Project name: 1w7b

Status: done

Started: 2026-04-15 13:08:36
Settings
Chain sequence(s) A: PSAYGSVKAYTNFDAERDALNIETAIKTKGVDEVTIVNILTNRSNEQRQDIAFAYQRRTKKELASALKSALSGHLETVILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGTDVPKWISIMTERSVPHLQKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQCIQNKPLYFADRLYDSMKGKGTRDKVLIRIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDYQKALLYLCGGDD
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]                                                (00:00:10)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:10)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:10)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:10)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:10)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:06:20)
[INFO]       Auto_mut: Residue number 24 from chain A and a score of 1.151 (tyrosine) selected for 
                       automated muatation                                                         (00:06:22)
[INFO]       Auto_mut: Residue number 185 from chain A and a score of 1.004 (valine) selected for  
                       automated muatation                                                         (00:06:22)
[INFO]       Auto_mut: Residue number 54 from chain A and a score of 0.879 (valine) selected for   
                       automated muatation                                                         (00:06:22)
[INFO]       Auto_mut: Residue number 186 from chain A and a score of 0.679 (isoleucine) selected  
                       for automated muatation                                                     (00:06:22)
[INFO]       Auto_mut: Residue number 298 from chain A and a score of 0.664 (valine) selected for  
                       automated muatation                                                         (00:06:22)
[INFO]       Auto_mut: Residue number 121 from chain A and a score of 0.640 (leucine) selected for 
                       automated muatation                                                         (00:06:22)
[INFO]       Auto_mut: Mutating residue number 24 from chain A (tyrosine) into glutamic acid       (00:06:22)
[INFO]       Auto_mut: Mutating residue number 185 from chain A (valine) into glutamic acid        (00:06:22)
[INFO]       Auto_mut: Mutating residue number 24 from chain A (tyrosine) into aspartic acid       (00:06:22)
[INFO]       Auto_mut: Mutating residue number 185 from chain A (valine) into lysine               (00:09:17)
[INFO]       Auto_mut: Mutating residue number 24 from chain A (tyrosine) into arginine            (00:09:17)
[INFO]       Auto_mut: Mutating residue number 24 from chain A (tyrosine) into lysine              (00:09:24)
[INFO]       Auto_mut: Mutating residue number 185 from chain A (valine) into aspartic acid        (00:12:10)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (valine) into glutamic acid         (00:12:21)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (valine) into aspartic acid         (00:12:26)
[INFO]       Auto_mut: Mutating residue number 185 from chain A (valine) into arginine             (00:14:58)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (valine) into arginine              (00:15:17)
[INFO]       Auto_mut: Mutating residue number 54 from chain A (valine) into lysine                (00:15:26)
[INFO]       Auto_mut: Mutating residue number 186 from chain A (isoleucine) into glutamic acid    (00:17:58)
[INFO]       Auto_mut: Mutating residue number 186 from chain A (isoleucine) into aspartic acid    (00:18:25)
[INFO]       Auto_mut: Mutating residue number 298 from chain A (valine) into glutamic acid        (00:18:45)
[INFO]       Auto_mut: Mutating residue number 186 from chain A (isoleucine) into lysine           (00:21:01)
[INFO]       Auto_mut: Mutating residue number 186 from chain A (isoleucine) into arginine         (00:21:32)
[INFO]       Auto_mut: Mutating residue number 298 from chain A (valine) into lysine               (00:21:47)
[INFO]       Auto_mut: Mutating residue number 298 from chain A (valine) into aspartic acid        (00:23:54)
[INFO]       Auto_mut: Mutating residue number 121 from chain A (leucine) into glutamic acid       (00:24:24)
[INFO]       Auto_mut: Mutating residue number 121 from chain A (leucine) into aspartic acid       (00:25:47)
