Project name: 1f0nv5

Status: done

Started: 2025-02-19 06:50:18
Settings
Chain sequence(s) A: SRPGLPVEYLQVPSPSMGRDIKVQFQSGGNNSPAVYLLDGLRAQDDVNGWLRNTPAFEWYYQSGLSIVMPVGGQSSFYSDWLKPACGKAGCQTYKWETFLTSELPQWLSANRAVKPTGSAAIGLSMAGSSAMILAAYHPQQFIYAGSLSALLDPSQGMGPAFIDAAMGDAGGYKAADMWGPSSDPAWERNDPTQQIPKLVANNTRLWVYCGNGTPNELGGANIPAEFLENFVRSSNLKFQDAYNAAGGHNAVFNFPPNGTHSWEYWGAQLNAMKGDLQSSLGAG
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                                          (00:04:02)
[INFO]       Auto_mut: Residue number 228 from chain A and a score of 1.966 (phenylalanine)        
                       selected for automated muatation                                            (00:04:04)
[INFO]       Auto_mut: Residue number 224 from chain A and a score of 1.754 (isoleucine) selected  
                       for automated muatation                                                     (00:04:04)
[INFO]       Auto_mut: Residue number 256 from chain A and a score of 1.555 (phenylalanine)        
                       selected for automated muatation                                            (00:04:04)
[INFO]       Auto_mut: Residue number 229 from chain A and a score of 1.290 (leucine) selected for 
                       automated muatation                                                         (00:04:04)
[INFO]       Auto_mut: Residue number 254 from chain A and a score of 1.258 (phenylalanine)        
                       selected for automated muatation                                            (00:04:04)
[INFO]       Auto_mut: Residue number 253 from chain A and a score of 1.024 (valine) selected for  
                       automated muatation                                                         (00:04:04)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into glutamic acid    (00:04:04)
[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 (00:04:04)
[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 (00:04:04)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into lysine           (00:05:17)
[INFO]       Auto_mut: Mutating residue number 228 from chain A (phenylalanine) into arginine      (00:05:18)
[INFO]       Auto_mut: Mutating residue number 228 from chain A (phenylalanine) into lysine        (00:05:22)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into aspartic acid    (00:06:36)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 256 from chain A (phenylalanine) into glutamic acid (00:06:51)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 256 from chain A (phenylalanine) into aspartic acid (00:06:59)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into arginine         (00:07:50)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (phenylalanine) into lysine        (00:08:02)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (phenylalanine) into arginine      (00:08:12)
[INFO]       Auto_mut: Mutating residue number 229 from chain A (leucine) into glutamic acid       (00:09:07)
[INFO]       Auto_mut: Mutating residue number 229 from chain A (leucine) into aspartic acid       (00:09:14)
[INFO]       Auto_mut: Mutating residue number 254 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 254 from chain A (phenylalanine) into glutamic acid (00:09:24)
[INFO]       Auto_mut: Mutating residue number 229 from chain A (leucine) into lysine              (00:10:27)
[INFO]       Auto_mut: Mutating residue number 229 from chain A (leucine) into arginine            (00:10:29)
[INFO]       Auto_mut: Mutating residue number 254 from chain A (phenylalanine) into lysine        (00:10:39)
[INFO]       Auto_mut: Mutating residue number 254 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 254 from chain A (phenylalanine) into aspartic acid (00:11:53)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (valine) into glutamic acid        (00:12:00)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (valine) into aspartic acid        (00:12:13)
[INFO]       Auto_mut: Mutating residue number 254 from chain A (phenylalanine) into arginine      (00:13:08)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (valine) into lysine               (00:13:21)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (valine) into arginine             (00:13:31)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 0.4036 kcal/mol, Difference in average    
                       score from the base case: -0.0478                                           (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       lysine: Energy difference: -0.2129 kcal/mol, Difference in average score    
                       from the base case: -0.0476                                                 (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 0.9083 kcal/mol, Difference in average    
