Project name: Tovhowani Mudau

Status: done

Started: 2024-01-28 09:12:12
Settings
Chain sequence(s) A: MEVLYSLSKTLKDARDKIVEGTLYSNVSDLIQQFNQMIATMNGNDFQTGGIGNLPIRNWTFDFGLLGTTLLNLDANYVETARTTIEYFIDFIDNVCMDEMARESQRNGPAPQSEALRKLAGIKFKRINFNNSSEYIENWNLQNRRQRTGFVFHKPNIFPYSASFTLNRSQPMHDNLMGTMWLNAGSEIQVAGFDYSCALNAPANIQQFEHIVQLRRALTTATITLLPDAERFSFPRVINSADGATTWFFNPIILRPNNVEVEFLLNGQIINTYQARFGTIVARNFDTIRLSFQLMRPPNMTPAVNALFPQAQPFQHHATVGLTLRIESAVCESVLADANETLLANVTAVRQEYAIPVGPVFPPGMNWTELITNYSPSREDNLQRVFTVASIRSMLIK
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                                          (00:04:35)
[INFO]       Auto_mut: Residue number 237 from chain A and a score of 2.048 (valine) selected for  
                       automated muatation                                                         (00:04:38)
[INFO]       Auto_mut: Residue number 248 from chain A and a score of 1.919 (phenylalanine)        
                       selected for automated muatation                                            (00:04:38)
[INFO]       Auto_mut: Residue number 24 from chain A and a score of 1.262 (tyrosine) selected for 
                       automated muatation                                                         (00:04:38)
[INFO]       Auto_mut: Residue number 151 from chain A and a score of 1.110 (valine) selected for  
                       automated muatation                                                         (00:04:38)
[INFO]       Auto_mut: Residue number 252 from chain A and a score of 1.026 (isoleucine) selected  
                       for automated muatation                                                     (00:04:38)
[INFO]       Auto_mut: Residue number 238 from chain A and a score of 0.958 (isoleucine) selected  
                       for automated muatation                                                     (00:04:38)
[INFO]       Auto_mut: Mutating residue number 237 from chain A (valine) into glutamic acid        (00:04:38)
[INFO]       Auto_mut: Mutating residue number 237 from chain A (valine) into aspartic acid        (00:04:38)
[INFO]       Auto_mut: Mutating residue number 248 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 248 from chain A (phenylalanine) into glutamic acid (00:04:38)
[INFO]       Auto_mut: Mutating residue number 237 from chain A (valine) into arginine             (00:06:39)
[INFO]       Auto_mut: Mutating residue number 237 from chain A (valine) into lysine               (00:06:39)
[INFO]       Auto_mut: Mutating residue number 248 from chain A (phenylalanine) into lysine        (00:06:41)
[INFO]       Auto_mut: Mutating residue number 248 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 248 from chain A (phenylalanine) into aspartic acid (00:08:43)
[INFO]       Auto_mut: Mutating residue number 24 from chain A (tyrosine) into glutamic acid       (00:08:45)
[INFO]       Auto_mut: Mutating residue number 24 from chain A (tyrosine) into aspartic acid       (00:09:06)
[INFO]       Auto_mut: Mutating residue number 248 from chain A (phenylalanine) into arginine      (00:10:45)
[INFO]       Auto_mut: Mutating residue number 24 from chain A (tyrosine) into lysine              (00:10:51)
[INFO]       Auto_mut: Mutating residue number 24 from chain A (tyrosine) into arginine            (00:11:09)
[INFO]       Auto_mut: Mutating residue number 151 from chain A (valine) into glutamic acid        (00:12:50)
[INFO]       Auto_mut: Mutating residue number 151 from chain A (valine) into aspartic acid        (00:12:53)
[INFO]       Auto_mut: Mutating residue number 252 from chain A (isoleucine) into glutamic acid    (00:13:20)
[INFO]       Auto_mut: Mutating residue number 151 from chain A (valine) into lysine               (00:14:51)
[INFO]       Auto_mut: Mutating residue number 151 from chain A (valine) into arginine             (00:14:53)
[INFO]       Auto_mut: Mutating residue number 252 from chain A (isoleucine) into lysine           (00:15:20)
[INFO]       Auto_mut: Mutating residue number 252 from chain A (isoleucine) into aspartic acid    (00:17:02)
[INFO]       Auto_mut: Mutating residue number 238 from chain A (isoleucine) into glutamic acid    (00:17:03)
[INFO]       Auto_mut: Mutating residue number 238 from chain A (isoleucine) into aspartic acid    (00:17:22)
[INFO]       Auto_mut: Mutating residue number 252 from chain A (isoleucine) into arginine         (00:19:04)
[INFO]       Auto_mut: Mutating residue number 238 from chain A (isoleucine) into lysine           (00:19:05)
