Project name: WT_amylase

Status: done

Started: 2026-04-14 12:49:53
Settings
Chain sequence(s) A: NGTLMQYFEWYMPNDGQHWKRLQNDSAYLAEHGITAVWIPPAYKGTSQADVGYGAYDLYDLGEFHQKGTVRTKYGTKGELQSAIKSLHSRDINVYGDVVINHKGGADATEDVTAVEVDPADRNRVISGEHLIKAWTHFHFPGRGSTYSDFKWHWYHFDGTDWDESRKLNRIYKFQGKAWDWEVSNENGNYDYLMYADIDYDHPDVAAEIKRWGTWYANELQLDGFRLDAVKHIKFSFLRDWVNHVREKTGKEMFTVAEYWQNDLGALENYLNKTNFNHSVFDVPLHYQFHAASTQGGGYDMRKLLNGTVVSKHPLKSVTFVDNHDTQPGQSLESTVQTWFKPLAYAFILTRESGYPQVFYGDMYGTKGDSQREIPALKHKIEPILKARKQYAYGAQHDYFDHHDIVGWTREGDSSVANSGLAALITDGPGGAKRMYVGRQNAGETWHDITGNRSEPVVINSEGWGEFHVNGGSVSIYVQR
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]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:09:40)
[INFO]       Auto_mut: Residue number 126 from chain A and a score of 1.421 (isoleucine) selected  
                       for automated muatation                                                     (00:09:45)
[INFO]       Auto_mut: Residue number 315 from chain A and a score of 1.116 (leucine) selected for 
                       automated muatation                                                         (00:09:45)
[INFO]       Auto_mut: Residue number 195 from chain A and a score of 0.904 (tyrosine) selected    
                       for automated muatation                                                     (00:09:45)
[INFO]       Auto_mut: Residue number 194 from chain A and a score of 0.885 (methionine) selected  
                       for automated muatation                                                     (00:09:45)
[INFO]       Auto_mut: Residue number 193 from chain A and a score of 0.794 (leucine) selected for 
                       automated muatation                                                         (00:09:45)
[INFO]       Auto_mut: Residue number 458 from chain A and a score of 0.786 (valine) selected for  
                       automated muatation                                                         (00:09:45)
[INFO]       Auto_mut: Mutating residue number 126 from chain A (isoleucine) into glutamic acid    (00:09:45)
[INFO]       Auto_mut: Mutating residue number 315 from chain A (leucine) into glutamic acid       (00:09:45)
[INFO]       Auto_mut: Mutating residue number 126 from chain A (isoleucine) into aspartic acid    (00:09:45)
[INFO]       Auto_mut: Mutating residue number 126 from chain A (isoleucine) into lysine           (00:13:38)
[INFO]       Auto_mut: Mutating residue number 315 from chain A (leucine) into lysine              (00:14:01)
[INFO]       Auto_mut: Mutating residue number 126 from chain A (isoleucine) into arginine         (00:14:23)
[INFO]       Auto_mut: Mutating residue number 315 from chain A (leucine) into aspartic acid       (00:17:47)
[INFO]       Auto_mut: Mutating residue number 195 from chain A (tyrosine) into glutamic acid      (00:18:11)
[INFO]       Auto_mut: Mutating residue number 195 from chain A (tyrosine) into aspartic acid      (00:18:56)
[INFO]       Auto_mut: Mutating residue number 315 from chain A (leucine) into arginine            (00:21:55)
[INFO]       Auto_mut: Mutating residue number 195 from chain A (tyrosine) into lysine             (00:22:29)
[INFO]       Auto_mut: Mutating residue number 195 from chain A (tyrosine) into arginine           (00:23:43)
[INFO]       Auto_mut: Mutating residue number 194 from chain A (methionine) into glutamic acid    (00:26:37)
[INFO]       Auto_mut: Mutating residue number 194 from chain A (methionine) into aspartic acid    (00:27:19)
[INFO]       Auto_mut: Mutating residue number 193 from chain A (leucine) into glutamic acid       (00:28:26)
[INFO]       Auto_mut: Mutating residue number 194 from chain A (methionine) into lysine           (00:31:09)
[INFO]       Auto_mut: Mutating residue number 194 from chain A (methionine) into arginine         (00:32:00)
[INFO]       Auto_mut: Mutating residue number 193 from chain A (leucine) into lysine              (00:33:16)
