Project name: 3-5M4

Status: done

Started: 2025-02-20 08:54:36
Settings
Chain sequence(s) A: FSRPGLPVEYLQVPSPSMGRDIKVQFQSGGNNSPAVYLLDGLRAQDDYNGWDINTPAFEWYYQSGLSIVMPVGGQSSFYSDWYSPACGKAGCQTYKWETFLTSELPQWLSANRAVKPTGSAAIGLSMAGSSAMILAAYHPQQFIYAGSLSALLDPSQGMGPSLIGLAMGDAGGYKAADMWGPSSDPAWERNDPTQQIPKLVANNTRLWVYCGNGTPNELGGANIPAEFLENFVRSSNLKFQDAYNAAGGHNAVFNFPPNGTHSWEYWGAQLNAMKGDLQSSLGAGFAVTNDGVI
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                                          (00:02:06)
[INFO]       Auto_mut: Residue number 294 from chain A and a score of 2.494 (isoleucine) selected  
                       for automated muatation                                                     (00:02:07)
[INFO]       Auto_mut: Residue number 286 from chain A and a score of 2.061 (phenylalanine)        
                       selected for automated muatation                                            (00:02:07)
[INFO]       Auto_mut: Residue number 293 from chain A and a score of 1.810 (valine) selected for  
                       automated muatation                                                         (00:02:07)
[INFO]       Auto_mut: Residue number 288 from chain A and a score of 1.664 (valine) selected for  
                       automated muatation                                                         (00:02:07)
[INFO]       Auto_mut: Residue number 228 from chain A and a score of 1.580 (phenylalanine)        
                       selected for automated muatation                                            (00:02:07)
[INFO]       Auto_mut: Residue number 224 from chain A and a score of 1.476 (isoleucine) selected  
                       for automated muatation                                                     (00:02:07)
[INFO]       Auto_mut: Mutating residue number 294 from chain A (isoleucine) into glutamic acid    (00:02:07)
[INFO]       Auto_mut: Mutating residue number 294 from chain A (isoleucine) into aspartic acid    (00:02:07)
[INFO]       Auto_mut: Mutating residue number 286 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 286 from chain A (phenylalanine) into glutamic acid (00:02:07)
[INFO]       Auto_mut: Mutating residue number 294 from chain A (isoleucine) into arginine         (00:03:09)
[INFO]       Auto_mut: Mutating residue number 294 from chain A (isoleucine) into lysine           (00:03:10)
[INFO]       Auto_mut: Mutating residue number 286 from chain A (phenylalanine) into lysine        (00:03:12)
[INFO]       Auto_mut: Mutating residue number 286 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 286 from chain A (phenylalanine) into aspartic acid (00:04:12)
[INFO]       Auto_mut: Mutating residue number 293 from chain A (valine) into glutamic acid        (00:04:13)
[INFO]       Auto_mut: Mutating residue number 293 from chain A (valine) into aspartic acid        (00:04:22)
[INFO]       Auto_mut: Mutating residue number 293 from chain A (valine) into lysine               (00:05:15)
[INFO]       Auto_mut: Mutating residue number 286 from chain A (phenylalanine) into arginine      (00:05:16)
[INFO]       Auto_mut: Mutating residue number 293 from chain A (valine) into arginine             (00:05:25)
[INFO]       Auto_mut: Mutating residue number 288 from chain A (valine) into glutamic acid        (00:06:20)
[INFO]       Auto_mut: Mutating residue number 288 from chain A (valine) into aspartic acid        (00:06:23)
[INFO]       Auto_mut: Mutating residue number 228 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 228 from chain A (phenylalanine) into glutamic acid (00:06:29)
[INFO]       Auto_mut: Mutating residue number 288 from chain A (valine) into lysine               (00:07:24)
[INFO]       Auto_mut: Mutating residue number 288 from chain A (valine) into arginine             (00:07:27)
[INFO]       Auto_mut: Mutating residue number 228 from chain A (phenylalanine) into lysine        (00:07:37)
