Project name: Val

Status: done

Started: 2026-02-09 18:37:38
Settings
Chain sequence(s) A: MAAPAAEAPLSAVKVVLEELEKKEKILVVQTAPSVRVAIGEEFGYAPGTISTGQMVAALRRLGFDYVFDTNFGADLTIMEEGSEFLERLEKGDLEDLPMFTSCCPGWVNLVEKVYPELRTRLSSAKSPQGMLSAMVKTYFAKKLGVEPEDIFHVSIMPCTAKKDEIKRPQQKIKLEDGREIQTTDVVLTTRELGKLIRMKKIPFANLPEEEYDAPLGISTGAAALFGVTGGVMEAALRTAYELKTGKALPKIVFEEVRGLKGVREAEIDLDGKKIRIAVVHGTANVRNLVEKILRREVKYHFVEVMACPGGCIGGGGQPYSRDPEILRKRAEAIYTIDERMTLRKSHENPAIKKLYEEYLEHPLSHKAHELLHTYYEDRSRKKRLAVKSAWSHPQFEK
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                                          (00:06:50)
[INFO]       Auto_mut: Residue number 387 from chain A and a score of 1.066 (valine) selected for  
                       automated muatation                                                         (00:06:52)
[INFO]       Auto_mut: Residue number 375 from chain A and a score of 1.066 (tyrosine) selected    
                       for automated muatation                                                     (00:06:52)
[INFO]       Auto_mut: Residue number 1 from chain A and a score of 1.062 (methionine) selected    
                       for automated muatation                                                     (00:06:52)
[INFO]       Auto_mut: Residue number 10 from chain A and a score of 0.712 (leucine) selected for  
                       automated muatation                                                         (00:06:52)
[INFO]       Auto_mut: Residue number 320 from chain A and a score of 0.672 (tyrosine) selected    
                       for automated muatation                                                     (00:06:52)
[INFO]       Auto_mut: Residue number 391 from chain A and a score of 0.642 (tryptophan) selected  
                       for automated muatation                                                     (00:06:52)
[INFO]       Auto_mut: Mutating residue number 387 from chain A (valine) into glutamic acid        (00:06:52)
[INFO]       Auto_mut: Mutating residue number 387 from chain A (valine) into aspartic acid        (00:06:52)
[INFO]       Auto_mut: Mutating residue number 375 from chain A (tyrosine) into glutamic acid      (00:06:52)
[INFO]       Auto_mut: Mutating residue number 387 from chain A (valine) into arginine             (00:10:30)
[INFO]       Auto_mut: Mutating residue number 387 from chain A (valine) into lysine               (00:10:38)
[INFO]       Auto_mut: Mutating residue number 375 from chain A (tyrosine) into lysine             (00:10:43)
[INFO]       Auto_mut: Mutating residue number 375 from chain A (tyrosine) into aspartic acid      (00:14:09)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into glutamic acid      (00:14:39)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into aspartic acid      (00:14:41)
[INFO]       Auto_mut: Mutating residue number 375 from chain A (tyrosine) into arginine           (00:17:56)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into lysine             (00:18:18)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into arginine           (00:18:23)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (leucine) into glutamic acid        (00:21:54)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (leucine) into aspartic acid        (00:21:58)
[INFO]       Auto_mut: Mutating residue number 320 from chain A (tyrosine) into glutamic acid      (00:22:03)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (leucine) into lysine               (00:25:46)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (leucine) into arginine             (00:25:50)
[INFO]       Auto_mut: Mutating residue number 320 from chain A (tyrosine) into lysine             (00:26:07)
[INFO]       Auto_mut: Mutating residue number 320 from chain A (tyrosine) into aspartic acid      (00:29:40)
[INFO]       Auto_mut: Mutating residue number 391 from chain A (tryptophan) into glutamic acid    (00:29:40)
[INFO]       Auto_mut: Mutating residue number 391 from chain A (tryptophan) into aspartic acid    (00:30:15)
[INFO]       Auto_mut: Mutating residue number 391 from chain A (tryptophan) into lysine           (00:33:22)
[INFO]       Auto_mut: Mutating residue number 320 from chain A (tyrosine) into arginine           (00:33:27)
[INFO]       Auto_mut: Mutating residue number 391 from chain A (tryptophan) into arginine         (00:33:56)
[INFO]       Auto_mut: Effect of mutation residue number 387 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.7344 kcal/mol, Difference in average score from 
