Project name: ph20

Status: done

Started: 2024-04-03 07:56:49
Settings
Chain sequence(s) A: LNFRAPPVIPNVPFLWAWNAPSEFCLGKFDEPLDMSLFSFIGSPRINATGQGVTIFYVDRLGYYPYIDSITGVTVNGGIPQKISLQDHLDKAKKDITFYMPVDNLGMAVIDWEEWRPTWARNWKPKDVYKNRSIELVQQQNVQLSLTEATEKAKQEFEKAGKDFLVETIKLGKLLRPNHLWGYYLFPDCYNHHYKKPGYNGSCFNVEIKRNDDLSWLWNESTALYPSIYLNTQQSPVAATLYVRNRVREAIRVSKIPDAKSPLPVFAYTRIVFTDQVLKFLSQDELVYTFGETVALGASGIVIWGTLSIMRSMKSCLLLDNYMETILNPYIINVTLAAKMCSQVLCQEQGVCIRKNWNSSDYLHLNPDNFAIQLEKGGKFTVRGKPTLEDLEQFSEKFYCSCYSTLSCKEKADVKDTDAVDVCIADGVCIDAFLKPPMETEEPQIFYNASPSTLS
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                                          (00:04:57)
[INFO]       Auto_mut: Residue number 481 from chain A and a score of 2.783 (phenylalanine)        
                       selected for automated muatation                                            (00:05:00)
[INFO]       Auto_mut: Residue number 480 from chain A and a score of 2.233 (isoleucine) selected  
                       for automated muatation                                                     (00:05:00)
[INFO]       Auto_mut: Residue number 482 from chain A and a score of 2.035 (tyrosine) selected    
                       for automated muatation                                                     (00:05:00)
[INFO]       Auto_mut: Residue number 105 from chain A and a score of 1.942 (isoleucine) selected  
                       for automated muatation                                                     (00:05:00)
[INFO]       Auto_mut: Residue number 108 from chain A and a score of 1.798 (valine) selected for  
                       automated muatation                                                         (00:05:00)
[INFO]       Auto_mut: Residue number 272 from chain A and a score of 1.514 (valine) selected for  
                       automated muatation                                                         (00:05:00)
[INFO]       Auto_mut: Mutating residue number 480 from chain A (isoleucine) into glutamic acid    (00:05:00)
[INFO]       Auto_mut: Mutating residue number 481 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 481 from chain A (phenylalanine) into glutamic acid (00:05:00)
[INFO]       Auto_mut: Mutating residue number 481 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 481 from chain A (phenylalanine) into aspartic acid (00:05:00)
[INFO]       Auto_mut: Mutating residue number 481 from chain A (phenylalanine) into arginine      (00:07:24)
[INFO]       Auto_mut: Mutating residue number 481 from chain A (phenylalanine) into lysine        (00:07:25)
[INFO]       Auto_mut: Mutating residue number 480 from chain A (isoleucine) into lysine           (00:07:26)
[INFO]       Auto_mut: Mutating residue number 480 from chain A (isoleucine) into aspartic acid    (00:09:50)
[INFO]       Auto_mut: Mutating residue number 482 from chain A (tyrosine) into glutamic acid      (00:09:56)
[INFO]       Auto_mut: Mutating residue number 482 from chain A (tyrosine) into aspartic acid      (00:09:57)
[INFO]       Auto_mut: Mutating residue number 480 from chain A (isoleucine) into arginine         (00:12:14)
[INFO]       Auto_mut: Mutating residue number 482 from chain A (tyrosine) into arginine           (00:12:19)
[INFO]       Auto_mut: Mutating residue number 482 from chain A (tyrosine) into lysine             (00:12:24)
[INFO]       Auto_mut: Mutating residue number 105 from chain A (isoleucine) into glutamic acid    (00:14:41)
[INFO]       Auto_mut: Mutating residue number 105 from chain A (isoleucine) into aspartic acid    (00:14:43)
[INFO]       Auto_mut: Mutating residue number 108 from chain A (valine) into glutamic acid        (00:14:56)
[INFO]       Auto_mut: Mutating residue number 105 from chain A (isoleucine) into arginine         (00:17:05)