[INFO]       Auto_mut: Mutating residue number 193 from chain A (leucine) into aspartic acid       (00:36:00)
[INFO]       Auto_mut: Mutating residue number 458 from chain A (valine) into glutamic acid        (00:36:36)
[INFO]       Auto_mut: Mutating residue number 458 from chain A (valine) into aspartic acid        (00:38:09)
[INFO]       Auto_mut: Mutating residue number 193 from chain A (leucine) into arginine            (00:40:08)
[INFO]       Auto_mut: Mutating residue number 458 from chain A (valine) into lysine               (00:40:37)
[INFO]       Auto_mut: Mutating residue number 458 from chain A (valine) into arginine             (00:42:03)
[INFO]       Auto_mut: Effect of mutation residue number 126 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 1.8227 kcal/mol, Difference in average    
                       score from the base case: -0.0325                                           (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 126 from chain A (isoleucine) into        
                       lysine: Energy difference: 0.5488 kcal/mol, Difference in average score     
                       from the base case: -0.0270                                                 (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 126 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 1.7626 kcal/mol, Difference in average    
                       score from the base case: -0.0319                                           (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 126 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.6277 kcal/mol, Difference in average score   
                       from the base case: -0.0296                                                 (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 315 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.0622 kcal/mol, Difference in average score from  
                       the base case: -0.0287                                                      (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 315 from chain A (leucine) into lysine:   
                       Energy difference: -0.2662 kcal/mol, Difference in average score from the   
                       base case: -0.0266                                                          (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 315 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.1335 kcal/mol, Difference in average score from  
                       the base case: -0.0283                                                      (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 315 from chain A (leucine) into arginine: 
                       Energy difference: 0.1024 kcal/mol, Difference in average score from the    
                       base case: -0.0276                                                          (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 195 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 2.0716 kcal/mol, Difference in average score from  
                       the base case: -0.0106                                                      (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 195 from chain A (tyrosine) into lysine:  
                       Energy difference: -0.0441 kcal/mol, Difference in average score from the   
                       base case: -0.0101                                                          (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 195 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 3.3047 kcal/mol, Difference in average score from  
                       the base case: -0.0102                                                      (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 195 from chain A (tyrosine) into          
                       arginine: Energy difference: 0.5748 kcal/mol, Difference in average score   