                       the base case: -0.0321                                                      (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 387 from chain A (valine) into lysine:    
                       Energy difference: -0.1617 kcal/mol, Difference in average score from the   
                       base case: -0.0360                                                          (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 387 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.7583 kcal/mol, Difference in average score from 
                       the base case: -0.0341                                                      (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 387 from chain A (valine) into arginine:  
                       Energy difference: -0.3382 kcal/mol, Difference in average score from the   
                       base case: -0.0317                                                          (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 375 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 0.3030 kcal/mol, Difference in average score from  
                       the base case: -0.0336                                                      (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 375 from chain A (tyrosine) into lysine:  
                       Energy difference: 0.4713 kcal/mol, Difference in average score from the    
                       base case: -0.0320                                                          (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 375 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 0.2762 kcal/mol, Difference in average score from  
                       the base case: -0.0334                                                      (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 375 from chain A (tyrosine) into          
                       arginine: Energy difference: 0.5829 kcal/mol, Difference in average score   
                       from the base case: -0.0358                                                 (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into glutamic 
                       acid: Energy difference: -0.3623 kcal/mol, Difference in average score from 
                       the base case: -0.0198                                                      (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into lysine:  
                       Energy difference: -0.0145 kcal/mol, Difference in average score from the   
                       base case: -0.0190                                                          (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into aspartic 
                       acid: Energy difference: -0.0779 kcal/mol, Difference in average score from 
                       the base case: -0.0197                                                      (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into          
                       arginine: Energy difference: -0.2753 kcal/mol, Difference in average score  
                       from the base case: -0.0200                                                 (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (leucine) into glutamic   
                       acid: Energy difference: 0.8415 kcal/mol, Difference in average score from  
                       the base case: -0.0399                                                      (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (leucine) into lysine:    
                       Energy difference: 0.1030 kcal/mol, Difference in average score from the    
                       base case: -0.0265                                                          (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (leucine) into aspartic   
                       acid: Energy difference: 1.3879 kcal/mol, Difference in average score from  
                       the base case: -0.0341                                                      (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (leucine) into arginine:  
                       Energy difference: 0.2084 kcal/mol, Difference in average score from the    
                       base case: -0.0321                                                          (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 320 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 0.4797 kcal/mol, Difference in average score from  