[INFO]       Auto_mut: Mutating residue number 105 from chain A (isoleucine) into lysine           (00:17:12)
[INFO]       Auto_mut: Mutating residue number 108 from chain A (valine) into lysine               (00:17:22)
[INFO]       Auto_mut: Mutating residue number 108 from chain A (valine) into aspartic acid        (00:19:32)
[INFO]       Auto_mut: Mutating residue number 272 from chain A (valine) into glutamic acid        (00:19:46)
[INFO]       Auto_mut: Mutating residue number 272 from chain A (valine) into aspartic acid        (00:19:55)
[INFO]       Auto_mut: Mutating residue number 108 from chain A (valine) into arginine             (00:21:56)
[INFO]       Auto_mut: Mutating residue number 272 from chain A (valine) into lysine               (00:22:11)
[INFO]       Auto_mut: Mutating residue number 272 from chain A (valine) into arginine             (00:22:26)
[INFO]       Auto_mut: Effect of mutation residue number 481 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: -0.2303 kcal/mol, Difference in average   
                       score from the base case: -0.0264                                           (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 481 from chain A (phenylalanine) into     
                       lysine: Energy difference: -1.9598 kcal/mol, Difference in average score    
                       from the base case: -0.0256                                                 (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 481 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: -1.4250 kcal/mol, Difference in average   
                       score from the base case: -0.0262                                           (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 481 from chain A (phenylalanine) into     
                       arginine: Energy difference: -2.0528 kcal/mol, Difference in average score  
                       from the base case: -0.0266                                                 (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 480 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 0.0189 kcal/mol, Difference in average    
                       score from the base case: -0.0266                                           (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 480 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.0329 kcal/mol, Difference in average score    
                       from the base case: -0.0258                                                 (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 480 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 0.0532 kcal/mol, Difference in average    
                       score from the base case: -0.0264                                           (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 480 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.1488 kcal/mol, Difference in average score   
                       from the base case: -0.0268                                                 (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 482 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 0.3702 kcal/mol, Difference in average score from  
                       the base case: -0.0224                                                      (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 482 from chain A (tyrosine) into lysine:  
                       Energy difference: -0.0281 kcal/mol, Difference in average score from the   
                       base case: -0.0217                                                          (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 482 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: -0.0647 kcal/mol, Difference in average score from 
