Project name: 1f0n_sv4

Status: done

Started: 2025-02-18 07:12:25
Settings
Chain sequence(s) A: SRPGLPVEYLQVPSPSMGRDIKVQFQSGGNNSPAVYLLDGLRAQDDYNGWDVNTPAFEWYYQSGLSIVMPVGGQSSFYSDWKSPACGKAGCQTYKWETFLTSELPQWLSANRAVKPTGSAAIGLSMAGSSAMILAAYHPQQFIYAGSLSALLDPSQGMGPSAIGAAMGDAGGYKAADMWGPSSDPAWERNDPTQQIPKLVANNTRLWVYCGNGTPNELGGANAGASAAENAVRSSNLKFQDAYNAAGGHNAVFNFPPNGTHSWEYWGAQLNAMKGDLQSSLGAG
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                                          (00:03:44)
[INFO]       Auto_mut: Residue number 256 from chain A and a score of 1.395 (phenylalanine)        
                       selected for automated muatation                                            (00:03:46)
[INFO]       Auto_mut: Residue number 53 from chain A and a score of 1.392 (valine) selected for   
                       automated muatation                                                         (00:03:46)
[INFO]       Auto_mut: Residue number 254 from chain A and a score of 1.051 (phenylalanine)        
                       selected for automated muatation                                            (00:03:46)
[INFO]       Auto_mut: Residue number 255 from chain A and a score of 0.777 (asparagine) selected  
                       for automated muatation                                                     (00:03:46)
[INFO]       Auto_mut: Residue number 210 from chain A and a score of 0.732 (tyrosine) selected    
                       for automated muatation                                                     (00:03:46)
[INFO]       Auto_mut: Residue number 253 from chain A and a score of 0.461 (valine) selected for  
                       automated muatation                                                         (00:03:46)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (valine) into glutamic acid         (00:03:46)
[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 (00:03:46)
[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 (00:03:46)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (phenylalanine) into arginine      (00:05:46)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (valine) into lysine                (00:05:50)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (phenylalanine) into lysine        (00:05:51)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (valine) into aspartic acid         (00:08:11)
[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 (00:08:14)
[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 (00:08:34)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (valine) into arginine              (00:10:01)
[INFO]       Auto_mut: Mutating residue number 254 from chain A (phenylalanine) into lysine        (00:10:08)
[INFO]       Auto_mut: Mutating residue number 254 from chain A (phenylalanine) into arginine      (00:10:27)
[INFO]       Auto_mut: Mutating residue number 255 from chain A (asparagine) into glutamic acid    (00:11:40)
[INFO]       Auto_mut: Mutating residue number 255 from chain A (asparagine) into aspartic acid    (00:11:41)
[INFO]       Auto_mut: Mutating residue number 210 from chain A (tyrosine) into glutamic acid      (00:12:20)
[INFO]       Auto_mut: Mutating residue number 255 from chain A (asparagine) into arginine         (00:14:00)
[INFO]       Auto_mut: Mutating residue number 255 from chain A (asparagine) into lysine           (00:14:20)
[INFO]       Auto_mut: Mutating residue number 210 from chain A (tyrosine) into lysine             (00:15:04)
[INFO]       Auto_mut: Mutating residue number 210 from chain A (tyrosine) into aspartic acid      (00:18:35)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (valine) into glutamic acid        (00:20:08)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (valine) into aspartic acid        (00:22:48)
[INFO]       Auto_mut: Mutating residue number 210 from chain A (tyrosine) into arginine           (00:23:13)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (valine) into lysine               (00:24:25)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (valine) into arginine             (00:25:43)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: -0.4933 kcal/mol, Difference in average   
                       score from the base case: -0.0255                                           (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       lysine: Energy difference: -0.1021 kcal/mol, Difference in average score    
                       from the base case: -0.0254                                                 (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: -0.7739 kcal/mol, Difference in average   
                       score from the base case: -0.0193                                           (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       arginine: Energy difference: -0.0530 kcal/mol, Difference in average score  
                       from the base case: -0.0284                                                 (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (valine) into glutamic    
                       acid: Energy difference: -0.3118 kcal/mol, Difference in average score from 
                       the base case: -0.0207                                                      (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (valine) into lysine:     
                       Energy difference: -0.8729 kcal/mol, Difference in average score from the   
                       base case: -0.0238                                                          (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (valine) into aspartic    
                       acid: Energy difference: 0.3286 kcal/mol, Difference in average score from  
                       the base case: -0.0252                                                      (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (valine) into arginine:   
                       Energy difference: -0.7016 kcal/mol, Difference in average score from the   
                       base case: -0.0252                                                          (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 2.4793 kcal/mol, Difference in average    
                       score from the base case: -0.0031                                           (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       lysine: Energy difference: 2.5046 kcal/mol, Difference in average score     
                       from the base case: -0.0059                                                 (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 3.3537 kcal/mol, Difference in average    