                       the base case: -0.0362                                                      (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 320 from chain A (tyrosine) into lysine:  
                       Energy difference: 0.6962 kcal/mol, Difference in average score from the    
                       base case: -0.0324                                                          (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 320 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 0.5078 kcal/mol, Difference in average score from  
                       the base case: -0.0294                                                      (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 320 from chain A (tyrosine) into          
                       arginine: Energy difference: 0.4994 kcal/mol, Difference in average score   
                       from the base case: -0.0356                                                 (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 391 from chain A (tryptophan) into        
                       glutamic acid: Energy difference: -0.1908 kcal/mol, Difference in average   
                       score from the base case: -0.0321                                           (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 391 from chain A (tryptophan) into        
                       lysine: Energy difference: -0.1289 kcal/mol, Difference in average score    
                       from the base case: -0.0311                                                 (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 391 from chain A (tryptophan) into        
                       aspartic acid: Energy difference: -0.3259 kcal/mol, Difference in average   
                       score from the base case: -0.0318                                           (00:37:41)
[INFO]       Auto_mut: Effect of mutation residue number 391 from chain A (tryptophan) into        
                       arginine: Energy difference: -0.2133 kcal/mol, Difference in average score  
                       from the base case: -0.0321                                                 (00:37:41)
[INFO]       Main:     Simulation completed successfully.                                          (00:37:50)
Show buried residues
Minimal score value
-4.6106
Maximal score value
1.0664
Average score
-0.8834
Total score value
-351.6036
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 1.0619
2 A A 0.5430
3 A A 0.2534
4 P A -0.2981
5 A A -0.4941
6 A A -0.8751
7 E A -1.6404
8 A A -0.6007
9 P A -0.1361
10 L A 0.7116
11 S A 0.1226
12 A A -0.0778
13 V A 0.0000
14 K A -0.9184
15 V A -0.2776
16 V A 0.0000
17 L A -1.4979
18 E A -2.6184
19 E A -2.9762
20 L A 0.0000
21 E A -3.8788
22 K A -4.5149
23 K A -4.6106
24 E A -4.0700
25 K A -3.2327
26 I A -1.5729
27 L A 0.0000
28 V A 0.0000
29 V A 0.0000
30 Q A 0.0000
31 T A 0.0000
32 A A 0.0000
33 P A 0.0000
34 S A 0.0000
35 V A 0.0000
36 R A 0.0000
37 V A 0.0000
38 A A 0.0000
39 I A 0.0000
40 G A 0.0000
41 E A -0.2060
42 E A -0.5276
43 F A -0.1230
44 G A -0.2824
45 Y A 0.1399
46 A A 0.0165
47 P A -0.5104
48 G A -0.5612
49 T A -0.0111
50 I A 0.4876
51 S A 0.0000
52 T A -0.5882
53 G A 0.0000
54 Q A -1.4000
55 M A 0.0000
56 V A 0.0000
57 A A 0.0000
58 A A 0.0000
59 L A 0.0000
60 R A -1.6729
61 R A -2.0747
62 L A 0.0000
63 G A -1.8413
64 F A 0.0000
65 D A -2.1879
66 Y A -0.6587
67 V A 0.0000
68 F A 0.0000
69 D A 0.0000
70 T A 0.0000
71 N A 0.0000
72 F A 0.0000
73 G A 0.0000
74 A A 0.0000
75 D A 0.0000
76 L A 0.0000
77 T A 0.0000
78 I A 0.0000
79 M A 0.0000
80 E A 0.0000
81 E A 0.0000
82 G A 0.0000
83 S A -0.2564
84 E A 0.0000
85 F A 0.0000
86 L A -1.2664
87 E A -2.4295
88 R A -2.6327
89 L A 0.0000
90 E A -3.3474
91 K A -3.6292
92 G A -3.1443
93 D A -3.3296
94 L A 0.0000
95 E A -3.4328
96 D A -3.1887
97 L A -1.8315
98 P A 0.0000
99 M A 0.0000
100 F A 0.0000
101 T A 0.0000
102 S A -0.0439
103 C A 0.0721
104 C A 0.0920
105 P A 0.0000
106 G A -0.1980
107 W A 0.0000
108 V A 0.0000
109 N A -0.7138
110 L A -0.2335
111 V A 0.0000
112 E A 0.0000
113 K A -1.6748
114 V A -0.7013
115 Y A 0.0000
116 P A -2.0255
117 E A -2.1827
118 L A 0.0000
119 R A -1.3848
120 T A -0.6287
121 R A -0.7983
122 L A 0.0000
123 S A 0.0000
124 S A 0.1707
125 A A 0.0000
126 K A 0.0000
127 S A 0.0000
128 P A -0.0090
129 Q A 0.0000
130 G A 0.0000
131 M A 0.0000
132 L A 0.0000
133 S A 0.0000
134 A A 0.0000
135 M A 0.0000
136 V A 0.0000
137 K A 0.0000
138 T A -1.1463
139 Y A 0.0000
140 F A 0.0000
141 A A 0.0000
142 K A -2.5368