                       from the base case: -0.0137                                                 (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 194 from chain A (methionine) into        
                       glutamic acid: Energy difference: 1.5030 kcal/mol, Difference in average    
                       score from the base case: -0.0127                                           (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 194 from chain A (methionine) into        
                       lysine: Energy difference: -0.1210 kcal/mol, Difference in average score    
                       from the base case: -0.0091                                                 (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 194 from chain A (methionine) into        
                       aspartic acid: Energy difference: 1.8470 kcal/mol, Difference in average    
                       score from the base case: -0.0110                                           (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 194 from chain A (methionine) into        
                       arginine: Energy difference: -0.4372 kcal/mol, Difference in average score  
                       from the base case: -0.0122                                                 (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 193 from chain A (leucine) into glutamic  
                       acid: Energy difference: 2.0258 kcal/mol, Difference in average score from  
                       the base case: -0.0094                                                      (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 193 from chain A (leucine) into lysine:   
                       Energy difference: 0.2114 kcal/mol, Difference in average score from the    
                       base case: -0.0085                                                          (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 193 from chain A (leucine) into aspartic  
                       acid: Energy difference: 3.5214 kcal/mol, Difference in average score from  
                       the base case: -0.0089                                                      (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 193 from chain A (leucine) into arginine: 
                       Energy difference: 0.0264 kcal/mol, Difference in average score from the    
                       base case: -0.0090                                                          (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 458 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.4996 kcal/mol, Difference in average score from 
                       the base case: -0.0289                                                      (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 458 from chain A (valine) into lysine:    
                       Energy difference: -1.3806 kcal/mol, Difference in average score from the   
                       base case: -0.0282                                                          (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 458 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.7183 kcal/mol, Difference in average score from 
                       the base case: -0.0287                                                      (00:46:06)
[INFO]       Auto_mut: Effect of mutation residue number 458 from chain A (valine) into arginine:  
                       Energy difference: -1.0483 kcal/mol, Difference in average score from the   
                       base case: -0.0275                                                          (00:46:06)
[INFO]       Main:     Simulation completed successfully.                                          (00:46:19)
Show buried residues
Minimal score value
-3.6618
Maximal score value
1.4213
Average score
-0.669
Total score value
-321.1351
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 N A -1.4703
2 G A -0.7697