[INFO]       Auto_mut: Mutating residue number 298 from chain A (valine) into arginine             (00:26:54)
[INFO]       Auto_mut: Mutating residue number 121 from chain A (leucine) into lysine              (00:27:13)
[INFO]       Auto_mut: Mutating residue number 121 from chain A (leucine) into arginine            (00:28:33)
[INFO]       Auto_mut: Effect of mutation residue number 24 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 0.8278 kcal/mol, Difference in average score from  
                       the base case: -0.0138                                                      (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 24 from chain A (tyrosine) into lysine:   
                       Energy difference: 0.2437 kcal/mol, Difference in average score from the    
                       base case: -0.0156                                                          (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 24 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 0.7460 kcal/mol, Difference in average score from  
                       the base case: -0.0076                                                      (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 24 from chain A (tyrosine) into arginine: 
                       Energy difference: 0.4382 kcal/mol, Difference in average score from the    
                       base case: -0.0190                                                          (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 185 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.6294 kcal/mol, Difference in average score from 
                       the base case: -0.0198                                                      (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 185 from chain A (valine) into lysine:    
                       Energy difference: -0.3976 kcal/mol, Difference in average score from the   
                       base case: -0.0274                                                          (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 185 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.6113 kcal/mol, Difference in average score from 
                       the base case: -0.0195                                                      (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 185 from chain A (valine) into arginine:  
                       Energy difference: -0.6360 kcal/mol, Difference in average score from the   
                       base case: -0.0167                                                          (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (valine) into glutamic    
                       acid: Energy difference: -1.0689 kcal/mol, Difference in average score from 
                       the base case: -0.0222                                                      (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (valine) into lysine:     
                       Energy difference: -0.6672 kcal/mol, Difference in average score from the   
                       base case: -0.0184                                                          (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (valine) into aspartic    
                       acid: Energy difference: -0.3987 kcal/mol, Difference in average score from 
                       the base case: -0.0194                                                      (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 54 from chain A (valine) into arginine:   
                       Energy difference: -0.8286 kcal/mol, Difference in average score from the   
                       base case: -0.0140                                                          (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 186 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 0.9319 kcal/mol, Difference in average    
                       score from the base case: -0.0148                                           (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 186 from chain A (isoleucine) into        
                       lysine: Energy difference: 0.4367 kcal/mol, Difference in average score     
