Project name: E2-solubility

Status: done

Started: 2024-06-25 09:02:29
Settings
Chain sequence(s) M: NFNVYKATRPYLAHCPDCGEGHSCHSPIALERIRNEATDGTLKIQVSLQIGIKTDDSHDWTKLRYMDSHTPADAERAGLLVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKISHTCTHPFHHEPPVIGRERFHSRPQHGKELPCSTYVQSTAATAEEIEVHMPPDTPDRTLMTQQSGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKIDQCHAAVTNHKNWQYNSPLVPRNAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVTMLLYPDHPTLLSYRNMGQEPNYHEEWVTHKKEVTLTVPTEGLEVTWGNNEPYKYWPQMSTNGTAHGHPHEIILYYYELYPTMTVVIVSVASFVLLSMVGTAVGMCVCARRRCITPYELTPGATVPFLLSLLCCV
input PDB
Selected Chain(s) M
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 M 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                                          (00:04:34)
[INFO]       Auto_mut: Residue number 378 from chain M and a score of 4.354 (leucine) selected for 
                       automated muatation                                                         (00:04:37)
[INFO]       Auto_mut: Residue number 376 from chain M and a score of 4.293 (phenylalanine)        
                       selected for automated muatation                                            (00:04:37)
[INFO]       Auto_mut: Residue number 373 from chain M and a score of 4.250 (valine) selected for  
                       automated muatation                                                         (00:04:37)
[INFO]       Auto_mut: Residue number 377 from chain M and a score of 4.247 (valine) selected for  
                       automated muatation                                                         (00:04:37)
[INFO]       Auto_mut: Residue number 379 from chain M and a score of 3.991 (leucine) selected for 
                       automated muatation                                                         (00:04:37)
[INFO]       Auto_mut: Residue number 370 from chain M and a score of 3.967 (isoleucine) selected  
                       for automated muatation                                                     (00:04:37)
[INFO]       Auto_mut: Mutating residue number 378 from chain M (leucine) into glutamic acid       (00:04:37)
[INFO]       Auto_mut: Mutating residue number 378 from chain M (leucine) into aspartic acid       (00:04:37)
[INFO]       Auto_mut: Mutating residue number 376 from chain M (phenylalanine) into glutamic acid 
                       Mutating residue number 376 from chain M (phenylalanine) into glutamic acid (00:04:37)
[INFO]       Auto_mut: Mutating residue number 376 from chain M (phenylalanine) into lysine        (00:06:42)
[INFO]       Auto_mut: Mutating residue number 378 from chain M (leucine) into arginine            (00:06:42)
[INFO]       Auto_mut: Mutating residue number 378 from chain M (leucine) into lysine              (00:06:50)
[INFO]       Auto_mut: Mutating residue number 376 from chain M (phenylalanine) into aspartic acid 
                       Mutating residue number 376 from chain M (phenylalanine) into aspartic acid (00:08:55)
[INFO]       Auto_mut: Mutating residue number 373 from chain M (valine) into glutamic acid        (00:08:59)
[INFO]       Auto_mut: Mutating residue number 373 from chain M (valine) into aspartic acid        (00:09:00)
[INFO]       Auto_mut: Mutating residue number 376 from chain M (phenylalanine) into arginine      (00:10:59)
[INFO]       Auto_mut: Mutating residue number 373 from chain M (valine) into lysine               (00:11:06)
[INFO]       Auto_mut: Mutating residue number 373 from chain M (valine) into arginine             (00:11:10)
[INFO]       Auto_mut: Mutating residue number 377 from chain M (valine) into glutamic acid        (00:13:11)
[INFO]       Auto_mut: Mutating residue number 377 from chain M (valine) into aspartic acid        (00:13:23)
[INFO]       Auto_mut: Mutating residue number 379 from chain M (leucine) into glutamic acid       (00:13:24)