143 K A -2.0938
144 L A -0.9587
145 G A -1.3519
146 V A -1.3201
147 E A -2.1335
148 P A -1.6577
149 E A -1.9775
150 D A -2.4398
151 I A 0.0000
152 F A 0.0000
153 H A 0.0000
154 V A 0.0000
155 S A 0.0000
156 I A 0.0000
157 M A 0.0000
158 P A 0.0000
159 C A -0.2124
160 T A -0.4063
161 A A -0.5147
162 K A 0.0000
163 K A -1.1678
164 D A -1.6669
165 E A 0.0000
166 I A 0.0000
167 K A -2.4739
168 R A -1.6033
169 P A -1.1922
170 Q A -0.5755
171 Q A 0.0000
172 K A -2.3942
173 I A 0.0000
174 K A -3.9232
175 L A -3.2016
176 E A -3.3972
177 D A -3.4506
178 G A -2.9207
179 R A -3.1711
180 E A -3.6322
181 I A 0.0000
182 Q A -1.8853
183 T A 0.0000
184 T A 0.0000
185 D A -0.9510
186 V A -0.3547
187 V A 0.0000
188 L A 0.0000
189 T A 0.0000
190 T A 0.0000
191 R A -0.7062
192 E A -0.9730
193 L A 0.0000
194 G A 0.0000
195 K A -1.6434
196 L A 0.0000
197 I A 0.0000
198 R A -1.9509
199 M A -0.9856
200 K A -1.8987
201 K A -2.3274
202 I A -1.6017
203 P A -1.3553
204 F A 0.0000
205 A A -0.5979
206 N A -1.5776
207 L A 0.0000
208 P A -1.5344
209 E A -2.6777
210 E A -2.2177
211 E A -2.2866
212 Y A -0.7482
213 D A -0.7035
214 A A -0.0858
215 P A -0.0266
216 L A 0.0000
217 G A 0.0222
218 I A 0.5484
219 S A 0.1965
220 T A 0.0000
221 G A 0.0000
222 A A 0.0000
223 A A 0.0000
224 A A 0.0000
225 L A 0.0000
226 F A 0.0000
227 G A 0.0000
228 V A 0.0000
229 T A 0.0000
230 G A 0.0000
231 G A 0.0000
232 V A 0.0000
233 M A 0.0000
234 E A 0.0000
235 A A 0.0000
236 A A 0.0000
237 L A 0.0000
238 R A 0.0000
239 T A 0.0000
240 A A 0.0000
241 Y A -0.7636
242 E A -0.7519
243 L A -0.1183
244 K A -1.0586
245 T A -1.4031
246 G A -1.2933
247 K A -2.1355
248 A A -0.9749
249 L A -0.7781
250 P A -1.0367
251 K A -1.5404
252 I A -0.3435
253 V A -0.6319
254 F A 0.0000
255 E A -2.4514
256 E A -2.6024
257 V A 0.0000
258 R A -1.3229
259 G A -1.2893
260 L A -0.5570
261 K A -1.4675
262 G A -0.8030
263 V A -0.8179
264 R A 0.0000
265 E A -2.5028
266 A A -2.5985
267 E A -3.3401
268 I A -2.5222
269 D A -3.3002
270 L A 0.0000
271 D A -3.2324
272 G A -2.6394
273 K A -3.3322
274 K A -3.7446
275 I A 0.0000
276 R A -2.9520
277 I A 0.0000
278 A A 0.0000
279 V A 0.0000
280 V A 0.0000
281 H A 0.0000
282 G A -0.3351
283 T A -0.5742
284 A A -0.7931
285 N A -1.2061
286 V A 0.0000
287 R A -1.6328
288 N A -2.0897
289 L A 0.0000
290 V A 0.0000
291 E A -2.3903
292 K A -3.0880
293 I A 0.0000
294 L A -2.3011
295 R A -3.6032
296 R A -4.1611
297 E A -3.6655
298 V A -2.4078
299 K A -2.9967
300 Y A 0.0000
301 H A -1.9286
302 F A 0.0000
303 V A 0.0000
304 E A 0.0000
305 V A 0.0000
306 M A 0.0000
307 A A -0.1421
308 C A -0.0470
309 P A -0.3737
310 G A 0.0000
311 G A 0.0000
312 C A 0.1063
313 I A 0.0000
314 G A -0.0539
315 G A 0.0000
316 G A -0.3105
317 G A 0.0000
318 Q A 0.0000
319 P A 0.0000
320 Y A 0.6721
321 S A -0.5929
322 R A -1.9915
323 D A -1.6401
324 P A -1.5888
325 E A -1.9569
326 I A -1.1570
327 L A -1.0203
328 R A -2.0195
329 K A -1.8854
330 R A 0.0000
331 A A 0.0000
332 E A -1.9627
333 A A 0.0000
334 I A 0.0000
335 Y A -1.0937
336 T A -1.4039
337 I A 0.0000
338 D A 0.0000
339 E A -2.5775
340 R A -2.6120
341 M A -1.2547
342 T A -0.6442
343 L A -0.6007
344 R A -0.9653
345 K A -0.7349
346 S A 0.0000
347 H A -1.2578
348 E A -2.0840
349 N A 0.0000
350 P A -1.4692
351 A A 0.0000
352 I A 0.0000
353 K A -3.7403
354 K A -3.4585
355 L A 0.0000
356 Y A 0.0000
357 E A -4.2491
358 E A -3.6479
359 Y A -2.1614
360 L A 0.0000
361 E A -3.7159
362 H A -2.5436
363 P A -0.9825
364 L A -1.1071
365 S A 0.0000
366 H A -2.4404
367 K A -2.6942
368 A A 0.0000
369 H A -2.0900
370 E A -3.0547
371 L A 0.0000
372 L A 0.0000
373 H A 0.0000
374 T A 0.0820
375 Y A 1.0660
376 Y A -0.3284
377 E A -1.8290
378 D A -3.5408
379 R A -2.9587
380 S A -3.1572
381 R A -4.0415
382 K A -3.9092
383 K A -3.4093
384 R A -2.0652
385 L A 0.2561
386 A A 0.4741
387 V A 1.0664
388 K A -0.6427
389 S A -0.2713
390 A A 0.0853
391 W A 0.6419
392 S A -0.5721
393 H A -1.2054
394 P A -1.2290
395 Q A -1.3153
396 F A -0.0641
397 E A -2.2458
398 K A -2.2745
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
VD387A -0.7583 -0.0341 View CSV PDB
VE387A -0.7344 -0.0321 View CSV PDB
WD391A -0.3259 -0.0318 View CSV PDB
WR391A -0.2133 -0.0321 View CSV PDB
ME1A -0.3623 -0.0198 View CSV PDB
MR1A -0.2753 -0.02 View CSV PDB
LK10A 0.103 -0.0265 View CSV PDB
LR10A 0.2084 -0.0321 View CSV PDB
YD375A 0.2762 -0.0334 View CSV PDB
YE375A 0.303 -0.0336 View CSV PDB
YE320A 0.4797 -0.0362 View CSV PDB
YR320A 0.4994 -0.0356 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018