Project name: 394eabd36a0721c

Status: done

Started: 2025-08-11 14:59:39
Settings
Chain sequence(s) B: AIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQKEPKNKTFLRCEAKNYSGRFTCWWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERVRGDNKEYEYSVECQEDSACPAAEESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKNLQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFCVQVQGKEKKDRVFTDKTSATVICRKNASISVRAQDRYYSSSWSEWASVPC
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                                          (00:03:56)
[INFO]       Auto_mut: Residue number 47 from chain B and a score of 1.852 (valine) selected for   
                       automated muatation                                                         (00:03:58)
[INFO]       Auto_mut: Residue number 290 from chain B and a score of 1.415 (phenylalanine)        
                       selected for automated muatation                                            (00:03:58)
[INFO]       Auto_mut: Residue number 268 from chain B and a score of 1.268 (tyrosine) selected    
                       for automated muatation                                                     (00:03:58)
[INFO]       Auto_mut: Residue number 314 from chain B and a score of 1.071 (tyrosine) selected    
                       for automated muatation                                                     (00:03:58)
[INFO]       Auto_mut: Residue number 23 from chain B and a score of 0.929 (isoleucine) selected   
                       for automated muatation                                                     (00:03:58)
[INFO]       Auto_mut: Residue number 76 from chain B and a score of 0.859 (threonine) selected    
                       for automated muatation                                                     (00:03:58)
[INFO]       Auto_mut: Mutating residue number 47 from chain B (valine) into glutamic acid         (00:03:58)
[INFO]       Auto_mut: Mutating residue number 47 from chain B (valine) into aspartic acid         (00:03:58)
[INFO]       Auto_mut: Mutating residue number 290 from chain B (phenylalanine) into glutamic acid 
                       Mutating residue number 290 from chain B (phenylalanine) into glutamic acid (00:03:58)
[INFO]       Auto_mut: Mutating residue number 47 from chain B (valine) into arginine              (00:06:00)
[INFO]       Auto_mut: Mutating residue number 290 from chain B (phenylalanine) into lysine        (00:06:16)
[INFO]       Auto_mut: Mutating residue number 47 from chain B (valine) into lysine                (00:06:21)
[INFO]       Auto_mut: Mutating residue number 290 from chain B (phenylalanine) into aspartic acid 
                       Mutating residue number 290 from chain B (phenylalanine) into aspartic acid (00:08:16)
[INFO]       Auto_mut: Mutating residue number 268 from chain B (tyrosine) into glutamic acid      (00:08:33)
[INFO]       Auto_mut: Mutating residue number 268 from chain B (tyrosine) into aspartic acid      (00:08:42)
[INFO]       Auto_mut: Mutating residue number 290 from chain B (phenylalanine) into arginine      (00:10:24)
[INFO]       Auto_mut: Mutating residue number 268 from chain B (tyrosine) into lysine             (00:10:40)
[INFO]       Auto_mut: Mutating residue number 268 from chain B (tyrosine) into arginine           (00:10:47)
[INFO]       Auto_mut: Mutating residue number 314 from chain B (tyrosine) into glutamic acid      (00:12:41)
[INFO]       Auto_mut: Mutating residue number 314 from chain B (tyrosine) into aspartic acid      (00:12:56)
[INFO]       Auto_mut: Mutating residue number 23 from chain B (isoleucine) into glutamic acid     (00:13:04)
[INFO]       Auto_mut: Mutating residue number 314 from chain B (tyrosine) into lysine             (00:14:52)
[INFO]       Auto_mut: Mutating residue number 314 from chain B (tyrosine) into arginine           (00:15:06)
[INFO]       Auto_mut: Mutating residue number 23 from chain B (isoleucine) into lysine            (00:15:27)
[INFO]       Auto_mut: Mutating residue number 23 from chain B (isoleucine) into aspartic acid     (00:17:21)
[INFO]       Auto_mut: Mutating residue number 76 from chain B (threonine) into glutamic acid      (00:17:24)
[INFO]       Auto_mut: Mutating residue number 76 from chain B (threonine) into aspartic acid      (00:17:44)
