Project name: HDA7

Status: done

Started: 2026-04-16 06:24:06
Settings
Chain sequence(s) A: GKRRVSYFYEPMIGDYYYGVNQPTKPQRIRVTHNLILSYNLHRHMEINHPDLADASDFEKFHSLEYINFLKSVTPETVTDPHPSVSENLKRFNVDVDWDGPVFHNLFDYCRAYAGGSISAAAKLNRQEADIAINWAGGMHHVKKDKASGFGYVNDVVLAILELLKSFKRVLYIEIGFPHGDEVEEAFKDTDRVMTVSFHKVGDTGDISDYGEGKGQYYSLNAPLKDGLDDFSLRGLFIPVIHRAMEIYEPEVIVLQCGADSLAGDPFGTFNLSIKGHGDCLQYVRSFNVPLMILGGGGYTLPNVARCWCYETAIAVGEQLDNDLPGNDYMKYFRPDYKLHILPTNRQNLNTRLDIITMRETLLAQLSLVMHAPSVP
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                                          (00:05:00)
[INFO]       Auto_mut: Residue number 274 from chain A and a score of 1.819 (phenylalanine)        
                       selected for automated muatation                                            (00:05:03)
[INFO]       Auto_mut: Residue number 382 from chain A and a score of 1.405 (valine) selected for  
                       automated muatation                                                         (00:05:03)
[INFO]       Auto_mut: Residue number 349 from chain A and a score of 1.264 (leucine) selected for 
                       automated muatation                                                         (00:05:03)
[INFO]       Auto_mut: Residue number 377 from chain A and a score of 1.157 (methionine) selected  
                       for automated muatation                                                     (00:05:03)
[INFO]       Auto_mut: Residue number 375 from chain A and a score of 0.931 (leucine) selected for 
                       automated muatation                                                         (00:05:03)
[INFO]       Auto_mut: Residue number 27 from chain A and a score of 0.846 (valine) selected for   
                       automated muatation                                                         (00:05:03)
[INFO]       Auto_mut: Mutating residue number 382 from chain A (valine) into glutamic acid        (00:05:03)
[INFO]       Auto_mut: Mutating residue number 274 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 274 from chain A (phenylalanine) into aspartic acid (00:05:03)
[INFO]       Auto_mut: Mutating residue number 274 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 274 from chain A (phenylalanine) into glutamic acid (00:05:03)
[INFO]       Auto_mut: Mutating residue number 274 from chain A (phenylalanine) into arginine      (00:07:33)
[INFO]       Auto_mut: Mutating residue number 382 from chain A (valine) into lysine               (00:07:40)
[INFO]       Auto_mut: Mutating residue number 274 from chain A (phenylalanine) into lysine        (00:07:40)
[INFO]       Auto_mut: Mutating residue number 382 from chain A (valine) into aspartic acid        (00:10:06)
[INFO]       Auto_mut: Mutating residue number 349 from chain A (leucine) into glutamic acid       (00:10:19)
[INFO]       Auto_mut: Mutating residue number 349 from chain A (leucine) into aspartic acid       (00:10:23)
[INFO]       Auto_mut: Mutating residue number 382 from chain A (valine) into arginine             (00:12:27)
[INFO]       Auto_mut: Mutating residue number 349 from chain A (leucine) into arginine            (00:12:45)
[INFO]       Auto_mut: Mutating residue number 349 from chain A (leucine) into lysine              (00:13:06)
[INFO]       Auto_mut: Mutating residue number 377 from chain A (methionine) into glutamic acid    (00:15:18)
[INFO]       Auto_mut: Mutating residue number 377 from chain A (methionine) into aspartic acid    (00:15:26)
[INFO]       Auto_mut: Mutating residue number 375 from chain A (leucine) into glutamic acid       (00:16:00)
[INFO]       Auto_mut: Mutating residue number 377 from chain A (methionine) into lysine           (00:17:42)