[INFO]       Auto_mut: Mutating residue number 238 from chain A (isoleucine) into arginine         (00:19:25)
[INFO]       Auto_mut: Effect of mutation residue number 237 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.5860 kcal/mol, Difference in average score from 
                       the base case: -0.0223                                                      (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 237 from chain A (valine) into lysine:    
                       Energy difference: -0.9739 kcal/mol, Difference in average score from the   
                       base case: -0.0214                                                          (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 237 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.1666 kcal/mol, Difference in average score from 
                       the base case: -0.0234                                                      (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 237 from chain A (valine) into arginine:  
                       Energy difference: -0.4238 kcal/mol, Difference in average score from the   
                       base case: -0.0279                                                          (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 248 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: -0.1868 kcal/mol, Difference in average   
                       score from the base case: -0.0272                                           (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 248 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.2879 kcal/mol, Difference in average score     
                       from the base case: -0.0262                                                 (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 248 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 0.5426 kcal/mol, Difference in average    
                       score from the base case: -0.0218                                           (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 248 from chain A (phenylalanine) into     
                       arginine: Energy difference: -0.0944 kcal/mol, Difference in average score  
                       from the base case: -0.0270                                                 (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 24 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 0.0393 kcal/mol, Difference in average score from  
                       the base case: -0.0128                                                      (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 24 from chain A (tyrosine) into lysine:   
                       Energy difference: 0.2303 kcal/mol, Difference in average score from the    
                       base case: -0.0177                                                          (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 24 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 0.2665 kcal/mol, Difference in average score from  
                       the base case: -0.0144                                                      (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 24 from chain A (tyrosine) into arginine: 
                       Energy difference: 0.4578 kcal/mol, Difference in average score from the    
                       base case: -0.0226                                                          (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 151 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.1264 kcal/mol, Difference in average score from  
                       the base case: -0.0269                                                      (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 151 from chain A (valine) into lysine:    
                       Energy difference: -0.3027 kcal/mol, Difference in average score from the   
                       base case: -0.0179                                                          (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 151 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.3428 kcal/mol, Difference in average score from  
                       the base case: -0.0274                                                      (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 151 from chain A (valine) into arginine:  
                       Energy difference: -0.1861 kcal/mol, Difference in average score from the   
                       base case: -0.0185                                                          (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 252 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 2.3723 kcal/mol, Difference in average    
