in average score from the   
                       base case: -0.0425                                                          (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 379 from chain B (leucine) into glutamic  
                       acid: Energy difference: 0.6277 kcal/mol, Difference in average score from  
                       the base case: -0.0419                                                      (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 379 from chain B (leucine) into lysine:   
                       Energy difference: 0.3243 kcal/mol, Difference in average score from the    
                       base case: -0.0421                                                          (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 379 from chain B (leucine) into aspartic  
                       acid: Energy difference: 1.2190 kcal/mol, Difference in average score from  
                       the base case: -0.0435                                                      (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 379 from chain B (leucine) into arginine: 
                       Energy difference: 0.5509 kcal/mol, Difference in average score from the    
                       base case: -0.0477                                                          (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 370 from chain B (valine) into glutamic   
                       acid: Energy difference: -0.7404 kcal/mol, Difference in average score from 
                       the base case: -0.0427                                                      (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 370 from chain B (valine) into lysine:    
                       Energy difference: -0.3945 kcal/mol, Difference in average score from the   
                       base case: -0.0438                                                          (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 370 from chain B (valine) into aspartic   
                       acid: Energy difference: -0.3899 kcal/mol, Difference in average score from 
                       the base case: -0.0431                                                      (00:22:06)
[INFO]       Auto_mut: Effect of mutation residue number 370 from chain B (valine) into arginine:  
                       Energy difference: -0.1596 kcal/mol, Difference in average score from the   
                       base case: -0.0465                                                          (00:22:06)
[INFO]       Main:     Simulation completed successfully.                                          (00:22:14)
Show buried residues
Minimal score value
-3.5878
Maximal score value
4.9025
Average score
-0.6109
Total score value
-255.9873
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
5 N B -1.5673
6 F B -1.1273
7 N B -1.7663
8 V B -0.7067
9 Y B 0.0000
10 K B -1.9306
11 A B -1.1911
12 T B 0.0000
13 R B 0.0000
14 P B 0.0000
15 Y B 0.0000
16 L B -0.3357
17 A B 0.0000
18 H B -0.9392
19 C B 0.0000
20 P B -1.1367
21 D B -1.7277
22 C B -1.3824
23 G B -1.6675
24 E B -2.5726
25 G B -2.0561
26 H B -2.0085
27 S B -1.4775
28 C B -0.8193
29 H B -1.1535
30 S B 0.0000
31 P B 0.0000
32 V B 0.0000
33 A B 0.0000
34 L B 0.0000
35 E B -0.7330