[INFO]       Auto_mut: Mutating residue number 228 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 228 from chain A (phenylalanine) into aspartic acid (00:08:29)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into glutamic acid    (00:08:36)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into aspartic acid    (00:08:53)
[INFO]       Auto_mut: Mutating residue number 228 from chain A (phenylalanine) into arginine      (00:09:36)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into lysine           (00:09:40)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into arginine         (00:09:57)
[INFO]       Auto_mut: Effect of mutation residue number 294 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -0.2263 kcal/mol, Difference in average   
                       score from the base case: -0.0273                                           (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 294 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.2462 kcal/mol, Difference in average score    
                       from the base case: -0.0265                                                 (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 294 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: -0.1908 kcal/mol, Difference in average   
                       score from the base case: -0.0271                                           (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 294 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.2820 kcal/mol, Difference in average score  
                       from the base case: -0.0256                                                 (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 286 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 1.1724 kcal/mol, Difference in average    
                       score from the base case: -0.0453                                           (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 286 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.1751 kcal/mol, Difference in average score     
                       from the base case: -0.0434                                                 (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 286 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 2.1336 kcal/mol, Difference in average    
                       score from the base case: -0.0449                                           (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 286 from chain A (phenylalanine) into     
                       arginine: Energy difference: 1.3785 kcal/mol, Difference in average score   
                       from the base case: -0.0456                                                 (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 293 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.0995 kcal/mol, Difference in average score from 
                       the base case: -0.0319                                                      (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 293 from chain A (valine) into lysine:    
                       Energy difference: -0.9085 kcal/mol, Difference in average score from the   
                       base case: -0.0309                                                          (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 293 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.4017 kcal/mol, Difference in average score from 
                       the base case: -0.0316                                                      (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 293 from chain A (valine) into arginine:  
                       Energy difference: -1.3012 kcal/mol, Difference in average score from the   
                       base case: -0.0315                                                          (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 288 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.5671 kcal/mol, Difference in average score from 
