Project name: 3-5M1

Status: done

Started: 2025-02-20 08:45:35
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]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:01:56)
[INFO]       Auto_mut: Residue number 294 from chain A and a score of 2.595 (isoleucine) selected  
                       for automated muatation                                                     (00:01:58)
[INFO]       Auto_mut: Residue number 286 from chain A and a score of 2.105 (phenylalanine)        
                       selected for automated muatation                                            (00:01:58)
[INFO]       Auto_mut: Residue number 293 from chain A and a score of 1.979 (valine) selected for  
                       automated muatation                                                         (00:01:58)
[INFO]       Auto_mut: Residue number 224 from chain A and a score of 1.826 (isoleucine) selected  
                       for automated muatation                                                     (00:01:58)
[INFO]       Auto_mut: Residue number 228 from chain A and a score of 1.783 (phenylalanine)        
                       selected for automated muatation                                            (00:01:58)
[INFO]       Auto_mut: Residue number 288 from chain A and a score of 1.694 (valine) selected for  
                       automated muatation                                                         (00:01:58)
[INFO]       Auto_mut: Mutating residue number 294 from chain A (isoleucine) into aspartic acid    (00:01:58)
[INFO]       Auto_mut: Mutating residue number 294 from chain A (isoleucine) into glutamic acid    (00:01:58)
[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 (00:01:58)
[INFO]       Auto_mut: Mutating residue number 294 from chain A (isoleucine) into arginine         (00:02:55)
[INFO]       Auto_mut: Mutating residue number 294 from chain A (isoleucine) into lysine           (00:02:55)
[INFO]       Auto_mut: Mutating residue number 286 from chain A (phenylalanine) into lysine        (00:02:57)
[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 (00:03:53)
[INFO]       Auto_mut: Mutating residue number 293 from chain A (valine) into glutamic acid        (00:03:53)
[INFO]       Auto_mut: Mutating residue number 293 from chain A (valine) into aspartic acid        (00:04:04)
[INFO]       Auto_mut: Mutating residue number 286 from chain A (phenylalanine) into arginine      (00:04:51)
[INFO]       Auto_mut: Mutating residue number 293 from chain A (valine) into lysine               (00:04:53)
[INFO]       Auto_mut: Mutating residue number 293 from chain A (valine) into arginine             (00:05:04)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into glutamic acid    (00:05:54)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into aspartic acid    (00:05:56)
[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 (00:06:05)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into arginine         (00:06:56)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into lysine           (00:06:58)
[INFO]       Auto_mut: Mutating residue number 228 from chain A (phenylalanine) into lysine        (00:07:10)
[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 (00:08:07)
[INFO]       Auto_mut: Mutating residue number 288 from chain A (valine) into glutamic acid        (00:08:10)
[INFO]       Auto_mut: Mutating residue number 288 from chain A (valine) into aspartic acid        (00:08:33)
[INFO]       Auto_mut: Mutating residue number 228 from chain A (phenylalanine) into arginine      (00:09:09)
[INFO]       Auto_mut: Mutating residue number 288 from chain A (valine) into lysine               (00:09:10)
[INFO]       Auto_mut: Mutating residue number 288 from chain A (valine) into arginine             (00:09:32)
[INFO]       Auto_mut: Effect of mutation residue number 294 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 0.0196 kcal/mol, Difference in average    
                       score from the base case: -0.0273                                           (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 294 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.7450 kcal/mol, Difference in average score    
                       from the base case: -0.0266                                                 (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 294 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 0.0272 kcal/mol, Difference in average    
                       score from the base case: -0.0271                                           (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 294 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.7720 kcal/mol, Difference in average score  
                       from the base case: -0.0274                                                 (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 286 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: -1.8071 kcal/mol, Difference in average   
