Project name: 3-5M5

Status: done

Started: 2025-02-20 08:55:03
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                                          (00:01:58)
[INFO]       Auto_mut: Residue number 294 from chain A and a score of 2.530 (isoleucine) selected  
                       for automated muatation                                                     (00:02:00)
[INFO]       Auto_mut: Residue number 286 from chain A and a score of 2.186 (phenylalanine)        
                       selected for automated muatation                                            (00:02:00)
[INFO]       Auto_mut: Residue number 293 from chain A and a score of 1.923 (valine) selected for  
                       automated muatation                                                         (00:02:00)
[INFO]       Auto_mut: Residue number 288 from chain A and a score of 1.564 (valine) selected for  
                       automated muatation                                                         (00:02:00)
[INFO]       Auto_mut: Residue number 1 from chain A and a score of 1.540 omitted from automated   
                       muatation (excluded by the user).                                           (00:02:00)
[INFO]       Auto_mut: Residue number 287 from chain A and a score of 1.529 (alanine) selected for 
                       automated muatation                                                         (00:02:00)
[INFO]       Auto_mut: Residue number 83 from chain A and a score of 0.910 (tyrosine) selected for 
                       automated muatation                                                         (00:02:00)
[INFO]       Auto_mut: Mutating residue number 294 from chain A (isoleucine) into glutamic acid    (00:02:00)
[INFO]       Auto_mut: Mutating residue number 294 from chain A (isoleucine) into aspartic acid    (00:02:00)
[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 (00:02:00)
[INFO]       Auto_mut: Mutating residue number 294 from chain A (isoleucine) into lysine           (00:02:52)
[INFO]       Auto_mut: Mutating residue number 294 from chain A (isoleucine) into arginine         (00:02:52)
[INFO]       Auto_mut: Mutating residue number 286 from chain A (phenylalanine) into lysine        (00:02:54)
[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 (00:03:46)
[INFO]       Auto_mut: Mutating residue number 293 from chain A (valine) into glutamic acid        (00:03:48)
[INFO]       Auto_mut: Mutating residue number 293 from chain A (valine) into aspartic acid        (00:03:52)
[INFO]       Auto_mut: Mutating residue number 286 from chain A (phenylalanine) into arginine      (00:04:39)
[INFO]       Auto_mut: Mutating residue number 293 from chain A (valine) into lysine               (00:04:41)
[INFO]       Auto_mut: Mutating residue number 293 from chain A (valine) into arginine             (00:04:45)
[INFO]       Auto_mut: Mutating residue number 288 from chain A (valine) into glutamic acid        (00:05:35)
[INFO]       Auto_mut: Mutating residue number 288 from chain A (valine) into aspartic acid        (00:05:38)
[INFO]       Auto_mut: Mutating residue number 287 from chain A (alanine) into glutamic acid       (00:05:41)
[INFO]       Auto_mut: Mutating residue number 288 from chain A (valine) into lysine               (00:06:29)
[INFO]       Auto_mut: Mutating residue number 288 from chain A (valine) into arginine             (00:06:31)
[INFO]       Auto_mut: Mutating residue number 287 from chain A (alanine) into lysine              (00:06:35)
[INFO]       Auto_mut: Mutating residue number 287 from chain A (alanine) into aspartic acid       (00:07:27)
[INFO]       Auto_mut: Mutating residue number 83 from chain A (tyrosine) into glutamic acid       (00:07:27)
[INFO]       Auto_mut: Mutating residue number 83 from chain A (tyrosine) into aspartic acid       (00:07:33)
[INFO]       Auto_mut: Mutating residue number 287 from chain A (alanine) into arginine            (00:08:19)
[INFO]       Auto_mut: Mutating residue number 83 from chain A (tyrosine) into lysine              (00:08:25)
[INFO]       Auto_mut: Mutating residue number 83 from chain A (tyrosine) into arginine            (00:08:27)
[INFO]       Auto_mut: Effect of mutation residue number 294 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 0.0865 kcal/mol, Difference in average    
                       score from the base case: -0.0279                                           (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 294 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.6419 kcal/mol, Difference in average score    
                       from the base case: -0.0272                                                 (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 294 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 0.0956 kcal/mol, Difference in average    
                       score from the base case: -0.0277                                           (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 294 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.9580 kcal/mol, Difference in average score  