                       the base case: -0.0388                                                      (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 288 from chain A (valine) into lysine:    
                       Energy difference: -0.4799 kcal/mol, Difference in average score from the   
                       base case: -0.0376                                                          (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 288 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.3729 kcal/mol, Difference in average score from 
                       the base case: -0.0385                                                      (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 288 from chain A (valine) into arginine:  
                       Energy difference: -0.8418 kcal/mol, Difference in average score from the   
                       base case: -0.0391                                                          (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 0.1868 kcal/mol, Difference in average    
                       score from the base case: -0.0451                                           (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       lysine: Energy difference: -0.1188 kcal/mol, Difference in average score    
                       from the base case: -0.0436                                                 (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 0.6122 kcal/mol, Difference in average    
                       score from the base case: -0.0502                                           (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       arginine: Energy difference: -0.2340 kcal/mol, Difference in average score  
                       from the base case: -0.0454                                                 (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -0.6204 kcal/mol, Difference in average   
                       score from the base case: -0.0449                                           (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.5064 kcal/mol, Difference in average score    
                       from the base case: -0.0463                                                 (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 0.1663 kcal/mol, Difference in average    
                       score from the base case: -0.0445                                           (00:11:02)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.5431 kcal/mol, Difference in average score  
                       from the base case: -0.0458                                                 (00:11:02)
[INFO]       Main:     Simulation completed successfully.                                          (00:11:07)
Show buried residues
Minimal score value
-2.9658
Maximal score value
2.4942
Average score
-0.4588
Total score value
-134.895
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 F A 1.3435
2 S A -0.2918
3 R A -1.7742
4 P A -1.1338
5 G A -1.0394
6 L A -0.6959
7 P A -0.3557
8 V A 0.0195
9 E A -0.3044
10 Y A 0.6260
11 L A 0.0000
12 Q A -1.8203
13 V A 0.0000
14 P A -1.6374
15 S A 0.0000
16 P A -1.0293
17 S A -0.7128
18 M A 0.0000
19 G A -1.3975
20 R A -2.0438
21 D A -2.7601
22 I A 0.0000
23 K A -1.3818
24 V A 0.0000
25 Q A 0.0000
26 F A 0.0000
27 Q A 0.0000
28 S A -0.9043
29 G A -1.0747
30 G A -1.6341
31 N A -2.3593
32 N A -2.5114
33 S A 0.0000
34 P A -1.0841
35 A A 0.0000
36 V A 0.0000
37 Y A 0.0000
38 L A 0.0000
39 L A 0.0000
40 D A 0.0000
41 G A 0.0000
42 L A -1.0970
43 R A -2.5038
44 A A 0.0000
45 Q A -2.4692
46 D A -2.9658
47 D A -2.0493
48 Y A -0.4392
49 N A 0.0000
50 G A 0.0000
51 W A 0.0000
52 D A 0.0000
53 I A 0.8777
54 N A -0.0834
55 T A 0.0000
56 P A -0.3457
57 A A 0.0000
58 F A 0.0000
59 E A -0.9580
60 W A -0.4594
61 Y A 0.0000
62 Y A -0.1104
63 Q A -0.7626
64 S A 0.0000
65 G A -0.5423
66 L A 0.0000
67 S A 0.0000
68 I A 0.0000
69 V A 0.0000
70 M A 0.0000
71 P A 0.0000
72 V A 0.0000
73 G A -1.5722
74 G A 0.0000