3 T A 0.0000
4 L A 0.0000
5 M A 0.0000
6 Q A 0.0000
7 Y A 0.0000
8 F A 0.0000
9 E A 0.0000
10 W A 0.0766
11 Y A -0.4624
12 M A 0.0000
13 P A -0.8673
14 N A -1.1141
15 D A -1.3148
16 G A 0.0000
17 Q A -1.6673
18 H A 0.0000
19 W A 0.0000
20 K A -2.3013
21 R A -1.9817
22 L A 0.0000
23 Q A -2.1174
24 N A -2.0990
25 D A -1.4914
26 S A 0.0000
27 A A -0.9752
28 Y A -0.7655
29 L A 0.0000
30 A A -1.4116
31 E A -2.1476
32 H A -1.4095
33 G A -1.3702
34 I A 0.0000
35 T A -1.1957
36 A A 0.0000
37 V A 0.0000
38 W A 0.0000
39 I A 0.0000
40 P A 0.0000
41 P A 0.0000
42 A A 0.0000
43 Y A 0.0000
44 K A 0.0000
45 G A 0.0000
46 T A -0.5012
47 S A -0.6839
48 Q A -0.7883
49 A A -0.5586
50 D A -0.4388
51 V A 0.0000
52 G A 0.0000
53 Y A 0.0000
54 G A 0.0000
55 A A 0.0000
56 Y A 0.0000
57 D A 0.0000
58 L A 0.0000
59 Y A 0.0000
60 D A 0.0000
61 L A 0.0000
62 G A 0.0000
63 E A -0.6272
64 F A -0.5388
65 H A -1.0242
66 Q A 0.0000
67 K A -1.0873
68 G A -0.9284
69 T A 0.0000
70 V A -0.1007
71 R A -0.5567
72 T A 0.0000
73 K A 0.0000
74 Y A 0.0000
75 G A 0.0000
76 T A -0.7481
77 K A -0.8913
78 G A -1.0392
79 E A -1.4528
80 L A 0.0000
81 Q A -1.5081
82 S A -1.5100
83 A A 0.0000
84 I A 0.0000
85 K A -2.5121
86 S A 0.0000
87 L A 0.0000
88 H A -2.2617
89 S A -1.8026
90 R A -2.3968
91 D A -2.7161
92 I A 0.0000
93 N A -1.5492
94 V A 0.0000
95 Y A 0.0000
96 G A 0.0000
97 D A 0.0000
98 V A 0.0000
99 V A 0.0000
100 I A 0.0000
101 N A 0.0000
102 H A 0.0000
103 K A 0.0000
104 G A 0.0000
105 G A -0.1918
106 A A 0.0000
107 D A -0.6288
108 A A -0.3835
109 T A -0.7735
110 E A -1.3307
111 D A -1.8108
112 V A 0.0000
113 T A -0.7866
114 A A 0.0000
115 V A -0.2309
116 E A -0.2262
117 V A 0.0000
118 D A -0.9528
119 P A -1.0360
120 A A -1.4009
121 D A -2.5767
122 R A 0.0000
123 N A -2.1554
124 R A -1.8305
125 V A 0.5106
126 I A 1.4213
127 S A 0.2473
128 G A -0.8239
129 E A -1.6599
130 H A -0.5654
131 L A 0.3718
132 I A 0.0000
133 K A -1.6624
134 A A 0.0000
135 W A -0.0535
136 T A 0.0000
137 H A -0.4172
138 F A 0.0000
139 H A -1.1640
140 F A 0.0000
141 P A -0.8506
142 G A -0.8818
143 R A 0.0000
144 G A -0.8856
145 S A -1.1153
146 T A -0.3374
147 Y A 0.1249
148 S A 0.0000
149 D A -1.8827
150 F A -1.1200
151 K A -1.0713
152 W A 0.0000
153 H A -0.0510
154 W A 0.1675
155 Y A 0.5510
156 H A 0.0000
157 F A 0.0000
158 D A 0.0000
159 G A 0.0000
160 T A 0.0000
161 D A -0.6358
162 W A -1.0499
163 D A 0.0000
164 E A -1.9330
165 S A -1.6887
166 R A -2.5590
167 K A -2.8052
168 L A -1.8784
169 N A -2.1996
170 R A -1.9096
171 I A -0.5494
172 Y A 0.0000
173 K A -0.7466
174 F A 0.0000
175 Q A -1.2368
176 G A -0.9101
177 K A -0.8302
178 A A -0.5214
179 W A -0.1589
180 D A 0.0000
181 W A 0.5299
182 E A -0.1081
183 V A 0.0000
184 S A 0.0000
185 N A -1.7722
186 E A -1.6322
187 N A -1.8229
188 G A -2.1441
189 N A 0.0000
190 Y A -0.6333
191 D A 0.0000
192 Y A 0.0000
193 L A 0.7939
194 M A 0.8851
195 Y A 0.9042
196 A A 0.0000
197 D A 0.0000
198 I A 0.0000
199 D A 0.0000
200 Y A 0.0000
201 D A -2.0577
202 H A -1.6281
203 P A -1.6667
204 D A -2.1933
205 V A 0.0000
206 A A -1.3279
207 A A -1.0583
208 E A 0.0000
209 I A 0.0000
210 K A -1.4550
211 R A -1.3142
212 W A 0.0000
213 G A 0.0000
214 T A -1.4309
215 W A -0.8966
216 Y A 0.0000
217 A A 0.0000
218 N A -1.9404
219 E A -1.3444
220 L A 0.0000
221 Q A -1.8252
222 L A 0.0000
223 D A -1.3227
224 G A 0.0000
225 F A 0.0000
226 R A 0.0000
227 L A 0.0000
228 D A 0.0000
229 A A 0.0000
230 V A 0.0000
231 K A -0.4300
232 H A 0.0000
233 I A 0.0000
234 K A -0.4453
235 F A 0.0000
236 S A -0.8184
237 F A 0.0000
238 L A 0.0000
239 R A -1.5807
240 D A -1.7462
241 W A 0.0000
242 V A 0.0000
243 N A -2.5474
244 H A -2.4133
245 V A 0.0000
246 R A -3.0481
247 E A -3.6618
248 K A -3.4095
249 T A -2.6222
250 G A -2.5040
251 K A -2.6628
252 E A -2.6880
253 M A 0.0000
254 F A -0.4230
255 T A 0.0000
256 V A 0.0000
257 A A 0.0000
258 E A 0.0000
259 Y A 0.0000
260 W A 0.0000
261 Q A -1.3216
262 N A -2.0308