[INFO]       Auto_mut: Mutating residue number 377 from chain M (valine) into lysine               (00:15:14)
[INFO]       Auto_mut: Mutating residue number 377 from chain M (valine) into arginine             (00:15:28)
[INFO]       Auto_mut: Mutating residue number 379 from chain M (leucine) into lysine              (00:15:32)
[INFO]       Auto_mut: Mutating residue number 379 from chain M (leucine) into aspartic acid       (00:17:24)
[INFO]       Auto_mut: Mutating residue number 370 from chain M (isoleucine) into glutamic acid    (00:17:40)
[INFO]       Auto_mut: Mutating residue number 370 from chain M (isoleucine) into aspartic acid    (00:17:42)
[INFO]       Auto_mut: Mutating residue number 379 from chain M (leucine) into arginine            (00:19:27)
[INFO]       Auto_mut: Mutating residue number 370 from chain M (isoleucine) into arginine         (00:19:45)
[INFO]       Auto_mut: Mutating residue number 370 from chain M (isoleucine) into lysine           (00:19:52)
[INFO]       Auto_mut: Effect of mutation residue number 378 from chain M (leucine) into glutamic  
                       acid: Energy difference: 0.5432 kcal/mol, Difference in average score from  
                       the base case: -0.0258                                                      (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 378 from chain M (leucine) into lysine:   
                       Energy difference: 0.1943 kcal/mol, Difference in average score from the    
                       base case: -0.0279                                                          (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 378 from chain M (leucine) into aspartic  
                       acid: Energy difference: 1.0226 kcal/mol, Difference in average score from  
                       the base case: -0.0253                                                      (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 378 from chain M (leucine) into arginine: 
                       Energy difference: 0.1100 kcal/mol, Difference in average score from the    
                       base case: -0.0268                                                          (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 376 from chain M (phenylalanine) into     
                       glutamic acid: Energy difference: 0.2777 kcal/mol, Difference in average    
                       score from the base case: -0.0329                                           (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 376 from chain M (phenylalanine) into     
                       lysine: Energy difference: -0.3283 kcal/mol, Difference in average score    
                       from the base case: -0.0344                                                 (00:22:08)
[INFO]       Auto_mut: Effect of mutation residue number 376 from chain M (phenylalanine) into     
                       aspartic acid: Energy difference: 0.5893 kcal/mol, Difference in average    
                       score from the base case: -0.0341                                           (00:22:08)
[INFO]       Auto_mut: Effect of mutation residue number 376 from chain M (phenylalanine) into     
                       arginine: Energy difference: 0.0422 kcal/mol, Difference in average score   
                       from the base case: -0.0356                                                 (00:22:08)
[INFO]       Auto_mut: Effect of mutation residue number 373 from chain M (valine) into glutamic   
                       acid: Energy difference: -0.2061 kcal/mol, Difference in average score from 
                       the base case: -0.0300                                                      (00:22:08)
[INFO]       Auto_mut: Effect of mutation residue number 373 from chain M (valine) into lysine:    
                       Energy difference: -0.4327 kcal/mol, Difference in average score from the   