75 Q A -1.4431
76 S A 0.0000
77 S A 0.0000
78 F A 0.0000
79 Y A 0.0000
80 S A 0.0000
81 D A -0.5598
82 W A 0.0000
83 Y A 0.9571
84 S A 0.0908
85 P A -0.1348
86 A A 0.0000
87 C A -0.4245
88 G A -1.3956
89 K A -1.9324
90 A A -0.8461
91 G A -0.5158
92 C A 0.1128
93 Q A -0.5086
94 T A -0.4449
95 Y A 0.0000
96 K A -0.8645
97 W A 0.0000
98 E A -0.5625
99 T A -0.5063
100 F A 0.0000
101 L A 0.0000
102 T A -0.3697
103 S A -0.5237
104 E A -0.6809
105 L A 0.0000
106 P A 0.0000
107 Q A -1.5530
108 W A -0.8421
109 L A 0.0000
110 S A -1.5544
111 A A -0.9572
112 N A -1.2645
113 R A -1.7037
114 A A -1.8580
115 V A 0.0000
116 K A -2.1132
117 P A -1.3238
118 T A -0.9359
119 G A -0.5915
120 S A 0.0000
121 A A 0.0000
122 A A 0.0000
123 I A 0.0000
124 G A 0.0000
125 L A 0.0000
126 S A 0.0749
127 M A 0.0000
128 A A 0.0000
129 G A 0.0000
130 S A 0.0000
131 S A 0.0000
132 A A 0.0000
133 M A 0.0000
134 I A 0.0000
135 L A 0.0000
136 A A 0.0000
137 A A 0.0000
138 Y A -0.2560
139 H A -0.4396
140 P A -0.9783
141 Q A -1.2847
142 Q A -0.8310
143 F A 0.0000
144 I A -0.3137
145 Y A 0.0000
146 A A 0.0000
147 G A 0.0000
148 S A 0.0000
149 L A 0.0000
150 S A 0.0000
151 A A 0.0000
152 L A 0.2232
153 L A 0.0000
154 D A -0.8688
155 P A 0.0000
156 S A -1.1675
157 Q A -1.1053
158 G A -0.3575
159 M A 0.5620
160 G A 0.0000
161 P A 0.0723
162 S A 0.4650
163 L A 0.9330
164 I A 0.0000
165 G A -0.0464
166 L A 0.7111
167 A A -0.3250
168 M A 0.0000
169 G A -1.3093
170 D A -2.0960
171 A A 0.0000
172 G A -1.8346
173 G A -1.6178
174 Y A 0.0000
175 K A -1.8425
176 A A -0.7342
177 A A -0.6792
178 D A -0.4919
179 M A 0.0000
180 W A 0.0000
181 G A 0.0000
182 P A -0.6345
183 S A -0.9259
184 S A -0.8721
185 D A -1.1067
186 P A -1.1797
187 A A 0.0000
188 W A 0.0000
189 E A -2.2214
190 R A -1.4031
191 N A 0.0000
192 D A 0.0000
193 P A 0.0000
194 T A -1.2172
195 Q A -1.5500
196 Q A 0.0000
197 I A 0.0000
198 P A -1.0072
199 K A -1.3365
200 L A 0.0000
201 V A -1.1907
202 A A -0.9123
203 N A -1.4572
204 N A -1.7787
205 T A 0.0000
206 R A -0.9490
207 L A 0.0000
208 W A 0.0000
209 V A 0.0000
210 Y A 0.0000
211 C A 0.0000
212 G A 0.0000
213 N A -0.8103
214 G A 0.0000
215 T A -1.0732
216 P A -1.2272
217 N A -1.4074
218 E A -1.8830
219 L A -0.9154
220 G A -1.1333
221 G A -0.9994
222 A A -0.5620
223 N A -0.5190
224 I A 1.4761
225 P A 0.7288
226 A A 0.1066
227 E A -0.0698
228 F A 1.5800
229 L A 1.1256
230 E A 0.0000
231 N A -0.7595
232 F A 0.2284
233 V A 0.0000
234 R A -0.4251
235 S A -0.6670
236 S A 0.0000
237 N A 0.0000
238 L A -0.5653
239 K A -1.8339
240 F A 0.0000
241 Q A -1.4606
242 D A -2.5043
243 A A -1.6987
244 Y A 0.0000
245 N A -2.1828
246 A A -1.2244
247 A A -0.9132
248 G A -1.0508
249 G A -1.6610
250 H A -1.6066
251 N A -1.2435
252 A A -0.5368
253 V A 0.2791
254 F A 0.5144
255 N A -0.0785
256 F A 0.0554
257 P A -0.2926
258 P A -0.5738
259 N A -0.7988
260 G A 0.0000
261 T A 0.0000
262 H A -0.6855
263 S A -0.6840
264 W A -0.6110
265 E A -1.3680
266 Y A 0.0000
267 W A 0.0000
268 G A 0.0000
269 A A -0.5635
270 Q A -0.6512
271 L A 0.0000
272 N A -0.9902
273 A A -0.6460
274 M A 0.0000
275 K A -1.0598
276 G A -1.0474
277 D A -0.8353
278 L A 0.0000
279 Q A -0.6907
280 S A -0.8292
281 S A -0.5448
282 L A -0.4131
283 G A -0.5148
284 A A -0.3728
285 G A 0.5307
286 F A 2.0605
287 A A 1.2322
288 V A 1.6637
289 T A -0.1621
290 N A -1.5220
291 D A -1.6164
292 G A -0.3285
293 V A 1.8103
294 I A 2.4942
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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
VR293A -1.3012 -0.0315 View CSV PDB
VR288A -0.8418 -0.0391 View CSV PDB
IE224A -0.6204 -0.0449 View CSV PDB
IR224A -0.5431 -0.0458 View CSV PDB
VK293A -0.9085 -0.0309 View CSV PDB
VE288A -0.5671 -0.0388 View CSV PDB
FR228A -0.234 -0.0454 View CSV PDB
FK228A -0.1188 -0.0436 View CSV PDB
IR294A -0.282 -0.0256 View CSV PDB
IE294A -0.2263 -0.0273 View CSV PDB
FK286A 0.1751 -0.0434 View CSV PDB
FE286A 1.1724 -0.0453 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018