                       score from the base case: -0.0470                                           (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.2567 kcal/mol, Difference in average score   
                       from the base case: -0.0500                                                 (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -1.0575 kcal/mol, Difference in average   
                       score from the base case: -0.0353                                           (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.3605 kcal/mol, Difference in average score    
                       from the base case: -0.0354                                                 (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: -0.0423 kcal/mol, Difference in average   
                       score from the base case: -0.0371                                           (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.4732 kcal/mol, Difference in average score  
                       from the base case: -0.0451                                                 (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: -0.7155 kcal/mol, Difference in average   
                       score from the base case: -0.0172                                           (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       lysine: Energy difference: -0.2570 kcal/mol, Difference in average score    
                       from the base case: -0.0298                                                 (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 0.0314 kcal/mol, Difference in average    
                       score from the base case: -0.0144                                           (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.2469 kcal/mol, Difference in average score   
                       from the base case: -0.0337                                                 (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 229 from chain A (leucine) into glutamic  
                       acid: Energy difference: 1.0984 kcal/mol, Difference in average score from  
                       the base case: -0.0060                                                      (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 229 from chain A (leucine) into lysine:   
                       Energy difference: 0.4858 kcal/mol, Difference in average score from the    
                       base case: -0.0120                                                          (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 229 from chain A (leucine) into aspartic  
                       acid: Energy difference: 1.6356 kcal/mol, Difference in average score from  
                       the base case: -0.0112                                                      (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 229 from chain A (leucine) into arginine: 
                       Energy difference: -0.1036 kcal/mol, Difference in average score from the   
                       base case: -0.0094                                                          (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 1.0803 kcal/mol, Difference in average    
                       score from the base case: -0.0229                                           (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       lysine: Energy difference: 4.2039 kcal/mol, Difference in average score     
                       from the base case: 0.0007                                                  (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 2.4943 kcal/mol, Difference in average    
                       score from the base case: -0.0125                                           (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       arginine: Energy difference: -0.2871 kcal/mol, Difference in average score  
                       from the base case: -0.0245                                                 (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.1702 kcal/mol, Difference in average score from 
                       the base case: -0.0302                                                      (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (valine) into lysine:    
                       Energy difference: -0.7770 kcal/mol, Difference in average score from the   
                       base case: -0.0131                                                          (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.1387 kcal/mol, Difference in average score from 
                       the base case: -0.0291                                                      (00:15:17)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (valine) into arginine:  
                       Energy difference: -0.2698 kcal/mol, Difference in average score from the   
                       base case: -0.0212                                                          (00:15:17)