                       from the base case: -0.0281                                                 (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 286 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: -0.3318 kcal/mol, Difference in average   
                       score from the base case: -0.0421                                           (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 286 from chain A (phenylalanine) into     
                       lysine: Energy difference: -0.1903 kcal/mol, Difference in average score    
                       from the base case: -0.0417                                                 (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 286 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: -0.2062 kcal/mol, Difference in average   
                       score from the base case: -0.0426                                           (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 286 from chain A (phenylalanine) into     
                       arginine: Energy difference: -0.6964 kcal/mol, Difference in average score  
                       from the base case: -0.0419                                                 (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 293 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.6383 kcal/mol, Difference in average score from 
                       the base case: -0.0340                                                      (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 293 from chain A (valine) into lysine:    
                       Energy difference: -0.3708 kcal/mol, Difference in average score from the   
                       base case: -0.0330                                                          (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 293 from chain A (valine) into aspartic   
                       acid: Energy difference: -1.4489 kcal/mol, Difference in average score from 
                       the base case: -0.0337                                                      (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 293 from chain A (valine) into arginine:  
                       Energy difference: -0.6011 kcal/mol, Difference in average score from the   
                       base case: -0.0342                                                          (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 288 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.5120 kcal/mol, Difference in average score from 
                       the base case: -0.0420                                                      (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 288 from chain A (valine) into lysine:    
                       Energy difference: -0.3602 kcal/mol, Difference in average score from the   
                       base case: -0.0408                                                          (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 288 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.1133 kcal/mol, Difference in average score from 
                       the base case: -0.0417                                                      (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 288 from chain A (valine) into arginine:  
                       Energy difference: -1.3333 kcal/mol, Difference in average score from the   
                       base case: -0.0423                                                          (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 287 from chain A (alanine) into glutamic  
                       acid: Energy difference: 0.1335 kcal/mol, Difference in average score from  
                       the base case: -0.0223                                                      (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 287 from chain A (alanine) into lysine:   
                       Energy difference: 1.4889 kcal/mol, Difference in average score from the    
                       base case: -0.0214                                                          (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 287 from chain A (alanine) into aspartic  
                       acid: Energy difference: -0.0360 kcal/mol, Difference in average score from 
                       the base case: -0.0223                                                      (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 287 from chain A (alanine) into arginine: 
                       Energy difference: -0.5440 kcal/mol, Difference in average score from the   
                       base case: -0.0227                                                          (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 83 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 1.4369 kcal/mol, Difference in average score from  
                       the base case: -0.0439                                                      (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 83 from chain A (tyrosine) into lysine:   
                       Energy difference: 0.6345 kcal/mol, Difference in average score from the    
                       base case: -0.0324                                                          (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 83 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 1.7026 kcal/mol, Difference in average score from  