                       base case: -0.0313                                                          (00:22:08)
[INFO]       Auto_mut: Effect of mutation residue number 373 from chain M (valine) into aspartic   
                       acid: Energy difference: 0.1149 kcal/mol, Difference in average score from  
                       the base case: -0.0318                                                      (00:22:08)
[INFO]       Auto_mut: Effect of mutation residue number 373 from chain M (valine) into arginine:  
                       Energy difference: -0.5632 kcal/mol, Difference in average score from the   
                       base case: -0.0336                                                          (00:22:08)
[INFO]       Auto_mut: Effect of mutation residue number 377 from chain M (valine) into glutamic   
                       acid: Energy difference: -0.1211 kcal/mol, Difference in average score from 
                       the base case: -0.0261                                                      (00:22:08)
[INFO]       Auto_mut: Effect of mutation residue number 377 from chain M (valine) into lysine:    
                       Energy difference: -0.2986 kcal/mol, Difference in average score from the   
                       base case: -0.0259                                                          (00:22:08)
[INFO]       Auto_mut: Effect of mutation residue number 377 from chain M (valine) into aspartic   
                       acid: Energy difference: 0.3492 kcal/mol, Difference in average score from  
                       the base case: -0.0252                                                      (00:22:08)
[INFO]       Auto_mut: Effect of mutation residue number 377 from chain M (valine) into arginine:  
                       Energy difference: -0.1437 kcal/mol, Difference in average score from the   
                       base case: -0.0287                                                          (00:22:08)
[INFO]       Auto_mut: Effect of mutation residue number 379 from chain M (leucine) into glutamic  
                       acid: Energy difference: 0.1143 kcal/mol, Difference in average score from  
                       the base case: -0.0293                                                      (00:22:08)
[INFO]       Auto_mut: Effect of mutation residue number 379 from chain M (leucine) into lysine:   
                       Energy difference: 0.0507 kcal/mol, Difference in average score from the    
                       base case: -0.0271                                                          (00:22:08)
[INFO]       Auto_mut: Effect of mutation residue number 379 from chain M (leucine) into aspartic  
                       acid: Energy difference: 0.4521 kcal/mol, Difference in average score from  
                       the base case: -0.0283                                                      (00:22:08)
[INFO]       Auto_mut: Effect of mutation residue number 379 from chain M (leucine) into arginine: 
                       Energy difference: -0.2739 kcal/mol, Difference in average score from the   
                       base case: -0.0285                                                          (00:22:08)
[INFO]       Auto_mut: Effect of mutation residue number 370 from chain M (isoleucine) into        
                       glutamic acid: Energy difference: 1.2630 kcal/mol, Difference in average    
                       score from the base case: -0.0239                                           (00:22:08)
[INFO]       Auto_mut: Effect of mutation residue number 370 from chain M (isoleucine) into        
                       lysine: Energy difference: 0.5958 kcal/mol, Difference in average score     
                       from the base case: -0.0263                                                 (00:22:08)