[INFO]       Auto_mut: Mutating residue number 377 from chain A (methionine) into arginine         (00:17:50)
[INFO]       Auto_mut: Mutating residue number 375 from chain A (leucine) into lysine              (00:18:24)
[INFO]       Auto_mut: Mutating residue number 375 from chain A (leucine) into aspartic acid       (00:19:59)
[INFO]       Auto_mut: Mutating residue number 27 from chain A (valine) into glutamic acid         (00:20:03)
[INFO]       Auto_mut: Mutating residue number 27 from chain A (valine) into aspartic acid         (00:20:58)
[INFO]       Auto_mut: Mutating residue number 27 from chain A (valine) into lysine                (00:22:19)
[INFO]       Auto_mut: Mutating residue number 375 from chain A (leucine) into arginine            (00:22:21)
[INFO]       Auto_mut: Mutating residue number 27 from chain A (valine) into arginine              (00:23:40)
[INFO]       Auto_mut: Effect of mutation residue number 274 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 1.1661 kcal/mol, Difference in average    
                       score from the base case: -0.0300                                           (00:25:59)
[INFO]       Auto_mut: Effect of mutation residue number 274 from chain A (phenylalanine) into     
                       lysine: Energy difference: -0.2775 kcal/mol, Difference in average score    
                       from the base case: -0.0293                                                 (00:25:59)
[INFO]       Auto_mut: Effect of mutation residue number 274 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 1.4701 kcal/mol, Difference in average    
                       score from the base case: -0.0280                                           (00:25:59)
[INFO]       Auto_mut: Effect of mutation residue number 274 from chain A (phenylalanine) into     
                       arginine: Energy difference: -2.0572 kcal/mol, Difference in average score  
                       from the base case: -0.0294                                                 (00:25:59)
[INFO]       Auto_mut: Effect of mutation residue number 382 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.2061 kcal/mol, Difference in average score from  
                       the base case: -0.0288                                                      (00:26:00)
[INFO]       Auto_mut: Effect of mutation residue number 382 from chain A (valine) into lysine:    
                       Energy difference: -0.2020 kcal/mol, Difference in average score from the   
                       base case: -0.0274                                                          (00:26:00)
[INFO]       Auto_mut: Effect of mutation residue number 382 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.4262 kcal/mol, Difference in average score from  
                       the base case: -0.0284                                                      (00:26:00)
[INFO]       Auto_mut: Effect of mutation residue number 382 from chain A (valine) into arginine:  
                       Energy difference: -1.1039 kcal/mol, Difference in average score from the   
                       base case: -0.0290                                                          (00:26:00)
[INFO]       Auto_mut: Effect of mutation residue number 349 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.1167 kcal/mol, Difference in average score from  
                       the base case: -0.0253                                                      (00:26:00)
[INFO]       Auto_mut: Effect of mutation residue number 349 from chain A (leucine) into lysine:   
                       Energy difference: -0.0341 kcal/mol, Difference in average score from the   