                       score from the base case: -0.0445                                           (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 286 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.2571 kcal/mol, Difference in average score     
                       from the base case: -0.0432                                                 (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 286 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 0.6111 kcal/mol, Difference in average    
                       score from the base case: -0.0442                                           (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 286 from chain A (phenylalanine) into     
                       arginine: Energy difference: -0.1986 kcal/mol, Difference in average score  
                       from the base case: -0.0444                                                 (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 293 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.7046 kcal/mol, Difference in average score from 
                       the base case: -0.0322                                                      (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 293 from chain A (valine) into lysine:    
                       Energy difference: -0.4578 kcal/mol, Difference in average score from the   
                       base case: -0.0312                                                          (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 293 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.1999 kcal/mol, Difference in average score from  
                       the base case: -0.0319                                                      (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 293 from chain A (valine) into arginine:  
                       Energy difference: -0.6511 kcal/mol, Difference in average score from the   
                       base case: -0.0324                                                          (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -0.7733 kcal/mol, Difference in average   
                       score from the base case: -0.0414                                           (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.2008 kcal/mol, Difference in average score    
                       from the base case: -0.0470                                                 (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 0.2437 kcal/mol, Difference in average    
                       score from the base case: -0.0450                                           (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.2835 kcal/mol, Difference in average score  
                       from the base case: -0.0481                                                 (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 0.1539 kcal/mol, Difference in average    
                       score from the base case: -0.0441                                           (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       lysine: Energy difference: -0.0892 kcal/mol, Difference in average score    
                       from the base case: -0.0471                                                 (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 0.6265 kcal/mol, Difference in average    
                       score from the base case: -0.0473                                           (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       arginine: Energy difference: -0.2524 kcal/mol, Difference in average score  
                       from the base case: -0.0552                                                 (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 288 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.5620 kcal/mol, Difference in average score from 
                       the base case: -0.0395                                                      (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 288 from chain A (valine) into lysine:    
                       Energy difference: -0.6521 kcal/mol, Difference in average score from the   
                       base case: -0.0383                                                          (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 288 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.3683 kcal/mol, Difference in average score from 
                       the base case: -0.0392                                                      (00:10:34)
[INFO]       Auto_mut: Effect of mutation residue number 288 from chain A (valine) into arginine:  
                       Energy difference: -0.7722 kcal/mol, Difference in average score from the   
                       base case: -0.0397                                                          (00:10:34)