                       from the base case: -0.0118                                                 (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 186 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 1.1111 kcal/mol, Difference in average    
                       score from the base case: -0.0281                                           (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 186 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.3662 kcal/mol, Difference in average score   
                       from the base case: -0.0127                                                 (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 298 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.4845 kcal/mol, Difference in average score from  
                       the base case: 0.0015                                                       (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 298 from chain A (valine) into lysine:    
                       Energy difference: -0.6108 kcal/mol, Difference in average score from the   
                       base case: 0.0043                                                           (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 298 from chain A (valine) into aspartic   
                       acid: Energy difference: 1.1450 kcal/mol, Difference in average score from  
                       the base case: 0.0033                                                       (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 298 from chain A (valine) into arginine:  
                       Energy difference: -1.9273 kcal/mol, Difference in average score from the   
                       base case: 0.0116                                                           (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 121 from chain A (leucine) into glutamic  
                       acid: Energy difference: -0.5568 kcal/mol, Difference in average score from 
                       the base case: -0.0110                                                      (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 121 from chain A (leucine) into lysine:   
                       Energy difference: -0.0562 kcal/mol, Difference in average score from the   
                       base case: -0.0112                                                          (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 121 from chain A (leucine) into aspartic  
                       acid: Energy difference: -0.1929 kcal/mol, Difference in average score from 
                       the base case: -0.0099                                                      (00:31:26)
[INFO]       Auto_mut: Effect of mutation residue number 121 from chain A (leucine) into arginine: 
                       Energy difference: -0.1395 kcal/mol, Difference in average score from the   
                       base case: -0.0083                                                          (00:31:26)
[INFO]       Main:     Simulation completed successfully.                                          (00:31:34)
Show buried residues
Minimal score value
-4.2125
Maximal score value
1.1515
Average score
-1.0865
Total score value
-346.6007
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
21 P A -0.3426
22 S A 0.0896
23 A A 0.4813
24 Y A 1.1515
25 G A 0.0000
26 S A -0.2568
27 V A 0.0000
28 K A -1.5685
29 A A -1.1108
30 Y A -0.4823
31 T A -0.6093
32 N A -1.1276
33 F A -0.7712
34 D A -1.8756
35 A A -1.7482
36 E A -2.8327
37 R A -2.0248
38 D A 0.0000
39 A A 0.0000
40 L A -1.2154
41 N A -1.4232
42 I A 0.0000
43 E A -1.4016
44 T A -1.2344
45 A A 0.0000
46 I A -1.3935
47 K A -2.3595
48 T A -1.9465
49 K A -2.3535
50 G A -1.6155
51 V A -1.1293
52 D A -0.8838
53 E A -0.1374
54 V A 0.8787
55 T A 0.1958
56 I A 0.0000
57 V A 0.0000
58 N A -0.5566
59 I A 0.0000
60 L A 0.0000
61 T A 0.0000
62 N A -1.1471
63 R A 0.0000
64 S A 0.0000
65 N A -1.7661
66 E A -2.4324
67 Q A -1.4853
68 R A 0.0000
69 Q A -1.2142
70 D A -1.7725
71 I A 0.0000
72 A A -0.9532
73 F A -0.3672
74 A A -1.8768
75 Y A 0.0000
76 Q A -3.3750
77 R A -3.8325
78 R A -3.8417
79 T A -3.2286
80 K A -3.9776
81 K A -3.4184
82 E A -2.7645
83 L A 0.0000
84 A A -1.1885
85 S A -1.3296
86 A A 0.0000
87 L A 0.0000
88 K A -1.9958
89 S A -1.1150
90 A A -1.0400
91 L A 0.0000
92 S A -1.1938
93 G A -1.2275
94 H A -1.4621
95 L A 0.0000
96 E A -1.3822
97 T A -1.1022
98 V A 0.0000
99 I A 0.0000
100 L A -0.5030