                       the base case: -0.0223                                                      (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 482 from chain A (tyrosine) into          
                       arginine: Energy difference: -0.2952 kcal/mol, Difference in average score  
                       from the base case: -0.0226                                                 (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 105 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 0.2159 kcal/mol, Difference in average    
                       score from the base case: -0.0263                                           (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 105 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.3826 kcal/mol, Difference in average score    
                       from the base case: -0.0215                                                 (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 105 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 0.3210 kcal/mol, Difference in average    
                       score from the base case: -0.0276                                           (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 105 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.2512 kcal/mol, Difference in average score  
                       from the base case: -0.0243                                                 (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 108 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.2300 kcal/mol, Difference in average score from 
                       the base case: -0.0314                                                      (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 108 from chain A (valine) into lysine:    
                       Energy difference: -0.8117 kcal/mol, Difference in average score from the   
                       base case: -0.0311                                                          (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 108 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.3314 kcal/mol, Difference in average score from  
                       the base case: -0.0303                                                      (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 108 from chain A (valine) into arginine:  
                       Energy difference: -1.0356 kcal/mol, Difference in average score from the   
                       base case: -0.0298                                                          (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 272 from chain A (valine) into glutamic   
                       acid: Energy difference: -1.9828 kcal/mol, Difference in average score from 
                       the base case: -0.0261                                                      (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 272 from chain A (valine) into lysine:    
                       Energy difference: -0.4240 kcal/mol, Difference in average score from the   
                       base case: -0.0261                                                          (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 272 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.8728 kcal/mol, Difference in average score from 
                       the base case: -0.0261                                                      (00:25:09)
[INFO]       Auto_mut: Effect of mutation residue number 272 from chain A (valine) into arginine:  
                       Energy difference: -0.7699 kcal/mol, Difference in average score from the   
                       base case: -0.0271                                                          (00:25:09)
[INFO]       Main:     Simulation completed successfully.                                          (00:25:17)
Show buried residues
Minimal score value
-3.8928
Maximal score value
2.783