[INFO]       Auto_mut: Mutating residue number 23 from chain B (isoleucine) into arginine          (00:19:29)
[INFO]       Auto_mut: Mutating residue number 76 from chain B (threonine) into lysine             (00:19:48)
[INFO]       Auto_mut: Mutating residue number 76 from chain B (threonine) into arginine           (00:19:51)
[INFO]       Auto_mut: Effect of mutation residue number 47 from chain B (valine) into glutamic    
                       acid: Energy difference: 0.2616 kcal/mol, Difference in average score from  
                       the base case: -0.0467                                                      (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 47 from chain B (valine) into lysine:     
                       Energy difference: -0.2220 kcal/mol, Difference in average score from the   
                       base case: -0.0370                                                          (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 47 from chain B (valine) into aspartic    
                       acid: Energy difference: 1.1232 kcal/mol, Difference in average score from  
                       the base case: -0.0497                                                      (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 47 from chain B (valine) into arginine:   
                       Energy difference: 0.0104 kcal/mol, Difference in average score from the    
                       base case: -0.0503                                                          (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 290 from chain B (phenylalanine) into     
                       glutamic acid: Energy difference: 0.8559 kcal/mol, Difference in average    
                       score from the base case: -0.0492                                           (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 290 from chain B (phenylalanine) into     
                       lysine: Energy difference: 1.0452 kcal/mol, Difference in average score     
                       from the base case: -0.0536                                                 (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 290 from chain B (phenylalanine) into     
                       aspartic acid: Energy difference: 1.8611 kcal/mol, Difference in average    
                       score from the base case: -0.0581                                           (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 290 from chain B (phenylalanine) into     
                       arginine: Energy difference: 1.4559 kcal/mol, Difference in average score   
                       from the base case: -0.0532                                                 (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 268 from chain B (tyrosine) into glutamic 
                       acid: Energy difference: 0.7468 kcal/mol, Difference in average score from  
                       the base case: -0.0521                                                      (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 268 from chain B (tyrosine) into lysine:  
                       Energy difference: 0.6202 kcal/mol, Difference in average score from the    
                       base case: -0.0505                                                          (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 268 from chain B (tyrosine) into aspartic 
                       acid: Energy difference: 1.0148 kcal/mol, Difference in average score from  
                       the base case: -0.0511                                                      (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 268 from chain B (tyrosine) into          
                       arginine: Energy difference: 0.6002 kcal/mol, Difference in average score   
                       from the base case: -0.0482                                                 (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 314 from chain B (tyrosine) into glutamic 
                       acid: Energy difference: 0.3463 kcal/mol, Difference in average score from  
                       the base case: -0.0518                                                      (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 314 from chain B (tyrosine) into lysine:  
                       Energy difference: 0.1969 kcal/mol, Difference in average score from the    