                       base case: -0.0234                                                          (00:26:00)
[INFO]       Auto_mut: Effect of mutation residue number 349 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.4817 kcal/mol, Difference in average score from  
                       the base case: -0.0245                                                      (00:26:00)
[INFO]       Auto_mut: Effect of mutation residue number 349 from chain A (leucine) into arginine: 
                       Energy difference: -0.1257 kcal/mol, Difference in average score from the   
                       base case: -0.0244                                                          (00:26:00)
[INFO]       Auto_mut: Effect of mutation residue number 377 from chain A (methionine) into        
                       glutamic acid: Energy difference: -0.0553 kcal/mol, Difference in average   
                       score from the base case: -0.0224                                           (00:26:00)
[INFO]       Auto_mut: Effect of mutation residue number 377 from chain A (methionine) into        
                       lysine: Energy difference: -0.3442 kcal/mol, Difference in average score    
                       from the base case: -0.0215                                                 (00:26:00)
[INFO]       Auto_mut: Effect of mutation residue number 377 from chain A (methionine) into        
                       aspartic acid: Energy difference: 0.5901 kcal/mol, Difference in average    
                       score from the base case: -0.0212                                           (00:26:00)
[INFO]       Auto_mut: Effect of mutation residue number 377 from chain A (methionine) into        
                       arginine: Energy difference: -0.7958 kcal/mol, Difference in average score  
                       from the base case: -0.0215                                                 (00:26:00)
[INFO]       Auto_mut: Effect of mutation residue number 375 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.6356 kcal/mol, Difference in average score from  
                       the base case: -0.0173                                                      (00:26:00)
[INFO]       Auto_mut: Effect of mutation residue number 375 from chain A (leucine) into lysine:   
                       Energy difference: 0.2174 kcal/mol, Difference in average score from the    
                       base case: -0.0178                                                          (00:26:00)
[INFO]       Auto_mut: Effect of mutation residue number 375 from chain A (leucine) into aspartic  
                       acid: Energy difference: 1.1394 kcal/mol, Difference in average score from  
                       the base case: -0.0147                                                      (00:26:00)
[INFO]       Auto_mut: Effect of mutation residue number 375 from chain A (leucine) into arginine: 
                       Energy difference: 0.3023 kcal/mol, Difference in average score from the    
                       base case: -0.0202                                                          (00:26:00)
[INFO]       Auto_mut: Effect of mutation residue number 27 from chain A (valine) into glutamic    
                       acid: Energy difference: -0.3841 kcal/mol, Difference in average score from 
                       the base case: -0.0386                                                      (00:26:00)
[INFO]       Auto_mut: Effect of mutation residue number 27 from chain A (valine) into lysine:     
                       Energy difference: -0.5323 kcal/mol, Difference in average score from the   