101 G A 0.0000
102 L A 0.0000
103 L A 0.0000
104 K A -0.8765
105 T A -0.8840
106 P A -0.9263
107 A A -0.9714
108 Q A -0.9779
109 Y A 0.0000
110 D A 0.0000
111 A A 0.0000
112 S A -0.4077
113 E A -0.8974
114 L A 0.0000
115 K A -1.0233
116 A A -1.1464
117 S A 0.0000
118 M A 0.0000
119 K A -2.0349
120 G A -0.8102
121 L A 0.6397
122 G A -0.5866
123 T A -1.4763
124 D A -2.2408
125 E A -2.5702
126 D A -2.6713
127 S A 0.0000
128 L A 0.0000
129 I A 0.0000
130 E A 0.0000
131 I A 0.0000
132 I A 0.0000
133 C A 0.0000
134 S A 0.0000
135 R A 0.0000
136 T A -0.9466
137 N A -2.2357
138 Q A -2.1660
139 E A -1.6191
140 L A 0.0000
141 Q A -2.6116
142 E A -2.0992
143 I A 0.0000
144 N A -2.4260
145 R A -2.5598
146 V A -1.9686
147 Y A 0.0000
148 K A -3.1449
149 E A -2.9948
150 M A -1.4666
151 Y A -1.3676
152 K A -2.5520
153 T A -2.2298
154 D A -2.9116
155 L A 0.0000
156 E A -2.4418
157 K A -2.4162
158 D A -1.7654
159 I A 0.0000
160 I A -0.8981
161 S A -0.8646
162 D A -1.1979
163 T A 0.0000
164 S A -1.2303
165 G A -1.5411
166 D A -1.9727
167 F A 0.0000
168 R A -1.8726
169 K A -1.9588
170 L A 0.0000
171 M A 0.0000
172 V A -1.2223
173 A A -1.5270
174 L A 0.0000
175 A A 0.0000
176 K A -2.4099
177 G A 0.0000
178 R A -3.3801
179 R A -2.8595
180 A A -2.5926
181 E A -3.1621
182 D A -2.4876
183 G A -1.4099
184 S A -0.3663
185 V A 1.0045
186 I A 0.6790
187 D A -0.5251
188 Y A 0.0323
189 E A -1.5702
190 L A -0.9266
191 I A 0.0000
192 D A -1.8295
193 Q A -1.7822
194 D A 0.0000
195 A A 0.0000
196 R A -2.5354
197 D A -2.1093
198 L A 0.0000
199 Y A -1.9423
200 D A -3.0837
201 A A 0.0000
202 G A 0.0000
203 V A -1.9488
204 K A -3.1450
205 R A -3.2491
206 K A -3.0589
207 G A -1.9622
208 T A -1.7371
209 D A -1.6998
210 V A -0.9496
211 P A -1.1082
212 K A -1.2578
213 W A 0.0000
214 I A 0.0000
215 S A -1.1190
216 I A 0.0000
217 M A 0.0000
218 T A -1.4993
219 E A -2.6080
220 R A -1.9223
221 S A 0.0000
222 V A -0.6318
223 P A -0.6587
224 H A -0.5435
225 L A 0.0000
226 Q A -1.7019
227 K A -1.7025
228 V A 0.0000
229 F A 0.0000
230 D A -3.3975
231 R A -2.7611
232 Y A 0.0000
233 K A -2.9339
234 S A -1.7404
235 Y A -1.3108
236 S A 0.0000
237 P A -0.8793
238 Y A -1.0270
239 D A -2.2866
240 M A 0.0000
241 L A -1.0174
242 E A -2.3872
243 S A 0.0000
244 I A 0.0000
245 R A -3.4585
246 K A -3.1534
247 E A -2.4967
248 V A -2.0651
249 K A -2.8465
250 G A -1.8917
251 D A -2.3264
252 L A 0.0000
253 E A 0.0000
254 N A -1.6690
255 A A 0.0000
256 F A 0.0000
257 L A -0.2552
258 N A 0.0000
259 L A 0.0000
260 V A 0.0000
261 Q A -0.5436
262 C A 0.0000
263 I A 0.0000
264 Q A -1.5860
265 N A -1.1543
266 K A -0.8475
267 P A 0.0000
268 L A -0.9144
269 Y A 0.0000
270 F A 0.0000
271 A A 0.0000
272 D A -0.9899
273 R A -0.8644
274 L A 0.0000
275 Y A -1.2208
276 D A -2.5403
277 S A 0.0000
278 M A 0.0000
279 K A -2.9535
280 G A -2.5672
281 K A -2.6307
282 G A -2.0122
283 T A -2.1020
284 R A -2.2749
285 D A -1.6183
286 K A -2.0925
287 V A -1.3747
288 L A 0.0000
289 I A 0.0000
290 R A 0.0000
291 I A 0.0000
292 M A 0.0000
293 V A 0.0000
294 S A -0.1238
295 R A 0.0000
296 S A 0.0000
297 E A -0.2668
298 V A 0.6644
299 D A 0.0000
300 M A 0.0000
301 L A -0.0214
302 K A -0.4893
303 I A 0.0000
304 R A 0.0000
305 S A -2.1991
306 E A -2.0864
307 F A 0.0000
308 K A -4.2125
309 R A -3.7885
310 K A -3.2497
311 Y A -2.2295
312 G A -2.6878
313 K A -2.7122
314 S A -2.4897
315 L A 0.0000
316 Y A -1.0477
317 Y A -0.8758
318 Y A -0.7902
319 I A 0.0000
320 Q A -1.7573
321 Q A -1.9331
322 D A -2.2590
323 T A -2.0808
324 K A -2.6516
325 G A -1.5139
326 D A -1.3618
327 Y A 0.0000
328 Q A -1.9295
329 K A -1.4072
330 A A 0.0000
331 L A 0.0000
332 L A 0.0000
333 Y A -0.1956
334 L A 0.0000
335 C A 0.0000
336 G A -1.0633
337 G A -1.3026
338 D A -3.0315
339 D A -2.8899
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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
VE54A -1.0689 -0.0222 View CSV PDB
VK185A -0.3976 -0.0274 View CSV PDB
VE185A -0.6294 -0.0198 View CSV PDB
VK54A -0.6672 -0.0184 View CSV PDB
LE121A -0.5568 -0.011 View CSV PDB
LD121A -0.1929 -0.0099 View CSV PDB
YK24A 0.2437 -0.0156 View CSV PDB
YR24A 0.4382 -0.019 View CSV PDB
IR186A 0.3662 -0.0127 View CSV PDB
IK186A 0.4367 -0.0118 View CSV PDB
VR298A -1.9273 0.0116 View CSV PDB
VK298A -0.6108 0.0043 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018