                       base case: -0.0472                                                          (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 314 from chain B (tyrosine) into aspartic 
                       acid: Energy difference: 0.6015 kcal/mol, Difference in average score from  
                       the base case: -0.0516                                                      (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 314 from chain B (tyrosine) into          
                       arginine: Energy difference: -0.7501 kcal/mol, Difference in average score  
                       from the base case: -0.0557                                                 (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 23 from chain B (isoleucine) into         
                       glutamic acid: Energy difference: 2.5710 kcal/mol, Difference in average    
                       score from the base case: -0.0422                                           (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 23 from chain B (isoleucine) into lysine: 
                       Energy difference: 0.9313 kcal/mol, Difference in average score from the    
                       base case: -0.0465                                                          (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 23 from chain B (isoleucine) into         
                       aspartic acid: Energy difference: 2.8329 kcal/mol, Difference in average    
                       score from the base case: -0.0514                                           (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 23 from chain B (isoleucine) into         
                       arginine: Energy difference: 1.1794 kcal/mol, Difference in average score   
                       from the base case: -0.0478                                                 (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 76 from chain B (threonine) into glutamic 
                       acid: Energy difference: -0.2015 kcal/mol, Difference in average score from 
                       the base case: -0.0322                                                      (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 76 from chain B (threonine) into lysine:  
                       Energy difference: -0.8749 kcal/mol, Difference in average score from the   
                       base case: -0.0232                                                          (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 76 from chain B (threonine) into aspartic 
                       acid: Energy difference: 0.5021 kcal/mol, Difference in average score from  
                       the base case: -0.0354                                                      (00:22:04)
[INFO]       Auto_mut: Effect of mutation residue number 76 from chain B (threonine) into          
                       arginine: Energy difference: -0.5107 kcal/mol, Difference in average score  
                       from the base case: -0.0409                                                 (00:22:04)
[INFO]       Main:     Simulation completed successfully.                                          (00:22:11)
Show buried residues
Minimal score value
-4.5698
Maximal score value
1.8521
Average score
-1.0314
Total score value
-312.5252
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
22 A B 0.3290
23 I B 0.9289
24 W B -0.1513
25 E B -2.3265
26 L B -1.6373
27 K B -3.1286
28 K B -3.2912
29 D B -2.5266
30 V B 0.0000
31 Y B -0.9786
32 V B 0.0000
33 V B 0.0000
34 E B -0.6330
35 L B 0.0000
36 D B -2.1468
37 W B -1.3881
38 Y B -0.1919
39 P B -0.5869
40 D B -1.8425
41 A B -1.5975
42 P B -1.6633
43 G B -2.2090
44 E B -1.3694
45 M B 0.1694
46 V B 0.0000
47 V B 1.8521
48 L B 0.0000
49 T B -0.2408
50 C B -1.4234
51 D B -2.1714
52 T B -1.5573
53 P B -1.6399
54 E B -3.0351
55 E B -2.6929
56 D B -2.8924
57 G B -1.9365
58 I B 0.0000
59 T B -0.2605
60 W B 0.0000
61 T B -0.6341
62 L B -1.1829
63 D B -2.7021
64 Q B -2.5445
65 S B -1.8558
66 S B -1.3299
67 E B -1.6776
68 V B 0.4193
69 L B 0.7912
70 G B 0.2815
71 S B -0.4542
72 G B -1.4333
73 K B -1.9689
74 T B -0.1273
75 L B 0.0000
76 T B 0.8592
77 I B 0.2585
78 Q B -1.0510
79 V B 0.0000
80 K B -3.3371
81 E B -2.7515
82 F B -1.1071
83 G B -1.4299