263 D A -2.1767
264 L A -1.5659
265 G A -1.2183
266 A A -1.3481
267 L A 0.0000
268 E A -1.4293
269 N A -1.5083
270 Y A 0.0000
271 L A 0.0000
272 N A -2.2020
273 K A -2.1300
274 T A 0.0000
275 N A -1.9942
276 F A -0.6178
277 N A -0.9218
278 H A 0.0000
279 S A 0.0000
280 V A 0.0000
281 F A 0.0000
282 D A 0.0000
283 V A 0.0000
284 P A 0.0000
285 L A 0.0000
286 H A 0.0000
287 Y A -0.1740
288 Q A -0.7115
289 F A 0.0000
290 H A -0.5993
291 A A -0.6121
292 A A 0.0000
293 S A 0.0000
294 T A -0.9479
295 Q A -1.4914
296 G A -1.1727
297 G A -1.1942
298 G A -1.2485
299 Y A 0.0000
300 D A -1.8892
301 M A 0.0000
302 R A -2.8237
303 K A -2.6604
304 L A 0.0000
305 L A -1.3311
306 N A -2.1667
307 G A -1.8011
308 T A 0.0000
309 V A 0.0000
310 V A -0.4834
311 S A -1.1099
312 K A -1.8778
313 H A -0.6587
314 P A -0.2465
315 L A 1.1162
316 K A 0.1469
317 S A 0.0000
318 V A 0.0000
319 T A 0.0000
320 F A 0.0000
321 V A 0.0000
322 D A 0.0000
323 N A 0.0000
324 H A 0.0000
325 D A -0.3498
326 T A 0.0000
327 Q A 0.0000
328 P A 0.0000
329 G A -1.3562
330 Q A -0.5579
331 S A -0.3965
332 L A -0.0774
333 E A -0.8138
334 S A 0.0000
335 T A -0.7593
336 V A 0.0000
337 Q A -0.9643
338 T A -0.4490
339 W A 0.1026
340 F A 0.0000
341 K A 0.0000
342 P A 0.0000
343 L A 0.0000
344 A A 0.0000
345 Y A 0.0000
346 A A 0.0000
347 F A 0.0000
348 I A 0.0000
349 L A 0.0000
350 T A 0.0000
351 R A -1.2820
352 E A -2.1295
353 S A -0.8302
354 G A -0.1584
355 Y A -0.0508
356 P A 0.0000
357 Q A 0.0000
358 V A 0.0000
359 F A 0.0000
360 Y A 0.0000
361 G A 0.0000
362 D A 0.0000
363 M A 0.0000
364 Y A 0.0502
365 G A 0.0000
366 T A -1.1562
367 K A -2.0047
368 G A -2.1987
369 D A -2.8750
370 S A -2.5738
371 Q A -2.6832
372 R A -3.0586
373 E A -2.4085
374 I A 0.0000
375 P A -0.6012
376 A A -0.1495
377 L A -0.4487
378 K A -0.8964
379 H A -1.4189
380 K A -1.2596
381 I A 0.0000
382 E A -1.0658
383 P A -0.9260
384 I A 0.0000
385 L A 0.0000
386 K A -1.6096
387 A A 0.0000
388 R A 0.0000
389 K A -1.8348
390 Q A -1.3653
391 Y A -0.9336
392 A A 0.0000
393 Y A -1.0603
394 G A -0.8587
395 A A -0.7503
396 Q A -1.1671
397 H A -0.8805
398 D A -1.3342
399 Y A -1.2851
400 F A -1.7426
401 D A -2.4135
402 H A -1.9009
403 H A -2.1709
404 D A 0.0000
405 I A 0.0000
406 V A 0.0000
407 G A 0.0000
408 W A 0.0000
409 T A 0.0000
410 R A 0.0000
411 E A -1.0087
412 G A -1.1173
413 D A -1.2991
414 S A -1.0254
415 S A -0.5774
416 V A -0.5142
417 A A -0.7234
418 N A -1.7651
419 S A -1.0831
420 G A 0.0000
421 L A 0.0000
422 A A 0.0000
423 A A 0.0000
424 L A 0.0000
425 I A 0.0000
426 T A 0.0000
427 D A 0.0000
428 G A -0.9848
429 P A -0.8169
430 G A -0.9977
431 G A -0.6590
432 A A -1.2173
433 K A -1.8748
434 R A -2.5967
435 M A 0.0000
436 Y A -1.1380
437 V A 0.0000
438 G A 0.0000
439 R A -3.1519
440 Q A -2.5159
441 N A 0.0000
442 A A -1.6941
443 G A -0.9863
444 E A -0.8123
445 T A -0.3737
446 W A 0.0000
447 H A -1.2843
448 D A 0.0000
449 I A -0.4758
450 T A -0.6829
451 G A -1.0280
452 N A -1.0618
453 R A -1.5262
454 S A -1.5607
455 E A -2.1598
456 P A -1.4460
457 V A 0.0000
458 V A 0.7862
459 I A 0.0000
460 N A -1.5169
461 S A -1.9074
462 E A -2.8171
463 G A 0.0000
464 W A -1.3776
465 G A 0.0000
466 E A -2.4576
467 F A 0.0000
468 H A -1.5588
469 V A 0.0000
470 N A -1.1586
471 G A -1.0823
472 G A -0.6522
473 S A -0.4838
474 V A 0.0000
475 S A 0.0000
476 I A 0.0000
477 Y A 0.0000
478 V A 0.0000
479 Q A -1.3959
480 R A -2.2836
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
VK458A -1.3806 -0.0282 View CSV PDB
VR458A -1.0483 -0.0275 View CSV PDB
LK315A -0.2662 -0.0266 View CSV PDB
MR194A -0.4372 -0.0122 View CSV PDB
MK194A -0.121 -0.0091 View CSV PDB
YK195A -0.0441 -0.0101 View CSV PDB
LE315A 0.0622 -0.0287 View CSV PDB
LR193A 0.0264 -0.009 View CSV PDB
IK126A 0.5488 -0.027 View CSV PDB
IR126A 0.6277 -0.0296 View CSV PDB
LK193A 0.2114 -0.0085 View CSV PDB
YR195A 0.5748 -0.0137 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018