Average score
-0.6244
Total score value
-284.0846
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
36 L A 0.8041
37 N A -0.4293
38 F A -0.1367
39 R A 0.0000
40 A A 0.0000
41 P A 0.1003
42 P A -0.0602
43 V A 0.4849
44 I A 0.2658
45 P A -0.5046
46 N A -1.1837
47 V A -0.0151
48 P A -0.3161
49 F A 0.0000
50 L A 0.0000
51 W A 0.0000
52 A A 0.0000
53 W A 0.0000
54 N A 0.0000
55 A A 0.0000
56 P A 0.0000
57 S A 0.0000
58 E A -1.1840
59 F A 0.1476
60 C A 0.0000
61 L A -0.8374
62 G A 0.0000
63 K A -1.0941
64 F A 0.0003
65 D A -1.9352
66 E A -2.3521
67 P A -1.5208
68 L A 0.0000
69 D A -1.1118
70 M A -0.3980
71 S A -0.7261
72 L A 0.0000
73 F A 0.0000
74 S A 0.2009
75 F A 0.0000
76 I A 0.5279
77 G A 0.0000
78 S A 0.0000
79 P A -0.1505
80 R A -0.4975
81 I A 0.6461
82 N A -0.4828
83 A A -0.3798
84 T A -0.0556
85 G A -0.3443
86 Q A -0.2523
87 G A -0.1197
88 V A 0.0000
89 T A 0.0000
90 I A 0.0000
91 F A 0.0000
92 Y A -0.0211
93 V A -0.4803
94 D A -1.1439
95 R A 0.0000
96 L A 0.0000
97 G A -1.2508
98 Y A -0.2949
99 Y A 0.0000
100 P A 0.0000
101 Y A 0.1678
102 I A 0.0000
103 D A 0.6350
104 S A 0.6815
105 I A 1.9416
106 T A 1.1405
107 G A 0.9928
108 V A 1.7976
109 T A 0.7173
110 V A 0.5297
111 N A -0.0869
112 G A -0.4259
113 G A 0.0000
114 I A 0.0000
115 P A 0.0000
116 Q A -1.5955
117 K A -1.6584
118 I A -0.8343
119 S A -0.9867
120 L A -1.0639
121 Q A -2.0369
122 D A -2.3312
123 H A 0.0000
124 L A -1.8161
125 D A -2.5567
126 K A -2.2624
127 A A 0.0000
128 K A -1.9683
129 K A -2.1512
130 D A 0.0000
131 I A 0.0000
132 T A -0.1133
133 F A 0.8548
134 Y A 0.0000
135 M A 0.0000
136 P A 0.5531
137 V A 0.9347
138 D A -0.8253
139 N A -1.3280
140 L A -0.3404
141 G A 0.0000
142 M A 0.0000
143 A A 0.0000
144 V A 0.0000
145 I A 0.0000
146 D A -0.2232
147 W A 0.0000
148 E A -1.0264
149 E A -0.8942
150 W A 0.0000
151 R A -0.4721
152 P A 0.0000
153 T A -1.0317
154 W A 0.0000
155 A A -0.1246
156 R A 0.0000
157 N A 0.0000
158 W A -0.3752
159 K A -1.6413
160 P A -1.2377
161 K A -1.0820
162 D A -1.1446
163 V A -0.7556
164 Y A 0.0000
165 K A -1.3862
166 N A -1.8625
167 R A -2.0081
168 S A 0.0000
169 I A -2.1236
170 E A -2.5554
171 L A -2.1836
172 V A 0.0000
173 Q A -1.6336
174 Q A -2.1094
175 Q A -2.0680
176 N A -1.3365
177 V A 0.1498
178 Q A -0.7538
179 L A -0.4897
180 S A 0.2101
181 L A 0.6337
182 T A -0.4519
183 E A -1.7569
184 A A 0.0000
185 T A -2.1414
186 E A -3.3253
187 K A -3.2528
188 A A 0.0000
189 K A -3.4862
190 Q A -3.8928
191 E A -3.8443
192 F A 0.0000
193 E A -2.7935
194 K A -3.2957
195 A A -2.1991
196 G A 0.0000
197 K A -1.8079
198 D A -1.3605
199 F A 0.0000
200 L A 0.0000
201 V A -0.9468
202 E A -1.3781
203 T A 0.0000
204 I A 0.0000
205 K A -0.8709
206 L A -0.3057
207 G A 0.0000
208 K A -0.3067
209 L A 0.9292
210 L A 0.3783
211 R A -0.4106
212 P A -0.8719
213 N A -1.3919
214 H A 0.0000
215 L A -0.0870
216 W A 0.0000
217 G A 0.0000
218 Y A 0.0000
219 Y A 0.0655
220 L A 0.1539
221 F A 0.2970
222 P A 0.0000
223 D A 0.0000
224 C A 0.0000
225 Y A 0.1052
226 N A 0.0000
227 H A -1.3761
228 H A -2.1165
229 Y A -1.9688
230 K A -3.0583
231 K A -3.0774
232 P A -1.8631
233 G A -1.4666
234 Y A -1.4988
235 N A -1.3004
236 G A 0.0000
237 S A -0.4049
238 C A -0.0073
239 F A 0.6205
240 N A -0.6141
241 V A 0.0676
242 E A 0.0000
243 I A -0.7333
244 K A -2.2398
245 R A -1.7590
246 N A 0.0000
247 D A -2.1863
248 D A -2.6932
249 L A 0.0000
250 S A -1.1171
251 W A -0.8220
252 L A 0.0000
253 W A 0.0000
254 N A -1.4903
255 E A -1.1898
256 S A 0.0000
257 T A -0.4207
258 A A 0.0000
259 L A 0.0000
260 Y A 0.0000
261 P A 0.0000
262 S A 0.0000
263 I A 0.0000
264 Y A 0.1149
265 L A 0.0000
266 N A -1.0792
267 T A -1.2979
268 Q A -1.6738
269 Q A -0.9144
270 S A -0.2439
271 P A 0.1032
272 V A 1.5137
273 A A 0.0000
274 A A 0.0000
275 T A 0.1545
276 L A 0.1364
277 Y A 0.0000
278 V A 0.0000
279 R A 0.0000