                       base case: -0.0377                                                          (00:26:00)
[INFO]       Auto_mut: Effect of mutation residue number 27 from chain A (valine) into aspartic    
                       acid: Energy difference: -0.0430 kcal/mol, Difference in average score from 
                       the base case: -0.0385                                                      (00:26:00)
[INFO]       Auto_mut: Effect of mutation residue number 27 from chain A (valine) into arginine:   
                       Energy difference: -1.0135 kcal/mol, Difference in average score from the   
                       base case: -0.0343                                                          (00:26:00)
[INFO]       Main:     Simulation completed successfully.                                          (00:26:08)
Show buried residues
Minimal score value
-4.0764
Maximal score value
1.8193
Average score
-0.7183
Total score value
-270.0869
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
8 G A -1.5551
9 K A -2.6103
10 R A -2.4000
11 R A -3.0696
12 V A 0.0000
13 S A 0.0000
14 Y A 0.0000
15 F A 0.0000
16 Y A 0.0000
17 E A 0.0000
18 P A -0.2039
19 M A 0.5595
20 I A 0.0000
21 G A 0.0000
22 D A -0.1155
23 Y A 0.1403
24 Y A 0.0000
25 Y A -0.3426
26 G A 0.0654
27 V A 0.8464
28 N A -0.7859
29 Q A -0.8001
30 P A -0.5998
31 T A -0.8896
32 K A -1.1468
33 P A -0.5847
34 Q A 0.0000
35 R A 0.0000
36 I A 0.0000
37 R A -0.4637
38 V A 0.0000
39 T A 0.0000
40 H A -0.2111
41 N A -0.6270
42 L A 0.0000
43 I A 0.0000
44 L A -0.0369
45 S A -0.3935
46 Y A -0.7955
47 N A -1.1740
48 L A 0.0000
49 H A -1.6870
50 R A -2.5974
51 H A -2.5631
52 M A -1.8376
53 E A -2.1450
54 I A -0.5388
55 N A -0.8763
56 H A -1.4576
57 P A 0.0000
58 D A -1.9737
59 L A -1.0778
60 A A 0.0000
61 D A -1.8842
62 A A -1.7913
63 S A -1.7745
64 D A -2.3127
65 F A 0.0000
66 E A -3.2251
67 K A -2.8077
68 F A 0.0000
69 H A 0.0000
70 S A -1.5499
71 L A -0.6354
72 E A -1.8084
73 Y A 0.0000
74 I A 0.0000
75 N A -2.1430
76 F A 0.0000
77 L A 0.0000
78 K A -1.8472
79 S A -1.2173
80 V A 0.0000
81 T A -0.9684
82 P A -1.1719
83 E A -2.1825
84 T A -1.4118
85 V A 0.0000
86 T A -1.5466
87 D A -2.4133
88 P A -2.0028
89 H A -1.8062
90 P A -1.5049
91 S A -1.1879
92 V A -1.5970
93 S A -2.1577
94 E A -3.3771
95 N A -2.6596
96 L A 0.0000
97 K A -4.0764
98 R A -3.8234
99 F A 0.0000
100 N A -3.5363
101 V A 0.0000
102 D A -2.6783
103 V A -1.5722
104 D A -2.0900
105 W A -1.0466
106 D A -0.8262
107 G A 0.0000
108 P A 0.0000
109 V A 0.0000
110 F A -0.2823
111 H A -0.4854
112 N A -0.5887
113 L A 0.0000
114 F A -0.7275
115 D A -0.7452
116 Y A 0.0000
117 C A 0.0000
118 R A -1.0124
119 A A 0.0000
120 Y A 0.0000
121 A A 0.0000
122 G A 0.0000
123 G A 0.0000
124 S A 0.0000
125 I A -0.0806
126 S A -0.5600
127 A A 0.0000
128 A A 0.0000
129 A A -1.2522
130 K A -1.8201
131 L A 0.0000
132 N A -2.2044
133 R A -3.1968
134 Q A -3.3518
135 E A -3.4508
136 A A 0.0000
137 D A -2.1197
138 I A 0.0000
139 A A 0.0000
140 I A 0.0000
141 N A 0.0000
142 W A 0.0000
143 A A 0.0000
144 G A 0.0000
145 G A 0.0000
146 M A 0.0000
147 H A 0.0000
148 H A -1.0387
149 V A 0.0000
150 K A -2.3862
151 K A -2.5618
152 D A -2.4197
153 K A -2.7368
154 A A 0.0000
155 S A -1.1769
156 G A -0.7953
157 F A -0.1584
158 G A 0.0000
159 Y A 0.0000
160 V A 0.0000
161 N A 0.0000
162 D A 0.0000
163 V A 0.0000
164 V A 0.0000
165 L A 0.0000
166 A A 0.0000
167 I A 0.0000
168 L A -0.2573
169 E A -0.4966
170 L A 0.0000
171 L A -1.0304
172 K A -1.8646
173 S A -1.6182
174 F A 0.0000
175 K A -1.7119
176 R A -1.5602
177 V A 0.0000
178 L A 0.0000
179 Y A 0.0000
180 I A 0.0000
181 E A 0.0000
182 I A 0.0000
183 G A 0.0000
