Project name: 3-5M3

Status: done

Started: 2025-02-20 08:53:59
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]                                                (00:00:09)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:09)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:09)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:09)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:09)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:02:10)
[INFO]       Auto_mut: Residue number 294 from chain A and a score of 2.558 (isoleucine) selected  
                       for automated muatation                                                     (00:02:12)
[INFO]       Auto_mut: Residue number 286 from chain A and a score of 2.112 (phenylalanine)        
                       selected for automated muatation                                            (00:02:12)
[INFO]       Auto_mut: Residue number 293 from chain A and a score of 1.852 (valine) selected for  
                       automated muatation                                                         (00:02:12)
[INFO]       Auto_mut: Residue number 288 from chain A and a score of 1.539 (valine) selected for  
                       automated muatation                                                         (00:02:12)
[INFO]       Auto_mut: Residue number 224 from chain A and a score of 1.470 (isoleucine) selected  
                       for automated muatation                                                     (00:02:12)
[INFO]       Auto_mut: Residue number 1 from chain A and a score of 1.417 omitted from automated   
                       muatation (excluded by the user).                                           (00:02:12)
[INFO]       Auto_mut: Residue number 228 from chain A and a score of 1.396 (phenylalanine)        
                       selected for automated muatation                                            (00:02:12)
[INFO]       Auto_mut: Mutating residue number 294 from chain A (isoleucine) into glutamic acid    (00:02:13)
[INFO]       Auto_mut: Mutating residue number 294 from chain A (isoleucine) into aspartic acid    (00:02:13)
[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 (00:02:13)
[INFO]       Auto_mut: Mutating residue number 294 from chain A (isoleucine) into arginine         (00:03:11)
[INFO]       Auto_mut: Mutating residue number 286 from chain A (phenylalanine) into lysine        (00:03:13)
[INFO]       Auto_mut: Mutating residue number 294 from chain A (isoleucine) into lysine           (00:03:13)
[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        (00:04:15)
[INFO]       Auto_mut: Mutating residue number 293 from chain A (valine) into aspartic acid        (00:04:20)
[INFO]       Auto_mut: Mutating residue number 286 from chain A (phenylalanine) into arginine      (00:05:12)
[INFO]       Auto_mut: Mutating residue number 293 from chain A (valine) into lysine               (00:05:17)
[INFO]       Auto_mut: Mutating residue number 293 from chain A (valine) into arginine             (00:05:21)
[INFO]       Auto_mut: Mutating residue number 288 from chain A (valine) into glutamic acid        (00:06:15)
[INFO]       Auto_mut: Mutating residue number 288 from chain A (valine) into aspartic acid        (00:06:19)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into glutamic acid    (00:06:23)
[INFO]       Auto_mut: Mutating residue number 288 from chain A (valine) into lysine               (00:07:17)
[INFO]       Auto_mut: Mutating residue number 288 from chain A (valine) into arginine             (00:07:19)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into lysine           (00:07:27)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into aspartic acid    (00:08:22)
[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 (00:08:22)
[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 (00:08:39)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into arginine         (00:09:23)
[INFO]       Auto_mut: Mutating residue number 228 from chain A (phenylalanine) into lysine        (00:09:30)
[INFO]       Auto_mut: Mutating residue number 228 from chain A (phenylalanine) into arginine      (00:09:41)
[INFO]       Auto_mut: Effect of mutation residue number 294 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -0.0745 kcal/mol, Difference in average   
                       score from the base case: -0.0221                                           (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 294 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.6458 kcal/mol, Difference in average score    
                       from the base case: -0.0213                                                 (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 294 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: -0.0705 kcal/mol, Difference in average   
                       score from the base case: -0.0219                                           (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 294 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.7393 kcal/mol, Difference in average score  