280 N A 0.0000
281 R A 0.0000
282 V A 0.0000
283 R A -1.1980
284 E A 0.0000
285 A A 0.0000
286 I A 0.0000
287 R A -0.8706
288 V A 0.0000
289 S A 0.0000
290 K A -1.0572
291 I A -0.7371
292 P A -1.2740
293 D A -2.0672
294 A A -1.2612
295 K A -1.7689
296 S A -1.3245
297 P A 0.0000
298 L A -0.4712
299 P A 0.0493
300 V A 0.0000
301 F A 0.0000
302 A A 0.0000
303 Y A 0.0000
304 T A 0.0000
305 R A 0.0000
306 I A 0.0000
307 V A 0.0000
308 F A 0.0000
309 T A -0.8120
310 D A -1.8249
311 Q A -1.0735
312 V A 0.0836
313 L A 0.7441
314 K A -0.7101
315 F A 0.0031
316 L A 0.0000
317 S A -1.2347
318 Q A -1.6961
319 D A -2.3254
320 E A -1.4099
321 L A 0.0000
322 V A -0.7206
323 Y A -0.1641
324 T A 0.0000
325 F A 0.0000
326 G A 0.0000
327 E A 0.0000
328 T A 0.0000
329 V A 0.0000
330 A A 0.0000
331 L A 0.0000
332 G A 0.0000
333 A A 0.0000
334 S A 0.0940
335 G A 0.0000
336 I A 0.0000
337 V A 0.0000
338 I A 0.0000
339 W A 0.1780
340 G A 0.0000
341 T A 0.0243
342 L A -0.0855
343 S A -0.0517
344 I A 0.0000
345 M A 0.0000
346 R A -1.7356
347 S A -0.9792
348 M A -0.0952
349 K A -1.3511
350 S A -0.5005
351 C A 0.0000
352 L A -0.0432
353 L A 0.3983
354 L A 0.0000
355 D A -0.9220
356 N A -0.7552
357 Y A 0.0000
358 M A 0.0000
359 E A -0.9255
360 T A -0.4282
361 I A -0.1597
362 L A 0.0000
363 N A 0.0000
364 P A -0.1188
365 Y A 0.0000
366 I A 0.0000
367 I A 0.0000
368 N A -0.3062
369 V A 0.0000
370 T A 0.0000
371 L A 0.0000
372 A A 0.0000
373 A A 0.0000
374 K A 0.0000
375 M A 0.0000
376 C A 0.0000
377 S A 0.0000
378 Q A -1.6463
379 V A 0.0000
380 L A 0.0000
381 C A 0.0000
382 Q A -2.6596
383 E A -2.2827
384 Q A -1.7612
385 G A 0.0000
386 V A -0.2102
387 C A 0.0000
388 I A 0.0000
389 R A 0.0000
390 K A -2.4567
391 N A -2.1964
392 W A -1.1400
393 N A -1.4915
394 S A -1.2685
395 S A -0.6824
396 D A -1.2267
397 Y A -0.1022
398 L A 0.0000
399 H A -0.3983
400 L A 0.0000
401 N A -1.4268
402 P A -1.4315
403 D A -2.2234
404 N A -2.2412
405 F A 0.0000
406 A A -1.3037
407 I A -0.5604
408 Q A -1.4581
409 L A -1.4807
410 E A -3.1057
411 K A -3.1181
412 G A -2.2757
413 G A -2.2933
414 K A -2.9185
415 F A 0.0000
416 T A -1.2997
417 V A -1.3435
418 R A -2.5684
419 G A -2.7172
420 K A -2.3876
421 P A 0.0000
422 T A -1.1844
423 L A -1.4106
424 E A -2.4550
425 D A 0.0000
426 L A 0.0000
427 E A -3.0979
428 Q A -2.7431
429 F A 0.0000
430 S A -2.4481
431 E A -2.9889
432 K A -2.5961
433 F A 0.0000
434 Y A -0.9257
435 C A -1.1144
436 S A 0.0000
437 C A -0.5746
438 Y A 0.0000
439 S A 0.0000
440 T A -0.1368
441 L A 0.0032
442 S A -0.5547
443 C A -1.6795
444 K A -2.7601
445 E A -2.8547
446 K A -2.4232
447 A A -1.6160
448 D A -2.1901
449 V A 0.0000
450 K A -3.0932
451 D A -3.2231
452 T A 0.0000
453 D A -2.1758
454 A A -1.1227
455 V A 0.0000
456 D A -2.1677
457 V A 0.0000
458 C A -0.6741
459 I A -0.2104
460 A A -0.8373
461 D A -2.0189
462 G A -1.2378
463 V A 0.0000
464 C A -0.9926
465 I A 0.0000
466 D A -2.5673
467 A A -1.1587
468 F A 0.4031
469 L A -0.5503
470 K A -1.0382
471 P A -0.5695
472 P A -0.4595
473 M A -0.4709
474 E A -2.2829
475 T A -2.1344
476 E A -3.3939
477 E A -3.1768
478 P A -1.4055
479 Q A -0.3860
480 I A 2.2330
481 F A 2.7830
482 Y A 2.0346
483 N A 0.1940
484 A A -0.0829
485 S A -0.5319
486 P A -0.4428
487 S A -0.0513
488 T A 0.4285
489 L A 1.3250
490 S A 0.4938
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
FR481A -2.0528 -0.0266 View CSV PDB
VE272A -1.9828 -0.0261 View CSV PDB
FK481A -1.9598 -0.0256 View CSV PDB
VR108A -1.0356 -0.0298 View CSV PDB
VK108A -0.8117 -0.0311 View CSV PDB
VD272A -0.8728 -0.0261 View CSV PDB
IK105A -0.3826 -0.0215 View CSV PDB
IR105A -0.2512 -0.0243 View CSV PDB
YR482A -0.2952 -0.0226 View CSV PDB
IK480A -0.0329 -0.0258 View CSV PDB
YD482A -0.0647 -0.0223 View CSV PDB
IE480A 0.0189 -0.0266 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018