84 D B -1.7346
85 A B 0.0000
86 G B -0.9259
87 Q B -1.3973
88 Y B 0.0000
89 T B -0.1843
90 C B 0.0000
91 H B -0.4667
92 K B -1.4690
93 G B -1.5166
94 G B -1.3339
95 E B -1.5032
96 V B 0.3980
97 L B -0.0488
98 S B -0.3817
99 H B -0.8628
100 S B 0.0000
101 L B -0.5411
102 L B 0.0000
103 L B 0.0000
104 L B 0.0000
105 H B 0.0000
106 K B -1.2280
107 K B -1.3961
108 E B -2.1829
109 D B -2.1791
110 G B -1.1050
111 I B 0.6224
112 W B 0.0677
113 S B -0.6863
114 T B -1.2757
115 D B -1.8942
116 I B 0.0000
117 L B 0.0000
118 K B -2.0451
119 D B -2.9175
120 Q B -2.9826
121 K B -4.5698
122 E B -3.8597
123 P B -3.0124
124 K B -4.0578
125 N B -4.0136
126 K B -3.5905
127 T B -2.9204
128 F B -1.6425
129 L B 0.0000
130 R B -0.7448
131 C B -0.3075
132 E B -1.1425
133 A B 0.0000
134 K B -2.0592
135 N B -1.3410
136 Y B -0.4636
137 S B -1.0790
138 G B 0.0000
139 R B -2.7809
140 F B 0.0000
141 T B -1.3438
142 C B 0.0000
143 W B -0.0426
144 W B 0.0000
145 L B 0.0000
146 T B 0.0000
147 T B -0.9904
148 I B -0.5887
149 S B -0.8217
150 T B -1.0980
151 D B -2.1777
152 L B -0.9743
153 T B -0.5053
154 F B 0.1632
155 S B -0.3022
156 V B -0.6383
157 K B -1.3799
158 S B -1.2350
159 S B -1.3446
160 R B -1.0270
161 G B -0.5666
162 S B -0.8530
163 S B -0.9007
164 D B -1.6622
165 P B -1.3722
166 Q B -2.0298
167 G B 0.0000
168 V B 0.0000
169 T B -1.4333
170 C B -1.3903
171 G B -1.0353
172 A B -0.5079
173 A B -0.1232
174 T B 0.0203
175 L B 0.3085
176 S B -0.3249
177 A B -1.0428
178 E B -2.4555
179 R B -2.6315
180 V B -1.6155
181 R B -2.9376
182 G B -2.4770
183 D B -3.0900
184 N B -2.9186
185 K B -2.9082
186 E B 0.0000
187 Y B -1.1008
188 E B 0.0000
189 Y B 0.2425
190 S B -0.1974
191 V B 0.0000
192 E B -2.2529
193 C B 0.0000
194 Q B -2.0643
195 E B -1.6980
196 D B -1.9719
197 S B -0.9885
198 A B -0.0881
199 C B 0.4443
200 P B -0.1204
201 A B -0.5005
202 A B -0.9147
203 E B -2.0126
204 E B -1.1884
205 S B -0.5042
206 L B 0.0557
207 P B -0.0528
208 I B 0.0000
209 E B -0.9161
210 V B 0.0000
211 M B -0.5976
212 V B 0.0000
213 D B 0.0000
214 A B 0.0000
215 V B -0.6479
216 H B -1.4568
217 K B -2.1453
218 L B -0.9197
219 K B -0.7196
220 Y B 0.0000
221 E B 0.0000
222 N B -0.8862
223 Y B 0.0000
224 T B -0.5409
225 S B -0.3155
226 S B -0.3284
227 F B -0.3244
228 F B -0.4488
229 I B 0.0000
230 R B -1.3468
231 D B -1.8022
232 I B -1.1605
233 I B 0.0000
234 K B -1.6975
235 P B 0.0000
236 D B -2.0334
237 P B -1.7433
238 P B 0.0000
239 K B -2.9995
240 N B -2.5043
241 L B -1.7061
242 Q B -2.1348
243 L B -1.1281
244 K B -2.2557
245 P B -1.6934
246 L B -1.7156
247 K B -2.6525
248 N B -2.5154
249 S B -1.9764
250 R B -2.3035
251 Q B -1.4096
252 V B -0.8658
253 E B -1.1745
254 V B 0.0000
255 S B -1.7956
256 W B 0.0000
257 E B -3.0713
258 Y B -1.7915
259 P B 0.0000
260 D B -2.3532
261 T B -1.2932
262 W B 0.0000
263 S B 0.0000
264 T B -0.3851
265 P B -0.1276
266 H B -0.3321
267 S B 0.2084
268 Y B 1.2685
269 F B 0.6619
270 S B 0.0489
271 L B 0.0000
272 T B -0.5820
273 F B 0.0000
274 C B 0.0000
275 V B 0.0000
276 Q B -1.8839
277 V B 0.0000
278 Q B -3.4453
279 G B -2.3650
280 K B -2.7874
284 E B -4.0240
285 K B -4.2056
286 K B -4.2150
287 D B -3.5710
288 R B -2.5762
289 V B 0.3554
290 F B 1.4146
291 T B -0.0638
292 D B -1.4702
293 K B -2.1042
294 T B -1.5377
295 S B -1.3122
296 A B -0.3559
297 T B -0.1641
298 V B 0.2446
299 I B 0.3013
300 C B -1.0968
301 R B -3.0895
302 K B -2.9581
303 N B -3.1203
304 A B -2.3916
305 S B -1.3883
306 I B 0.0000
307 S B -0.7542
308 V B 0.0000
309 R B -0.9343
310 A B 0.0000
311 Q B -0.7185
312 D B 0.0000
313 R B -0.6757
314 Y B 1.0710
315 Y B 0.4573
316 S B -0.2478
317 S B 0.0000
318 S B -0.7633
319 W B -0.5650
320 S B 0.0000
321 E B -2.0664
322 W B -0.9093
323 A B -0.9310
324 S B -0.4927
325 V B -0.2010
326 P B -0.5179
327 C B -0.7173
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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
YR314B -0.7501 -0.0557 View CSV PDB
TR76B -0.5107 -0.0409 View CSV PDB
TK76B -0.8749 -0.0232 View CSV PDB
VK47B -0.222 -0.037 View CSV PDB
VR47B 0.0104 -0.0503 View CSV PDB
YK314B 0.1969 -0.0472 View CSV PDB
YK268B 0.6202 -0.0505 View CSV PDB
YR268B 0.6002 -0.0482 View CSV PDB
FE290B 0.8559 -0.0492 View CSV PDB
FK290B 1.0452 -0.0536 View CSV PDB
IK23B 0.9313 -0.0465 View CSV PDB
IR23B 1.1794 -0.0478 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018