184 F A 0.3841
185 P A 0.0082
186 H A 0.0000
187 G A 0.0000
188 D A -1.4052
189 E A 0.0000
190 V A 0.0000
191 E A 0.0000
192 E A -2.3625
193 A A -1.4101
194 F A 0.0000
195 K A -2.8919
196 D A -3.7367
197 T A -2.2749
198 D A -1.5868
199 R A -1.3188
200 V A 0.0000
201 M A 0.0000
202 T A 0.0000
203 V A 0.0000
204 S A 0.0000
205 F A 0.0000
206 H A 0.0000
207 K A -0.7181
208 V A -0.5476
209 G A -1.4608
210 D A -2.2652
211 T A -1.6536
212 G A 0.0000
213 D A -2.1039
214 I A -0.6139
215 S A -0.8131
216 D A -1.5268
217 Y A -0.7051
218 G A -2.3611
219 E A -3.4479
220 G A -2.9385
221 K A -3.1322
222 G A 0.0000
223 Q A -2.2264
224 Y A -0.6006
225 Y A 0.0000
226 S A 0.0000
227 L A 0.0000
228 N A 0.0000
229 A A 0.0000
230 P A -0.4324
231 L A 0.0000
232 K A -0.9141
233 D A -1.4372
234 G A 0.0000
235 L A 0.0000
236 D A -0.9087
237 D A -0.8170
238 F A 0.3275
239 S A 0.0000
240 L A 0.0000
241 R A -1.6146
242 G A -0.7269
243 L A 0.0000
244 F A 0.0000
245 I A -0.7305
246 P A -1.0106
247 V A 0.0000
248 I A 0.0000
249 H A -1.5342
250 R A -2.2371
251 A A 0.0000
252 M A -1.8624
253 E A -2.5411
254 I A -1.0508
255 Y A 0.0000
256 E A -2.4926
257 P A 0.0000
258 E A -1.7172
259 V A 0.0000
260 I A 0.0000
261 V A 0.0000
262 L A 0.0000
263 Q A 0.0000
264 C A 0.0000
265 G A 0.0000
266 A A 0.0000
267 D A 0.0000
268 S A 0.0000
269 L A 0.0000
270 A A 0.0000
271 G A -0.4339
272 D A 0.0000
273 P A 0.6255
274 F A 1.8193
275 G A 0.6303
276 T A -0.5883
277 F A 0.0000
278 N A 0.0000
279 L A 0.0000
280 S A 0.0000
281 I A 0.0000
282 K A -1.3567
283 G A 0.0000
284 H A 0.0000
285 G A 0.0000
286 D A -1.9638
287 C A 0.0000
288 L A 0.0000
289 Q A -1.1834
290 Y A -0.7011
291 V A 0.0000
292 R A -0.8294
293 S A -0.5536
294 F A -0.4909
295 N A -1.2986
296 V A -0.8340
297 P A -0.9332
298 L A 0.0000
299 M A 0.0000
300 I A 0.0000
301 L A 0.0000
302 G A 0.0000
303 G A 0.0000
304 G A 0.1967
305 G A 0.0000
306 Y A 0.6746
307 T A 0.3323
308 L A 0.3775
309 P A -0.1228
310 N A -0.0029
311 V A 0.0000
312 A A 0.0000
313 R A 0.0000
314 C A 0.0000
315 W A 0.0000
316 C A 0.0000
317 Y A -0.4977
318 E A 0.0000
319 T A 0.0000
320 A A 0.0000
321 I A 0.0000
322 A A 0.0000
323 V A 0.0000
324 G A -1.3476
325 E A -1.5591
326 Q A -1.9002
327 L A -1.8443
328 D A -2.9400
329 N A -2.4751
330 D A -3.0476
331 L A 0.0000
332 P A -1.0971
333 G A -1.0404
334 N A -1.3092
335 D A -2.0827
336 Y A -1.2412
337 M A -1.3503
338 K A -2.1277
339 Y A -0.9026
340 F A 0.0000
341 R A -2.8468
342 P A -2.3444
343 D A -2.6903
344 Y A -1.9854
345 K A -2.3616
346 L A 0.0000
347 H A -0.8599
348 I A 0.3508
349 L A 1.2641
350 P A -0.1322
351 T A -1.1978
352 N A -2.4116
353 R A -3.2406
354 Q A -2.5642
355 N A -1.7906
356 L A -0.7420
357 N A 0.0000
358 T A -0.4358
359 R A -0.8374
360 L A 0.6547
361 D A -0.0956
362 I A 0.0000
363 I A 0.1169
364 T A -0.3417
365 M A -0.2535
366 R A -0.8132
367 E A -1.6986
368 T A -0.7615
369 L A 0.0000
370 L A -0.6760
371 A A -0.1869
372 Q A 0.0000
373 L A 0.0000
374 S A 0.4750
375 L A 0.9313
376 V A 0.0000
377 M A 1.1565
378 H A -0.0684
379 A A -0.1303
380 P A -0.3542
381 S A 0.3100
382 V A 1.4045
383 P A 0.1513
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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
FR274A -2.0572 -0.0294 View CSV PDB
VR27A -1.0135 -0.0343 View CSV PDB
VR382A -1.1039 -0.029 View CSV PDB
VK27A -0.5323 -0.0377 View CSV PDB
MR377A -0.7958 -0.0215 View CSV PDB
FK274A -0.2775 -0.0293 View CSV PDB
VK382A -0.202 -0.0274 View CSV PDB
MK377A -0.3442 -0.0215 View CSV PDB
LR349A -0.1257 -0.0244 View CSV PDB
LK349A -0.0341 -0.0234 View CSV PDB
LK375A 0.2174 -0.0178 View CSV PDB
LR375A 0.3023 -0.0202 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018