[INFO]       Auto_mut: Effect of mutation residue number 370 from chain M (isoleucine) into        
                       aspartic acid: Energy difference: 1.8727 kcal/mol, Difference in average    
                       score from the base case: -0.0231                                           (00:22:08)
[INFO]       Auto_mut: Effect of mutation residue number 370 from chain M (isoleucine) into        
                       arginine: Energy difference: 1.1936 kcal/mol, Difference in average score   
                       from the base case: -0.0275                                                 (00:22:08)
[INFO]       Main:     Simulation completed successfully.                                          (00:22:15)
Show buried residues
Minimal score value
-3.7898
Maximal score value
4.3538
Average score
-0.7256
Total score value
-300.3798
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 M -1.5211
6 F M -1.4544
7 N M -1.9915
8 V M -0.9142
9 Y M 0.0000
10 K M -2.3950
11 A M -1.3708
12 T M -0.8608
13 R M -0.7895
14 P M 0.0000
15 Y M 0.0000
16 L M 0.1915
17 A M 0.0000
18 H M -1.1213
19 C M 0.0000
20 P M -1.3055
21 D M -1.9809
22 C M -1.6113
23 G M -1.8623
24 E M -2.6804
25 G M -2.1846
26 H M -2.0912
27 S M -1.6301
28 C M -1.0219
29 H M -1.1836
30 S M 0.0000
31 P M -0.3916
32 I M 0.0000
33 A M 0.0000
34 L M 0.0000
35 E M -1.3957
36 R M -2.3007
37 I M -1.7321
38 R M -2.7802
39 N M -3.0536
40 E M -2.7732
41 A M -1.6051
42 T M -0.8523
43 D M -1.0737
44 G M -1.7293
45 T M 0.0000
46 L M 0.0000
47 K M 0.0000
48 I M 0.0000
49 Q M -0.8225
50 V M 0.0000
51 S M 0.0000
52 L M 0.0000
53 Q M 0.0000
54 I M 0.0000
55 G M 0.0000
56 I M 0.0000
57 K M -1.9534
58 T M -2.0623
59 D M -2.7349
60 D M -2.8635
61 S M -2.0551
62 H M -1.9156
63 D M -1.0902
64 W M -0.2001
65 T M -0.8589
66 K M -1.7712
67 L M 0.0000
68 R M 0.0000
69 Y M 0.0000
70 M M -0.8121
71 D M -1.6648
72 S M -1.1043
73 H M -1.1507
74 T M -0.9343
75 P M -1.0145
76 A M -1.0224
77 D M -2.0124
78 A M -2.1325
79 E M -2.5180
80 R M -1.4827
81 A M -0.7124
82 G M -0.4760
83 L M 0.3478
84 L M 0.9571
85 V M 0.0000
86 R M -1.2739
87 T M 0.0000
88 S M -1.2518
89 A M -0.7401
90 P M -0.6971
91 C M -0.6222
92 T M -0.3005
93 I M 0.4102
94 T M -0.2287
95 G M -0.1522
96 T M 0.0063
97 M M 0.0000
98 G M 0.0000
99 H M -0.1562
100 F M 0.0000
101 I M 0.0000
102 L M 0.0000
103 A M 0.0000
104 R M -1.7699
105 C M -1.4012
106 P M -1.7606
107 K M -2.8965
108 G M -2.6030
109 E M -2.8718
110 T M -1.6750
111 L M 0.0000
112 T M -0.4480
113 V M 0.0000
114 G M 0.0316
115 F M 0.0000
116 T M -0.8484
117 D M -1.6645
118 S M -1.9245
119 R M -2.3757
120 K M -1.9637
121 I M 0.0653
122 S M -0.2379
123 H M -0.0840
124 T M -0.2588
125 C M 0.0000
126 T M -0.6447
127 H M -0.8285
128 P M -0.9570
129 F M -0.9906
130 H M -2.3344
131 H M -2.6544
132 E M -2.7404
133 P M -1.4286
134 P M -0.1843
135 V M 0.9321
136 I M 0.3351
137 G M -0.8782
138 R M -1.2918
139 E M 0.0000
140 R M -1.7975
141 F M -1.2401
142 H M -1.5887
143 S M -1.7639
144 R M -2.8476
145 P M -2.6242
146 Q M -2.5657
147 H M -2.7128
148 G M -3.2234
149 K M -3.3673
150 E M -3.1202
151 L M -1.3286
152 P M -0.7559
153 C M -0.5582
154 S M -0.4303
155 T M -0.3174
156 Y M 0.0000
157 V M 0.1530
158 Q M -0.8460
159 S M -0.5103
160 T M -0.4535
161 A M -0.3602
162 A M -0.5861
163 T M -0.8203
164 A M -1.2882
165 E M -2.6276
166 E M -3.1242
167 I M -2.0841
168 E M -2.8475
169 V M 0.0000
170 H M -2.7700
171 M M -1.8752
172 P M -1.7754
173 P M -2.0227
174 D M -2.8067
175 T M -1.4870
176 P M -1.6291
177 D M -1.6401
178 R M -2.2044
179 T M -1.0014
180 L M -0.8665
181 M M -1.0120
182 T M -1.5055
183 Q M -2.4880
184 Q M -2.3617
185 S M -1.8502
186 G M -2.2044
187 N M -2.1061
188 V M 0.0000
189 K M -1.0090
190 I M 0.0000
191 T M -1.0119
192 V M 0.0000
193 N M -1.8146
194 G M -1.2392
195 Q M -1.1535
196 T M -0.8441
197 V M 0.0000
198 R M -2.4224
199 Y M 0.0000
200 K M -3.3176
201 C M 0.0000
202 N M -2.9081