[INFO]       Main:     Simulation completed successfully.                                          (00:10:40)
Show buried residues
Minimal score value
-2.9252
Maximal score value
2.5951
Average score
-0.439
Total score value
-129.0606
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 1.4608
2 S A -0.1949
3 R A -1.6787
4 P A -1.0989
5 G A -1.0393
6 L A -0.6943
7 P A -0.5791
8 V A -0.2888
9 E A -0.3148
10 Y A 0.5773
11 L A 0.0000
12 Q A -1.8393
13 V A 0.0000
14 P A -1.5636
15 S A 0.0000
16 P A -0.9786
17 S A -0.7225
18 M A 0.0000
19 G A -1.3145
20 R A -1.9201
21 D A -2.6169
22 I A 0.0000
23 K A -1.6288
24 V A 0.0000
25 Q A 0.0000
26 F A 0.0000
27 Q A 0.0000
28 S A -0.9532
29 G A -1.0575
30 G A -1.6818
31 N A -2.3191
32 N A -2.4236
33 S A 0.0000
34 P A -0.9675
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 -1.0798
43 R A -2.4931
44 A A 0.0000
45 Q A -2.3503
46 D A -2.9252
47 D A -1.9552
48 Y A -0.2994
49 N A 0.0000
50 G A 0.0000
51 W A 0.0000
52 D A 0.0000
53 I A 1.0564
54 N A -0.0528
55 T A 0.0000
56 P A -0.0952
57 A A 0.0000
58 F A 0.0000
59 E A -0.5737
60 W A -0.2382
61 Y A 0.0000
62 Y A -0.0642
63 Q A -0.8113
64 S A 0.0000
65 G A -0.6565
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 0.0000
74 G A 0.0000
75 Q A -1.4458
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 -0.6465
82 W A 0.0000
83 Y A 0.9573
84 S A 0.1034
85 P A -0.2951
86 A A 0.0000
87 C A -0.5131
88 G A -1.4795
89 K A -1.9427
90 A A -0.8450
91 G A -0.5571
92 C A 0.1005
93 Q A -0.4471
94 T A -0.4083
95 Y A 0.0000
96 K A -0.8834
97 W A 0.0000
98 E A -0.6139
99 T A -0.5734
100 F A 0.0000
101 L A 0.0000
102 T A -0.4184
103 S A -0.6510
104 E A -0.7593
105 L A 0.0000
106 P A 0.0000
107 Q A -1.5531
108 W A -0.8843
109 L A 0.0000
110 S A -1.4598
111 A A -0.9473
112 N A -1.3409
113 R A -1.7182
114 A A -1.7907
115 V A 0.0000
116 K A -1.8315
117 P A -1.1898
118 T A -0.8208
119 G A -0.4864
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 0.0720
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 -0.2323
139 H A -0.4136
140 P A -0.8914
141 Q A -1.2247
142 Q A 0.0000
143 F A 0.0000
144 I A -0.1900
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 0.0523
153 L A 0.0000
154 D A -1.0197
155 P A 0.0000
156 S A -1.2264
157 Q A -1.1993
158 G A -0.4030
159 M A 0.5801
160 G A 0.0000
161 P A 0.0577
162 S A 0.4707
163 L A 0.9224
164 I A 0.0000
165 G A 0.0022
166 L A 0.7584
167 A A -0.2894
168 M A 0.0000
169 G A -1.2697
170 D A -2.1018
171 A A 0.0000
172 G A -1.8447
173 G A -1.6502
174 Y A 0.0000
175 K A -1.8541
176 A A -0.8276
177 A A -0.6604
178 D A -0.4668
179 M A 0.0000
180 W A 0.0000
181 G A 0.0000
182 P A -0.6354
183 S A -0.9432
184 S A -0.8733
185 D A -1.1128
186 P A -1.1723
187 A A -0.8385
188 W A 0.0000
189 E A -2.2045
190 R A -1.4026
191 N A 0.0000
192 D A 0.0000
193 P A 0.0000
194 T A -1.2687
195 Q A -1.4656
196 Q A 0.0000
197 I A 0.0000
198 P A -0.9692
199 K A -1.2538
200 L A 0.0000
201 V A -1.2644
202 A A -0.9449
203 N A -1.5225
204 N A -1.7760
205 T A 0.0000
206 R A -0.8214
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 -0.7499
214 G A 0.0000
215 T A -0.7337
216 P A -1.0616
217 N A -1.3800
218 E A -1.9197
219 L A -0.6475
220 G A -0.8794
221 G A -0.6555
222 A A -0.4292
223 N A 0.0638
224 I A 1.8264
225 P A 0.8812
226 A A 0.0000
227 E A 0.4484
228 F A 1.7831
229 L A 1.0269
230 E A 0.0000
231 N A -0.7192
232 F A 0.1959
233 V A 0.0000
234 R A -0.6270
235 S A -0.6629
236 S A 0.0000
237 N A 0.0000
238 L A -0.6175
239 K A -2.1483
240 F A 0.0000
241 Q A -1.7263
242 D A -2.7312
243 A A -1.8683
244 Y A 0.0000
245 N A -2.4721
246 A A -1.3544
247 A A -1.0093
248 G A -1.1396
249 G A -1.7812
250 H A -1.6800
251 N A -1.3111
252 A A -0.5753
253 V A 0.2678
254 F A 0.5240
255 N A 0.1052
256 F A 0.1726
257 P A -0.3069
258 P A -0.6207
259 N A -0.9184
260 G A 0.0000
261 T A 0.0000
262 H A -0.3800
263 S A 0.0000
264 W A -0.3927
265 E A -1.1877
266 Y A 0.0000
267 W A 0.0000
268 G A 0.0000
269 A A -0.4181
270 Q A -0.5603
271 L A 0.0000
272 N A -0.8649
273 A A -0.6016
274 M A 0.0000
275 K A -1.0328
276 G A -1.0971
277 D A -0.8538
278 L A 0.0000
279 Q A -0.7923
280 S A -0.8598
281 S A -0.5619
282 L A -0.3995
283 G A -0.5505
284 A A -0.3145
285 G A 0.3944
286 F A 2.1053
287 A A 1.4878
288 V A 1.6940
289 T A -0.2128
290 N A -1.5682
291 D A -1.7335
292 G A -0.4678
293 V A 1.9793
294 I A 2.5951
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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
FE286A -1.8071 -0.0445 View CSV PDB
IE224A -0.7733 -0.0414 View CSV PDB
VR288A -0.7722 -0.0397 View CSV PDB
VK288A -0.6521 -0.0383 View CSV PDB
FR228A -0.2524 -0.0552 View CSV PDB
VE293A -0.7046 -0.0322 View CSV PDB
IR224A -0.2835 -0.0481 View CSV PDB
VR293A -0.6511 -0.0324 View CSV PDB
IR294A -0.772 -0.0274 View CSV PDB
IK294A -0.745 -0.0266 View CSV PDB
FR286A -0.1986 -0.0444 View CSV PDB
FK228A -0.0892 -0.0471 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018