[INFO]       Main:     Simulation completed successfully.                                          (00:15:24)
Show buried residues
Minimal score value
-3.2525
Maximal score value
1.9662
Average score
-0.5491
Total score value
-155.9353
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
2 S A -1.0745
3 R A -1.7225
4 P A -1.1667
5 G A -0.9022
6 L A -0.4426
7 P A -0.1044
8 V A 0.2152
9 E A -0.1971
10 Y A 0.1255
11 L A 0.0000
12 Q A -1.3610
13 V A 0.0000
14 P A -1.2938
15 S A 0.0000
16 P A -0.9410
17 S A -0.7043
18 M A 0.0000
19 G A -1.3357
20 R A -1.8551
21 D A -2.1562
22 I A 0.0000
23 K A -1.4762
24 V A 0.0000
25 Q A 0.0000
26 F A 0.0000
27 Q A 0.0000
28 S A -0.8034
29 G A -1.1322
30 G A -1.5881
31 N A -2.3559
32 N A -2.5034
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 -0.6257
42 L A -1.1267
43 R A -2.5560
44 A A 0.0000
45 Q A -2.6007
46 D A -3.2525
47 D A -2.6720
48 V A -1.4783
49 N A 0.0000
50 G A 0.0000
51 W A 0.0000
52 L A -0.7184
53 R A -1.6627
54 N A -0.9204
55 T A 0.0000
56 P A -0.7917
57 A A 0.0000
58 F A 0.0000
59 E A -0.5721
60 W A -0.2426
61 Y A 0.0000
62 Y A -0.0631
63 Q A -1.0871
64 S A 0.0000
65 G A -1.0223
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 -1.8182
74 G A -1.1636
75 Q A -1.5748
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 -0.6702
82 W A 0.0000
83 L A -0.0129
84 K A -1.6839
85 P A -1.1031
86 A A 0.0000
87 C A -0.5562
88 G A -1.1018
89 K A -1.8151
90 A A -0.7907
91 G A -0.4600
92 C A 0.1530
93 Q A -0.7057
94 T A -0.7485
95 Y A 0.0000
96 K A -0.8389
97 W A 0.0000
98 E A 0.0000
99 T A -0.4272
100 F A 0.0000
101 L A 0.0000
102 T A -0.3985
103 S A -0.6529
104 E A -0.8115
105 L A 0.0000
106 P A 0.0000
107 Q A -1.4866
108 W A -0.6050
109 L A 0.0000
110 S A -1.3891
111 A A -0.7797
112 N A -1.0332
113 R A -1.5640
114 A A -1.7449
115 V A 0.0000
116 K A -2.2056
117 P A -1.3576
118 T A -1.0182
119 G A -0.6438
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 0.3293
126 S A -0.0100
127 M A -0.0481
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 -0.1425
139 H A -0.5334
140 P A -0.9924
141 Q A -1.3928
142 Q A -0.9945
143 F A 0.0000
144 I A -0.4548
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 0.3022
153 L A 0.0000
154 D A -1.1167
155 P A 0.0000
156 S A -1.3093
157 Q A -1.5470
158 G A -0.5483
159 M A 0.5337
160 G A -0.0025
161 P A 0.0000
162 A A 0.1016
163 F A 0.5890
164 I A 0.0000
165 D A -1.3211
166 A A -0.9473
167 A A -1.1506
168 M A 0.0000
169 G A -1.8895
170 D A -2.5640
171 A A 0.0000
172 G A -1.7354
173 G A -1.7696
174 Y A 0.0000
175 K A -2.4087
176 A A 0.0000
177 A A -1.1361
178 D A -1.2084
179 M A 0.0000
180 W A 0.0000
181 G A 0.0000
182 P A -0.8312
183 S A -0.9689
184 S A -0.8587
185 D A -1.1664
186 P A -1.1224
187 A A -0.8265
188 W A 0.0000
189 E A -1.9583
190 R A -1.3933
191 N A 0.0000
192 D A 0.0000
193 P A 0.0000
194 T A -1.2399
195 Q A -1.5817
196 Q A 0.0000
197 I A 0.0000
198 P A -1.0715
199 K A -1.4578
200 L A 0.0000
201 V A -1.3338
202 A A -0.9476
203 N A -1.5192
204 N A -1.7361
205 T A 0.0000
206 R A -1.3548
207 L A 0.0000
208 W A 0.0000
209 V A 0.0000
210 Y A 0.7809
211 C A 0.0000
212 G A 0.0000
213 N A -0.4147
214 G A 0.0000
215 T A -0.7246
216 P A -1.5086
217 N A -2.1238
218 E A -2.1770
219 L A -0.7481
220 G A -0.8866
221 G A -0.5591
222 A A -0.6577
223 N A -0.0225
224 I A 1.7537
225 P A 0.8377
226 A A 0.0000
227 E A 0.4141
228 F A 1.9662
229 L A 1.2895
230 E A 0.0000
231 N A -0.4971
232 F A 0.8437
233 V A 0.0000
234 R A -0.4761
235 S A -0.7821
236 S A -0.9263
237 N A 0.0000
238 L A -0.7846
239 K A -2.4859
240 F A 0.0000
241 Q A -1.6053
242 D A -2.7734
243 A A -1.8784
244 Y A 0.0000
245 N A -2.4044
246 A A -1.2843
247 A A -0.9331
248 G A -1.1355
249 G A -1.7786
250 H A -1.6655
251 N A -1.3038
252 A A -0.3291
253 V A 1.0241
254 F A 1.2575
255 N A 1.0137
256 F A 1.5554
257 P A 0.4157
258 P A -0.3333
259 N A -0.7772
260 G A 0.0000
261 T A 0.0000
262 H A 0.0473
263 S A 0.0613
264 W A 0.5285
265 E A 0.1447
266 Y A 0.0000
267 W A 0.0000
268 G A 0.0000
269 A A -0.0226
270 Q A 0.0000
271 L A 0.0000
272 N A -0.6976
273 A A -0.7223
274 M A 0.0000
275 K A -1.4388
276 G A -1.7334
277 D A -2.2278
278 L A 0.0000
279 Q A -1.4463
280 S A -1.2996
281 S A -0.9809
282 L A -0.6214
283 G A -0.8692
284 A A -1.0222
285 G A -0.8989
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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
IE224A -1.0575 -0.0353 View CSV PDB
IR224A -0.4732 -0.0451 View CSV PDB
FK228A -0.2129 -0.0476 View CSV PDB
FK256A -0.257 -0.0298 View CSV PDB
FE256A -0.7155 -0.0172 View CSV PDB
VE253A -0.1702 -0.0302 View CSV PDB
FR254A -0.2871 -0.0245 View CSV PDB
VD253A -0.1387 -0.0291 View CSV PDB
LR229A -0.1036 -0.0094 View CSV PDB
FR228A 0.2567 -0.05 View CSV PDB
LK229A 0.4858 -0.012 View CSV PDB
FE254A 1.0803 -0.0229 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018