                       from the base case: -0.0223                                                 (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 286 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 0.7218 kcal/mol, Difference in average    
                       score from the base case: -0.0338                                           (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 286 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.5299 kcal/mol, Difference in average score     
                       from the base case: -0.0381                                                 (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 286 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 0.4724 kcal/mol, Difference in average    
                       score from the base case: -0.0391                                           (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 286 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.1014 kcal/mol, Difference in average score   
                       from the base case: -0.0398                                                 (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 293 from chain A (valine) into glutamic   
                       acid: Energy difference: 2.0554 kcal/mol, Difference in average score from  
                       the base case: -0.0271                                                      (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 293 from chain A (valine) into lysine:    
                       Energy difference: -0.2384 kcal/mol, Difference in average score from the   
                       base case: -0.0261                                                          (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 293 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.1687 kcal/mol, Difference in average score from  
                       the base case: -0.0269                                                      (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 293 from chain A (valine) into arginine:  
                       Energy difference: -0.3846 kcal/mol, Difference in average score from the   
                       base case: -0.0273                                                          (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 288 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.9905 kcal/mol, Difference in average score from 
                       the base case: -0.0341                                                      (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 288 from chain A (valine) into lysine:    
                       Energy difference: -0.5496 kcal/mol, Difference in average score from the   
                       base case: -0.0329                                                          (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 288 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.5554 kcal/mol, Difference in average score from 
                       the base case: -0.0338                                                      (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 288 from chain A (valine) into arginine:  
                       Energy difference: -0.9262 kcal/mol, Difference in average score from the   
                       base case: -0.0343                                                          (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -0.8256 kcal/mol, Difference in average   
                       score from the base case: -0.0366                                           (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.2829 kcal/mol, Difference in average score    
                       from the base case: -0.0435                                                 (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 0.2781 kcal/mol, Difference in average    
                       score from the base case: -0.0395                                           (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.3173 kcal/mol, Difference in average score  
                       from the base case: -0.0477                                                 (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 0.5042 kcal/mol, Difference in average    
                       score from the base case: -0.0399                                           (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.0398 kcal/mol, Difference in average score     
                       from the base case: -0.0384                                                 (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 1.0028 kcal/mol, Difference in average    
                       score from the base case: -0.0344                                           (00:10:56)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       arginine: Energy difference: -0.0495 kcal/mol, Difference in average score  