                       score from the base case: -0.0027                                           (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 252 from chain A (isoleucine) into        
                       lysine: Energy difference: 1.6199 kcal/mol, Difference in average score     
                       from the base case: -0.0019                                                 (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 252 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 2.6565 kcal/mol, Difference in average    
                       score from the base case: 0.0032                                            (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 252 from chain A (isoleucine) into        
                       arginine: Energy difference: 1.9870 kcal/mol, Difference in average score   
                       from the base case: -0.0023                                                 (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 238 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 2.2281 kcal/mol, Difference in average    
                       score from the base case: 0.0021                                            (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 238 from chain A (isoleucine) into        
                       lysine: Energy difference: 1.9641 kcal/mol, Difference in average score     
                       from the base case: 0.0077                                                  (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 238 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 2.0142 kcal/mol, Difference in average    
                       score from the base case: 0.0028                                            (00:21:37)
[INFO]       Auto_mut: Effect of mutation residue number 238 from chain A (isoleucine) into        
                       arginine: Energy difference: 2.3876 kcal/mol, Difference in average score   
                       from the base case: 0.0048                                                  (00:21:37)
[INFO]       Main:     Simulation completed successfully.                                          (00:21:45)
Show buried residues
Minimal score value
-3.8443
Maximal score value
2.0478
Average score
-0.7296
Total score value
-289.6372
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 -0.6620
2 E A -1.6869
3 V A 0.0000
4 L A 0.0000
5 Y A -0.3919
6 S A 0.0000
7 L A 0.0000
8 S A 0.0000
9 K A -1.0841
10 T A 0.0000
11 L A 0.0000
12 K A -1.8696
13 D A -1.6626
14 A A 0.0000
15 R A -2.5315
16 D A -2.4005
17 K A -1.4615
18 I A 0.0000
19 V A -1.9727
20 E A -2.5604
21 G A -1.1728
22 T A -0.4849
23 L A 0.6587
24 Y A 1.2624
25 S A -0.1457
26 N A -1.5538
27 V A 0.0000
28 S A -1.5958
29 D A -2.8033
30 L A 0.0000
31 I A 0.0000
32 Q A -2.0563
33 Q A -1.5195
34 F A 0.0000
35 N A 0.0000
36 Q A -0.8340
37 M A 0.0000
38 I A 0.0000
39 A A -0.3862
40 T A 0.0000
41 M A 0.0000
42 N A -1.5442
43 G A -1.5333
44 N A -1.8248
45 D A -2.8483
46 F A 0.0000
47 Q A -2.2257
48 T A 0.0000
49 G A -0.5643
50 G A -0.2803
51 I A -0.2074
52 G A -1.3853
53 N A -1.4981
54 L A 0.0000
55 P A -0.1541
56 I A 0.6144
57 R A -1.0835
58 N A -2.0710
59 W A 0.0000
60 T A -1.8583
61 F A 0.0000
62 D A -2.0294
63 F A -0.5459
64 G A -0.0246
65 L A 0.8736
66 L A 0.0000
67 G A -0.1215
68 T A -0.3665
69 T A 0.2298
70 L A 0.7723
71 L A 0.9561
72 N A -0.9294
73 L A -0.8258
74 D A -2.2090
75 A A -1.8274
76 N A -2.5139
77 Y A -1.8318
78 V A -1.9213
79 E A -2.6516
80 T A -1.5388
81 A A 0.0000
82 R A -2.2845
83 T A -1.2325
84 T A 0.0000
85 I A 0.0000
86 E A -1.6593
87 Y A -0.8188
88 F A 0.0000
89 I A -1.0244
90 D A -1.5543
91 F A 0.0000
92 I A 0.0000
93 D A -0.5787
94 N A 0.0000
95 V A 0.0000
96 C A 0.0000
97 M A 0.0000
98 D A 0.0000
99 E A 0.0000
100 M A 0.0000
101 A A 0.0000
102 R A -0.3210
103 E A -1.0354
104 S A 0.0000
105 Q A -2.8756
106 R A -3.2414
107 N A -2.5722
108 G A 0.0000
109 P A -1.2478
110 A A -1.0960
111 P A -1.4614
112 Q A -1.4296
113 S A 0.0000
114 E A -3.0823
115 A A 0.0000
116 L A 0.0000
117 R A -3.2588
118 K A -3.0288
119 L A 0.0000
120 A A -1.4091
121 G A -0.7569
122 I A 0.6220
123 K A -0.8404
124 F A 0.0000
125 K A -1.6460
126 R A -2.1591
127 I A 0.0000
128 N A -1.7542
129 F A -0.9626
130 N A -1.5828
131 N A -1.9697
132 S A -1.1232
133 S A -1.5416
134 E A -2.2258
135 Y A -0.3169
136 I A -0.6061
137 E A -2.1311
138 N A -1.7977
139 W A -0.3746