36 R B -1.7087
37 I B -1.3768
38 R B -2.4634
39 N B -2.4375
40 E B -2.4257
41 A B 0.0000
42 T B -0.6563
43 D B -0.5730
44 G B -1.3155
45 T B 0.0000
46 L B 0.0000
47 K B 0.0000
48 I B 0.0000
49 Q B 0.0000
50 V B 0.0000
51 S B 0.0000
52 L B 0.0000
53 Q B 0.0000
54 I B 0.0000
55 G B 0.0000
56 I B 0.0000
57 K B -2.3812
58 T B -1.8273
59 D B -2.6204
60 D B -2.4276
61 S B -2.0229
62 H B -1.9349
63 D B -1.0062
64 W B -0.4301
65 T B -1.1307
66 K B -1.8938
67 L B 0.0000
68 R B 0.0000
69 Y B 0.0000
70 M B 0.0000
71 D B -1.6725
72 N B -1.7357
73 H B -0.8286
74 M B 0.0357
75 P B -0.5196
76 A B -0.8844
77 D B -1.9547
78 A B 0.0000
79 E B -1.9330
80 R B -1.5715
81 A B -0.7598
82 G B -0.5070
83 L B -0.1585
84 F B 0.0456
85 V B 0.0000
86 R B -1.2654
87 T B -1.8195
88 S B -1.3821
89 A B -0.8323
90 P B -0.7830
91 C B -0.6704
92 T B -0.3416
93 I B 0.3233
94 T B -0.2021
95 G B 0.0000
96 T B -0.0749
97 M B 0.0000
98 G B 0.0000
99 H B 0.0000
100 F B 0.0000
101 I B 0.0000
102 L B 0.0000
103 A B 0.0000
104 R B -1.2584
105 C B -1.2919
106 P B -1.9332
107 K B -3.0371
108 G B -2.5678
109 E B -2.8450
110 T B -1.7172
111 L B 0.0000
112 T B -0.7991
113 A B 0.0000
114 G B 0.0000
115 F B 0.0000
116 T B -0.9368
117 D B 0.0000
118 S B -1.8784
119 R B -2.4793
120 K B -2.2393
121 I B -0.5770
122 S B -0.5299
123 H B -0.2235
124 S B -0.1505
125 C B 0.0000
126 T B -0.7150
127 H B -0.9022
128 P B -1.0318
129 F B -1.0338
130 H B -2.2972
131 H B 0.0000
132 D B -2.7825
133 P B -1.3070
134 P B -0.0818
135 V B 0.8233
136 I B 0.2913
137 G B -0.4920
138 R B -0.4708
139 E B 0.0000
140 K B -0.7402
141 F B -0.9609
142 H B -1.4668
143 S B -1.5222
144 R B -2.5442
145 P B -2.4761
146 Q B -2.6347
147 H B -2.8691
148 G B -3.0964
149 K B -2.9160
150 E B -3.0877
151 L B -1.3542
152 P B -1.0647
153 C B 0.0000
154 S B -0.6510
155 T B -0.4224
156 Y B 0.0000
157 V B 0.0130
158 Q B -0.8820
159 S B -0.3993
160 T B -0.3810
161 A B -0.2762
162 A B -0.4872
163 T B -0.9976
164 T B -1.4338
165 E B -2.8734
166 E B -3.3457
167 I B -2.1432
168 E B -3.0530
169 V B 0.0000
170 H B 0.0000
171 M B -1.3739
172 P B 0.0000
173 P B -1.2590
174 D B -1.4213
175 T B -0.9292
176 P B -1.1792
177 D B -1.6344
178 R B -2.3707
179 T B -1.0695
180 L B 0.0000
181 M B 0.0000
182 S B -1.2220
183 Q B -1.8060
184 Q B -1.5784
185 S B -1.3666
186 G B -1.7954
187 N B -2.0561
188 V B 0.0000
189 K B -1.2818
190 I B 0.0000
191 T B -0.8992
192 V B -1.1928
193 N B -1.6763
194 G B -1.3249
195 Q B -1.2349
196 T B -0.5478
197 V B 0.0000
198 R B -0.9491
199 Y B 0.0000
200 K B -2.4216
201 C B 0.0000
202 N B -2.7758
203 C B -2.1383
204 G B -1.7789
205 G B -1.7585
206 S B -1.8846
207 N B -2.8248
208 E B -2.9740
209 G B -1.0134
210 L B 0.6115
211 T B -0.0313
212 T B -0.4528
213 T B -0.6929
214 D B -1.4428
215 K B -0.9910
216 V B -0.7218
217 I B 0.0000
218 N B -2.3516
219 N B -2.5038
220 C B 0.0000
221 K B -3.0309
222 V B -2.5233
223 D B -2.9803
224 Q B -2.4953
225 C B 0.0000
226 H B -2.3174
227 A B 0.0000
228 A B 0.0000
229 V B 0.0000
230 T B -0.8850
231 N B -1.4276
232 H B -2.0824
233 K B -2.3539
234 K B -1.5811
235 W B -1.0050
236 Q B 0.0000
237 Y B 0.0000
238 N B -1.1491
239 S B 0.0000
240 P B -0.3396
241 L B 0.3866
242 V B -0.0973
243 P B -1.0402
244 R B -2.4269
245 N B 0.0000
246 A B -1.3789