                       from the base case: -0.0403                                                 (00:10:56)
[INFO]       Main:     Simulation completed successfully.                                          (00:11:01)
Show buried residues
Minimal score value
-2.8717
Maximal score value
2.558
Average score
-0.432
Total score value
-127.0043
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 1.4174
2 S A -0.1502
3 R A -1.6747
4 P A -1.0641
5 G A -0.9549
6 L A -0.5309
7 P A -0.1575
8 V A 0.0899
9 E A -0.2653
10 Y A 0.6328
11 L A 0.0000
12 Q A -1.8285
13 V A 0.0000
14 P A -1.6480
15 S A 0.0000
16 P A -1.0352
17 S A -0.7273
18 M A 0.0000
19 G A -1.4091
20 R A -2.0683
21 D A -2.7752
22 I A 0.0000
23 K A -1.3879
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 -1.0828
30 G A -1.6337
31 N A -2.2224
32 N A -2.2040
33 S A 0.0000
34 P A 0.0000
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 -0.8693
43 R A -2.1267
44 A A 0.0000
45 Q A -2.2844
46 D A -2.8717
47 D A -1.9925
48 Y A -0.3449
49 N A 0.0000
50 G A 0.0000
51 W A 0.0000
52 D A 0.0000
53 I A 0.8452
54 N A -0.0689
55 T A 0.0000
56 P A -0.0292
57 A A 0.0000
58 F A 0.0000
59 E A -0.3763
60 W A -0.1143
61 Y A 0.0000
62 Y A 0.1257
63 Q A -1.0270
64 S A 0.0000
65 G A -0.7843
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 -1.5133
74 G A -0.9706
75 Q A -1.1813
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 -0.6564
82 W A 0.0000
83 Y A 0.9420
84 S A 0.0850
85 P A -0.1608
86 A A 0.0000
87 C A -0.5055
88 G A -1.3265
89 K A -1.9812
90 A A -0.8674
91 G A -0.5581
92 C A 0.0743
93 Q A -0.5609
94 T A -0.4814
95 Y A 0.0000
96 K A -0.8906
97 W A 0.0000
98 E A -0.5743
99 T A -0.5162
100 F A 0.0000
101 L A 0.0000
102 T A -0.3691
103 S A -0.5162
104 E A -0.6759
105 L A 0.0000
106 P A 0.0000
107 Q A -1.4471
108 W A -0.8572
109 L A 0.0000
110 S A -1.3037
111 A A -0.8647
112 N A -1.2779
113 R A -1.5969
114 A A -1.6462
115 V A 0.0000
116 K A -1.2689
117 P A -0.9554
118 T A -0.7165
119 G A -0.4539
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 0.0700
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 -0.2422
139 H A -0.4460
140 P A -0.9660
141 Q A -1.2786
142 Q A -0.7378
143 F A 0.0000
144 I A -0.3190
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 0.1868
153 L A 0.0000
154 D A 0.0000
155 P A 0.0000
156 S A -1.0740
157 Q A -1.1063
158 G A -0.3618
159 M A 0.5948
160 G A 0.0000
161 P A 0.0828
162 S A 0.4548
163 L A 0.8602
164 I A 0.0000
165 G A -0.0849
166 L A 0.6436
167 A A -0.3471
168 M A 0.0000
169 G A -1.4819
170 D A -1.9679
171 A A 0.0000
172 G A 0.0000
173 G A -1.8258
174 Y A 0.0000
175 K A -1.7138
176 A A -0.7667
177 A A -0.6530
178 D A -0.4563
179 M A 0.0000
180 W A 0.0000
181 G A 0.0000
182 P A -0.6322
183 S A -0.8945
184 S A -0.8324
185 D A -1.0613
186 P A -1.0823
187 A A -0.7464
188 W A 0.0000
189 E A -1.9315
190 R A -1.2680
191 N A 0.0000
192 D A 0.0000
193 P A 0.0000
194 T A -1.1513
195 Q A -1.5156
196 Q A 0.0000
197 I A 0.0000
198 P A -1.0289
199 K A -1.3321
200 L A 0.0000
201 V A -1.2637
202 A A -0.9415
203 N A -1.4795
204 N A -1.8490
205 T A 0.0000
206 R A -0.9499
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 -0.9109
214 G A 0.0000
215 T A -0.9595
216 P A -1.2757
217 N A -1.4955
218 E A -1.9079
219 L A -0.8122
220 G A -1.0238
221 G A -0.8885
222 A A -0.6921
223 N A -0.3447
224 I A 1.4705
225 P A 0.7013
226 A A 0.0000
227 E A -0.3211
228 F A 1.3962
229 L A 0.7734
230 E A 0.0000
231 N A -0.8791
232 F A 0.1241
233 V A 0.0000
234 R A -0.6604
235 S A -0.6030
236 S A 0.0000
237 N A 0.0000
238 L A -0.5201
239 K A -1.7278
240 F A 0.0000
241 Q A -1.4549
242 D A -2.4917
243 A A -1.6955
244 Y A 0.0000
245 N A -2.2555
246 A A -1.2573
247 A A -0.9449
248 G A -1.0878
249 G A -1.7243
250 H A -1.6878
251 N A -1.3484
252 A A -0.6367
253 V A 0.1499
254 F A 0.5015
255 N A 0.0574
256 F A 0.1235
257 P A -0.2853
258 P A -0.6169
259 N A -0.9322
260 G A 0.0000
261 T A 0.0000
262 H A -0.6049
263 S A -0.6853
264 W A -0.4478
265 E A -1.0605
266 Y A 0.0000
267 W A 0.0000
268 G A 0.0000
269 A A -0.4306
270 Q A -0.5567
271 L A 0.0000
272 N A -0.8420
273 A A -0.5837
274 M A 0.0000
275 K A -1.0169
276 G A -1.0475
277 D A -0.8735
278 L A 0.0000
279 Q A -0.8019
280 S A -0.6642
281 S A -0.6040
282 L A 0.0000
283 G A -0.3406
284 A A -0.3505
285 G A 0.2720
286 F A 2.1125
287 A A 1.1516
288 V A 1.5391
289 T A -0.2235
290 N A -1.4666
291 D A -1.6190
292 G A -0.1343
293 V A 1.8520
294 I A 2.5580
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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
VE288A -0.9905 -0.0341 View CSV PDB
VR288A -0.9262 -0.0343 View CSV PDB
IE224A -0.8256 -0.0366 View CSV PDB
IR224A -0.3173 -0.0477 View CSV PDB
IR294A -0.7393 -0.0223 View CSV PDB
IK294A -0.6458 -0.0213 View CSV PDB
VR293A -0.3846 -0.0273 View CSV PDB
FR228A -0.0495 -0.0403 View CSV PDB
VK293A -0.2384 -0.0261 View CSV PDB
FK228A 0.0398 -0.0384 View CSV PDB
FR286A 0.1014 -0.0398 View CSV PDB
FD286A 0.4724 -0.0391 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018