                       the base case: -0.0426                                                      (00:09:42)
[INFO]       Auto_mut: Effect of mutation residue number 83 from chain A (tyrosine) into arginine: 
                       Energy difference: 0.5295 kcal/mol, Difference in average score from the    
                       base case: -0.0378                                                          (00:09:42)
[INFO]       Main:     Simulation completed successfully.                                          (00:09:49)
Show buried residues
Minimal score value
-2.9015
Maximal score value
2.5299
Average score
-0.4768
Total score value
-140.1871
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 1.5395
2 S A 0.0522
3 R A -1.2041
4 P A -0.8621
5 G A -0.8986
6 L A -0.5795
7 P A -0.2576
8 V A 0.0034
9 E A -0.3007
10 Y A 0.6128
11 L A 0.0000
12 Q A -1.8312
13 V A 0.0000
14 P A -1.6177
15 S A 0.0000
16 P A -1.0238
17 S A -0.6928
18 M A 0.0000
19 G A -1.3906
20 R A -2.0587
21 D A -2.7671
22 I A 0.0000
23 K A -1.4024
24 V A 0.0000
25 Q A 0.0000
26 F A 0.0000
27 Q A 0.0000
28 S A -0.9452
29 G A -1.1214
30 G A -1.6092
31 N A -2.2429
32 N A -2.2358
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 -0.9906
43 R A -2.4152
44 A A 0.0000
45 Q A -2.3794
46 D A -2.9015
47 D A -1.9926
48 Y A -0.3657
49 N A 0.0000
50 G A 0.0000
51 W A 0.0000
52 D A 0.0000
53 I A 0.8590
54 N A -0.1401
55 T A 0.0000
56 P A 0.0179
57 A A 0.0000
58 F A 0.0000
59 E A -0.4837
60 W A -0.2413
61 Y A 0.0000
62 Y A -0.0873
63 Q A -1.1155
64 S A 0.0000
65 G A -0.8163
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 -1.3098
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 -0.5793
82 W A 0.0000
83 Y A 0.9103
84 S A 0.0546
85 P A -0.1535
86 A A 0.0000
87 C A -0.4338
88 G A -1.4061
89 K A -1.9104
90 A A -0.8344
91 G A -0.5126
92 C A 0.1103
93 Q A -0.4943
94 T A -0.4394
95 Y A 0.0000
96 K A -0.8022
97 W A 0.0000
98 E A 0.0000
99 T A -0.4216
100 F A 0.0000
101 L A 0.0000
102 T A -0.3273
103 S A -0.5044
104 E A -0.6510
105 L A 0.0000
106 P A 0.0000
107 Q A -1.4479
108 W A -0.8486
109 L A 0.0000
110 S A -1.3108
111 A A -0.8630
112 N A -1.2632
113 R A -1.6250
114 A A -1.6674
115 V A 0.0000
116 K A -1.3024
117 P A -0.9789
118 T A -0.5882
119 G A -0.4011
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 0.0147
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 -0.2325
139 H A -0.4022
140 P A -0.9172
141 Q A -1.2468
142 Q A -0.7199
143 F A 0.0000
144 I A -0.1902
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 0.0996
153 L A 0.0000
154 D A -0.9992
155 P A 0.0000
156 S A -1.1539
157 Q A -1.2280
158 G A -0.5235
159 M A 0.3828
160 G A 0.0000
161 P A -0.0915
162 S A 0.2368
163 L A 0.7200
164 I A 0.0000
165 G A -0.2361
166 L A 0.3908
167 A A -0.4285
168 M A 0.0000
169 G A -1.3821
170 D A -2.2650
171 A A 0.0000
172 G A 0.0000
173 G A -1.6191
174 Y A 0.0000
175 K A -1.8935
176 A A -0.8129
177 A A -0.7143
178 D A -0.5735
179 M A 0.0000
180 W A 0.0000
181 G A 0.0000
182 P A -0.6391
183 S A -0.8734
184 S A -0.7813
185 D A -0.9922
186 P A -1.0084
187 A A 0.0000
188 W A 0.0000
189 E A -1.8376
190 R A -1.2980
191 N A 0.0000
192 D A 0.0000
193 P A 0.0000
194 T A -1.3778
195 Q A -1.7886
196 Q A 0.0000
197 I A 0.0000
198 P A -1.0932
199 K A -1.4019
200 L A 0.0000
201 V A -1.2954
202 A A -0.9617
203 N A -1.4777
204 N A -1.8398
205 T A 0.0000
206 R A -0.9257
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 -1.1197
214 G A 0.0000
215 T A -1.4709
216 P A -1.8386
217 N A -2.3690
218 E A -2.3564
219 L A -1.4188
220 G A -1.2435
221 G A -0.9879
222 A A -0.7956
223 N A -1.4410
224 I A -0.2968
225 P A -0.4034
226 A A -0.6817
227 E A -0.7960
228 F A 0.5047
229 L A 0.4311
230 E A 0.0000
231 N A -1.0324
232 F A 0.1041
233 V A 0.0000
234 R A -0.5525
235 S A -0.7289
236 S A 0.0000
237 N A 0.0000
238 L A -0.6064
239 K A -2.0496
240 F A 0.0000
241 Q A -1.6231
242 D A -2.6522
243 A A -1.8660
244 Y A 0.0000
245 N A -2.4507
246 A A -1.3430
247 A A -0.9926
248 G A -1.1156
249 G A -1.7789
250 H A -1.6999
251 N A -1.3402
252 A A -0.6247
253 V A 0.2137
254 F A 0.4824
255 N A 0.0446
256 F A 0.0143
257 P A -0.4823
258 P A -0.8212
259 N A -1.4580
260 G A 0.0000
261 T A 0.0000
262 H A -0.6808
263 S A -0.6893
264 W A -0.7267
265 E A -1.7113
266 Y A -0.8901
267 W A 0.0000
268 G A 0.0000
269 A A -0.6363
270 Q A -0.6157
271 L A 0.0000
272 N A -0.8850
273 A A -0.6150
274 M A 0.0000
275 K A -1.0328
276 G A -1.0909
277 D A -0.8360
278 L A 0.0000
279 Q A -0.7883
280 S A -0.6620
281 S A -0.5808
282 L A 0.0000
283 G A -0.4280
284 A A 0.0000
285 G A 0.2839
286 F A 2.1860
287 A A 1.5286
288 V A 1.5639
289 T A -0.0461
290 N A -1.5448
291 D A -1.5855
292 G A -0.2505
293 V A 1.9233
294 I A 2.5299
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
VR288A -1.3333 -0.0423 View CSV PDB
VD293A -1.4489 -0.0337 View CSV PDB
FR286A -0.6964 -0.0419 View CSV PDB
VE288A -0.512 -0.042 View CSV PDB
IR294A -0.958 -0.0281 View CSV PDB
VE293A -0.6383 -0.034 View CSV PDB
FE286A -0.3318 -0.0421 View CSV PDB
IK294A -0.6419 -0.0272 View CSV PDB
AR287A -0.544 -0.0227 View CSV PDB
AD287A -0.036 -0.0223 View CSV PDB
YR83A 0.5295 -0.0378 View CSV PDB
YK83A 0.6345 -0.0324 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018