247 E B -2.1087
248 L B -1.2906
249 G B -2.1142
250 D B -3.1034
251 R B -3.1828
252 K B -3.2032
253 G B -2.6895
254 K B -3.2348
255 I B 0.0000
256 H B -1.6642
257 I B -0.9961
258 P B 0.0000
259 F B 0.0000
260 P B 0.1678
261 L B 0.4748
262 A B 0.0116
263 N B -1.0549
264 A B -0.8860
265 T B -1.2911
266 C B -1.8745
267 R B -3.5878
268 V B 0.0000
269 P B 0.0000
270 K B -3.4856
271 A B -2.6377
272 R B -2.9467
273 N B -1.7835
274 P B 0.0000
275 T B 0.0808
276 V B 1.2599
277 T B 1.1792
278 Y B 0.9791
279 G B -0.7417
280 K B -2.0030
281 N B -1.2263
282 Q B -0.5301
283 V B 0.0000
284 I B 1.0352
285 M B 0.0000
286 L B -0.3915
287 L B 0.0000
288 Y B -1.7035
289 P B -1.8679
290 D B -2.4587
291 H B -1.3489
292 P B -0.2985
293 T B 0.0000
294 L B 0.0877
295 L B 0.0000
296 S B 0.0000
297 Y B -1.2785
298 R B -2.4113
299 N B -2.5257
300 M B -1.9687
301 G B -2.6357
302 E B -3.2384
303 E B -3.3478
304 P B -2.5678
305 N B -2.4714
306 Y B -1.3794
307 Q B -2.0170
308 E B -1.5370
309 E B -0.4403
310 W B 0.7764
311 V B 0.0000
312 M B -0.0893
313 H B -1.8981
314 K B -2.7617
315 K B -2.2779
316 E B -2.0443
317 V B 0.0000
318 V B 0.9854
319 L B 0.0000
320 T B -0.3441
321 V B 0.0000
322 P B -0.7367
323 T B -0.7886
324 E B -1.8813
325 G B 0.0000
326 L B 0.0000
327 E B -1.0297
328 V B 0.0000
329 T B -1.1069
330 W B 0.0000
331 G B 0.0000
332 N B -1.6875
333 N B -2.1900
334 E B -2.3860
335 P B -1.3925
336 Y B -0.8928
337 K B -1.6408
338 Y B -0.5953
339 W B 0.0455
340 P B -0.4676
341 Q B -0.4404
342 L B 0.6772
343 S B -0.5707
344 T B -0.8096
345 N B -0.7914
346 G B -0.1562
347 T B -0.4877
348 A B -1.0733
349 H B -1.6530
350 G B -1.8951
351 H B -2.0670
352 P B -1.8750
353 H B -2.2314
354 E B -1.7296
355 I B 0.1720
356 I B 1.3431
357 L B 1.3427
358 Y B 1.0705
359 Y B 1.9985
360 Y B 1.7531
361 E B 0.7490
362 L B 1.6940
363 Y B 2.0790
364 P B 1.4345
365 T B 1.2667
366 M B 2.3513
367 T B 2.7986
368 V B 3.4273
369 V B 3.9493
370 V B 4.3177
371 V B 4.1308
372 S B 3.5528
373 V B 4.3795
374 A B 3.7948
375 T B 3.6688
376 F B 4.9025
377 I B 4.8570
378 L B 4.5700
379 L B 4.3572
380 S B 3.1797
381 M B 3.3539
382 V B 3.3247
383 G B 1.8914
384 M B 2.3491
385 A B 1.9890
386 A B 1.6922
387 G B 1.7860
388 M B 2.0530
389 C B 1.4708
390 I B 1.8512
391 C B 0.7364
392 A B -0.2361
393 R B -0.9340
394 R B -2.2862
395 R B -2.4439
396 C B -0.8431
397 I B -0.9363
398 T B -1.1377
399 P B -0.2923
400 Y B 0.4774
401 E B -0.8382
402 L B 0.8844
403 T B 0.3272
404 P B -0.1590
405 G B -0.1556
406 A B 0.0654
407 T B 0.2188
408 V B 1.1525
409 P B 1.3718
410 F B 2.9076
411 L B 2.4059
412 L B 1.8528
413 S B 1.6071
414 L B 3.0118
415 V B 3.0152
416 C B 2.1804
417 C B 1.0847
418 V B 0.9467
419 R B -1.2302
420 T B -0.3311
421 A B -1.0121
422 K B -1.9434
423 A B -0.6052
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
VE370B -0.7404 -0.0427 View CSV PDB
VK370B -0.3945 -0.0438 View CSV PDB
VK373B -0.377 -0.0342 View CSV PDB
VE373B -0.2066 -0.0378 View CSV PDB
IR377B -0.1081 -0.0415 View CSV PDB
LR378B 0.0229 -0.0403 View CSV PDB
LK378B 0.0652 -0.0384 View CSV PDB
IK377B 0.1165 -0.0481 View CSV PDB
FR376B 0.1404 -0.0433 View CSV PDB
FK376B 0.3252 -0.0443 View CSV PDB
LK379B 0.3243 -0.0421 View CSV PDB
LR379B 0.5509 -0.0477 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018