203 C M -2.3694
204 G M -1.5652
205 G M -1.3545
206 S M -2.2239
207 N M -2.9586
208 E M -3.1704
209 G M -1.3325
210 L M 0.2050
211 T M -0.4354
212 T M -0.8143
213 T M -1.3201
214 D M -2.1393
215 K M -1.0024
216 V M 0.4679
217 I M 0.0000
218 N M -1.9811
219 N M -2.5125
220 C M -2.6655
221 K M -3.2971
222 I M -2.2666
223 D M -3.0509
224 Q M -2.9529
225 C M -2.5882
226 H M -2.5970
227 A M 0.0000
228 A M 0.0000
229 V M -1.4137
230 T M -1.5811
231 N M -2.3472
232 H M -1.9986
233 K M -2.1701
234 N M -1.5572
235 W M -1.2388
236 Q M -0.6494
237 Y M -0.7360
238 N M -1.7094
239 S M 0.0000
240 P M -0.3516
241 L M 0.2356
242 V M -0.3623
243 P M -1.5789
244 R M -3.0822
245 N M -3.0888
246 A M -1.9415
247 E M -1.9834
248 L M -0.6459
249 G M -2.3796
250 D M -3.2818
251 R M -3.7898
252 K M -3.2880
253 G M -2.2902
254 K M -2.5566
255 I M 0.0000
256 H M -1.5651
257 I M -0.8930
258 P M 0.0000
259 F M 0.0000
260 P M 0.1338
261 L M 0.5776
262 A M 0.1777
263 N M -0.6629
264 V M 0.1428
265 T M -0.8380
266 C M -1.6484
267 R M -3.4414
268 V M 0.0000
269 P M 0.0000
270 K M -2.5205
271 A M -2.1341
272 R M -2.8627
273 N M -2.0451
274 P M -0.5144
275 T M 0.1598
276 V M 1.5660
277 T M 1.0858
278 Y M 0.6624
279 G M -1.1955
280 K M -2.4697
281 N M -2.1820
282 Q M -1.6646
283 V M 0.0000
284 T M 0.2214
285 M M 0.0000
286 L M -0.3709
287 L M 0.0000
288 Y M -1.2982
289 P M -1.7640
290 D M -2.5157
291 H M -1.6576
292 P M -1.0283
293 T M 0.0000
294 L M -0.6372
295 L M 0.0000
296 S M -0.9788
297 Y M -0.9256
298 R M -1.7178
299 N M -1.9352
300 M M -1.9033
301 G M -2.0841
302 Q M -2.6469
303 E M -2.9391
304 P M -2.0832
305 N M -1.8436
306 Y M -0.7657
307 H M -1.8967
308 E M -2.3364
309 E M -1.5767
310 W M -0.0536
311 V M 0.0000
312 T M -1.0243
313 H M -2.0817
314 K M -2.6733
315 K M -2.0351
316 E M -1.9930
317 V M -0.5854
318 T M -0.3889
319 L M -0.2053
320 T M -0.9139
321 V M 0.0000
322 P M -0.6938
323 T M -0.8936
324 E M -1.4838
325 G M 0.0000
326 L M 0.0000
327 E M -1.1146
328 V M 0.0000
329 T M -0.8503
330 W M 0.0000
331 G M 0.0000
332 N M -1.6143
333 N M -2.1104
334 E M -2.0057
335 P M -1.4687
336 Y M -1.1513
337 K M -1.4323
338 Y M -0.4284
339 W M 0.0899
340 P M -0.6859
341 Q M -0.8654
342 M M 0.0152
343 S M -0.7247
344 T M -0.6344
345 N M -1.4159
346 G M -0.4768
347 T M -0.4735
348 A M -0.1798
349 H M -1.4417
350 G M -1.6868
351 H M -1.8130
352 P M -1.1046
353 H M -0.9672
354 E M -0.7270
355 I M 0.5592
356 I M 1.7908
357 L M 1.6466
358 Y M 1.1060
359 Y M 2.0734
360 Y M 1.9115
361 E M -0.2426
362 L M 1.0458
363 Y M 1.6715
364 P M 1.1830
365 T M 1.3565
366 M M 2.5920
367 T M 0.0000
368 V M 3.4754
369 V M 3.9351
370 I M 3.9671
371 V M 3.7202
372 S M 3.2695
373 V M 4.2498
374 A M 3.4893
375 S M 3.1923
376 F M 4.2926
377 V M 4.2469
378 L M 4.3538
379 L M 3.9914
380 S M 2.8490
381 M M 3.3844
382 V M 3.3736
383 G M 1.9267
384 T M 1.5830
385 A M 1.9653
386 V M 2.7352
387 G M 1.7823
388 M M 1.9619
389 C M 1.5225
390 V M 1.1921
391 C M 0.5017
392 A M -0.4407
393 R M -0.8018
394 R M -2.3116
395 R M -2.5484
396 C M -0.9128
397 I M -0.5076
398 T M -1.2333
399 P M -0.4602
400 Y M 0.1396
401 E M -0.8510
402 L M 0.6405
403 T M 0.0392
404 P M -0.3370
405 G M -0.5542
406 A M -0.1671
407 T M 0.1152
408 V M 1.1553
409 P M 1.6789
410 F M 3.2756
411 L M 3.5122
412 L M 3.2115
413 S M 3.0487
414 L M 3.9170
415 L M 3.7678
416 C M 2.8096
417 C M 1.5442
418 V M 2.9040
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
VR373M -0.5632 -0.0336 View CSV PDB
VK373M -0.4327 -0.0313 View CSV PDB
FK376M -0.3283 -0.0344 View CSV PDB
LR379M -0.2739 -0.0285 View CSV PDB
VK377M -0.2986 -0.0259 View CSV PDB
VR377M -0.1437 -0.0287 View CSV PDB
FR376M 0.0422 -0.0356 View CSV PDB
LK379M 0.0507 -0.0271 View CSV PDB
LR378M 0.11 -0.0268 View CSV PDB
LK378M 0.1943 -0.0279 View CSV PDB
IK370M 0.5958 -0.0263 View CSV PDB
IR370M 1.1936 -0.0275 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018