140 N A -1.1300
141 L A -1.3362
142 Q A -2.3252
143 N A -2.3838
144 R A -2.6984
145 R A -3.8443
146 Q A -3.6207
147 R A -3.4333
148 T A -2.0666
149 G A -1.1329
150 F A 0.0942
151 V A 1.1101
152 F A 0.0000
153 H A -1.7478
154 K A -2.4526
155 P A 0.0000
156 N A -2.1989
157 I A -0.9202
158 F A 0.0000
159 P A -0.5965
160 Y A 0.1926
161 S A 0.3384
162 A A 0.2769
163 S A 0.1229
164 F A 0.3605
165 T A -0.1331
166 L A -0.5323
167 N A -1.4695
168 R A -1.5459
169 S A -1.6328
170 Q A -1.4922
171 P A -0.9182
172 M A -0.1844
173 H A -1.7884
174 D A -2.1289
175 N A -1.7582
176 L A 0.0000
177 M A -0.8023
178 G A 0.0000
179 T A -0.4402
180 M A 0.0000
181 W A 0.0925
182 L A 0.0000
183 N A 0.0000
184 A A -0.2898
185 G A -1.2574
186 S A 0.0000
187 E A -0.9878
188 I A 0.0000
189 Q A 0.0000
190 V A 0.0000
191 A A 0.0000
192 G A 0.0000
193 F A 0.0000
194 D A 0.0000
195 Y A 0.0000
196 S A 0.0000
197 C A 0.0000
198 A A 0.0000
199 L A -0.7813
200 N A -1.5327
201 A A -0.9469
202 P A -0.6844
203 A A -0.4735
204 N A -0.8857
205 I A -0.4561
206 Q A -0.8371
207 Q A -1.8335
208 F A 0.0000
209 E A -2.2710
210 H A 0.0000
211 I A -0.5101
212 V A 0.0000
213 Q A -1.6997
214 L A -1.6244
215 R A -2.4658
216 R A -2.1653
217 A A -1.7135
218 L A 0.0000
219 T A -0.8930
220 T A -0.3664
221 A A 0.0000
222 T A -0.4461
223 I A 0.0000
224 T A -0.4270
225 L A 0.0000
226 L A -0.2849
227 P A -1.0438
228 D A -1.6650
229 A A 0.0000
230 E A -2.3883
231 R A -1.9770
232 F A 0.0000
233 S A -0.5346
234 F A 0.3943
235 P A 0.7517
236 R A 0.9729
237 V A 2.0478
238 I A 0.9580
239 N A -0.5091
240 S A -1.1929
241 A A -1.3651
242 D A -2.1871
243 G A -1.5749
244 A A -0.9765
245 T A -0.7931
246 T A 0.0054
247 W A 0.0000
248 F A 1.9192
249 F A 0.0000
250 N A 0.4843
251 P A 0.0000
252 I A 1.0256
253 I A 0.5378
254 L A -0.2059
255 R A -1.8522
256 P A 0.0000
257 N A -2.1685
258 N A -2.4864
259 V A 0.0000
260 E A -2.2298
261 V A 0.0000
262 E A -0.8158
263 F A 0.0000
264 L A 0.0000
265 L A -0.8739
266 N A -1.4622
267 G A -1.1850
268 Q A -0.9395
269 I A 0.5049
270 I A 0.4796
271 N A 0.0551
272 T A -0.3504
273 Y A -0.9494
274 Q A -2.1025
275 A A -1.8594
276 R A -1.9876
277 F A -0.3229
278 G A -0.2980
279 T A -0.1723
280 I A 0.0000
281 V A 0.7182
282 A A 0.0000
283 R A -1.6778
284 N A -1.1848
285 F A 0.0000
286 D A -1.6174
287 T A 0.0000
288 I A 0.0000
289 R A -1.5564
290 L A 0.0000
291 S A -2.0058
292 F A 0.0000
293 Q A -1.7401
294 L A 0.0000
295 M A -0.4138
296 R A 0.0000
297 P A -0.4372
298 P A -0.9261
299 N A -1.4012
300 M A -0.6158
301 T A -0.4059
302 P A -0.3980
303 A A 0.0725
304 V A 0.1142
305 N A -0.7325
306 A A -0.2142
307 L A 0.1592
308 F A 0.0000
309 P A -1.0501
310 Q A -1.6491
311 A A -1.1628
312 Q A -2.0802
313 P A -1.8304
314 F A 0.0000
315 Q A -1.1278
316 H A -0.1707
317 H A 0.0000
318 A A 0.0000
319 T A 0.0000
320 V A 0.0000
321 G A 0.0000
322 L A 0.0000
323 T A 0.0000
324 L A 0.0000
325 R A -1.3838
326 I A 0.0000
327 E A -1.9607
328 S A -0.9541
329 A A 0.0000
330 V A 0.1876
331 C A 0.0000
332 E A -2.1259
333 S A 0.0000
334 V A -1.8357
335 L A 0.0000
336 A A 0.0000
337 D A -2.7229
338 A A -1.4793
339 N A -2.0374
340 E A -1.6382
341 T A -0.7336
342 L A -0.4278
343 L A -0.4651
344 A A -0.2948
345 N A -0.4619
346 V A 0.0000
347 T A -0.4732
348 A A -0.9586
349 V A 0.0000
350 R A 0.0000
351 Q A -1.9626
352 E A -2.5416
353 Y A -1.6555
354 A A -1.1067
355 I A 0.0000
356 P A 0.1524
357 V A 0.9415
358 G A 0.2439
359 P A -0.1990
360 V A 0.0000
361 F A 0.2869
362 P A 0.0885
363 P A -0.2170
364 G A -0.7261
365 M A -0.9195
366 N A -1.6122
367 W A -0.9634
368 T A -1.0741
369 E A -1.9218
370 L A -1.0476
371 I A -0.9230
372 T A -0.8345
373 N A -1.5528
374 Y A 0.0000
375 S A 0.0000
376 P A -1.6057
377 S A -1.8449
378 R A -1.6802
379 E A -0.6613
380 D A -1.1781
381 N A 0.0000
382 L A 0.0000
383 Q A -0.5628
384 R A 0.0000
385 V A 0.0000
386 F A 0.0000
387 T A 0.0000
388 V A 0.0000
389 A A 0.0000
390 S A -0.1064
391 I A 0.0000
392 R A -0.2731
393 S A -0.3184
394 M A -0.3706
395 L A 0.0000
396 I A -0.3988
397 K A -1.4389
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
VK237A -0.9739 -0.0214 View CSV PDB
VR237A -0.4238 -0.0279 View CSV PDB
FE248A -0.1868 -0.0272 View CSV PDB
FR248A -0.0944 -0.027 View CSV PDB
VK151A -0.3027 -0.0179 View CSV PDB
VR151A -0.1861 -0.0185 View CSV PDB
YE24A 0.0393 -0.0128 View CSV PDB
YK24A 0.2303 -0.0177 View CSV PDB
IK252A 1.6199 -0.0019 View CSV PDB
IR252A 1.987 -0.0023 View CSV PDB
IE238A 2.2281 0.0021 View CSV PDB
ID238A 2.0142 0.0028 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018