                       score from the base case: -0.0171                                           (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       arginine: Energy difference: 2.5167 kcal/mol, Difference in average score   
                       from the base case: -0.0136                                                 (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 255 from chain A (asparagine) into        
                       glutamic acid: Energy difference: 0.2333 kcal/mol, Difference in average    
                       score from the base case: 0.0020                                            (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 255 from chain A (asparagine) into        
                       lysine: Energy difference: -0.9780 kcal/mol, Difference in average score    
                       from the base case: -0.0022                                                 (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 255 from chain A (asparagine) into        
                       aspartic acid: Energy difference: 0.1361 kcal/mol, Difference in average    
                       score from the base case: 0.0058                                            (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 255 from chain A (asparagine) into        
                       arginine: Energy difference: -0.5242 kcal/mol, Difference in average score  
                       from the base case: -0.0074                                                 (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 210 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: -7.3831 kcal/mol, Difference in average score from 
                       the base case: 0.0023                                                       (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 210 from chain A (tyrosine) into lysine:  
                       Energy difference: -4.9227 kcal/mol, Difference in average score from the   
                       base case: 0.0077                                                           (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 210 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: -7.4231 kcal/mol, Difference in average score from 
                       the base case: 0.0046                                                       (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 210 from chain A (tyrosine) into          
                       arginine: Energy difference: -5.1511 kcal/mol, Difference in average score  
                       from the base case: 0.0066                                                  (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.6561 kcal/mol, Difference in average score from  
                       the base case: -0.0201                                                      (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (valine) into lysine:    
                       Energy difference: -0.2864 kcal/mol, Difference in average score from the   
                       base case: -0.0053                                                          (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.7741 kcal/mol, Difference in average score from  
                       the base case: -0.0100                                                      (00:27:36)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (valine) into arginine:  
                       Energy difference: -1.2788 kcal/mol, Difference in average score from the   
                       base case: -0.0075                                                          (00:27:36)
[INFO]       Main:     Simulation completed successfully.                                          (00:27:43)
Show buried residues
Minimal score value
-3.3615
Maximal score value
1.3954
Average score
-0.6204
Total score value
-176.2074
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 -1.1759
3 R A -1.9202
4 P A -1.2581
5 G A -0.9473
6 L A -0.4781
7 P A -0.0847
8 V A 0.1919
9 E A -0.2992
10 Y A -0.0270
11 L A 0.0000
12 Q A -1.4329
13 V A 0.0000
14 P A -1.3112
15 S A 0.0000
16 P A -0.9483
17 S A -0.7167
18 M A 0.0000
19 G A -1.3516
20 R A -1.8894
21 D A -2.1880
22 I A 0.0000
23 K A -1.4685
24 V A 0.0000
25 Q A 0.0000
26 F A 0.0000
27 Q A 0.0000
28 S A -0.7957
29 G A -1.1203
30 G A -1.5750
31 N A -2.3361
32 N A -2.4632
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 -0.7659
42 L A -1.2256
43 R A -2.6855
44 A A 0.0000
45 Q A -2.9698
46 D A -3.3615
47 D A -2.6136
48 Y A -0.4477
49 N A 0.0000
50 G A -0.1425
51 W A 0.0000
52 D A 0.4820
53 V A 1.3917
54 N A -0.3581
55 T A 0.0000
56 P A -0.5053
57 A A 0.0000
58 F A 0.0000
59 E A -0.6822
60 W A -0.2653
61 Y A 0.0000
62 Y A -0.0508
63 Q A -1.0836
64 S A 0.0000
65 G A -1.0212
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 -1.8922
74 G A -1.2365
75 Q A -1.6824
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 -1.2481
82 W A 0.0000
83 K A -2.0847
84 S A -1.4747
85 P A -0.8985
86 A A 0.0000
87 C A -0.2592
88 G A -1.0954
89 K A -1.8328
90 A A -0.7933
91 G A -0.4489
92 C A 0.1914
93 Q A -0.5126
94 T A -0.7739
95 Y A 0.0000
96 K A -1.1310
97 W A 0.0000
98 E A -0.5725
99 T A -0.5334
100 F A 0.0000
101 L A 0.0000
102 T A -0.4631
103 S A -0.6791
104 E A -0.8320
105 L A 0.0000
106 P A 0.0000
107 Q A -1.4737
108 W A -0.6048
109 L A 0.0000
110 S A -1.3615
111 A A -0.7734
112 N A -1.0467
113 R A -1.5505
114 A A -1.7185
115 V A 0.0000
116 K A -2.0987
117 P A -1.3055
118 T A -0.9790
119 G A -0.6118
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 -0.1587
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 -0.3313
139 H A -0.6139
140 P A -1.0206
141 Q A -1.4022
142 Q A -0.9879
143 F A 0.0000
144 I A -0.4330
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 0.2742
153 L A 0.0000
154 D A -0.9912
155 P A 0.0000
156 S A -1.3426
157 Q A -1.5446
158 G A -0.6403
159 M A 0.3846
160 G A 0.0000
161 P A -0.3396
162 S A -0.1565
163 A A 0.1463
164 I A 0.0000
165 G A -0.8059
166 A A -0.8270
167 A A -1.0935
168 M A 0.0000
169 G A -1.7850
170 D A -2.4752
171 A A 0.0000
172 G A -1.7616
173 G A -1.7589
174 Y A 0.0000
175 K A -2.0567
176 A A -1.1166
177 A A -1.1817
178 D A -1.4349
179 M A 0.0000
180 W A 0.0000
181 G A 0.0000
182 P A -0.8081
183 S A -0.8601
184 S A -0.7589
185 D A -1.0128
186 P A -1.1376
187 A A -1.2582
188 W A 0.0000
189 E A -2.1265
190 R A -1.8211
191 N A 0.0000
192 D A 0.0000
193 P A 0.0000
194 T A -1.2255
195 Q A -1.6390
196 Q A 0.0000
197 I A 0.0000
198 P A -1.0689
199 K A -1.4807
200 L A 0.0000
201 V A -1.3312
202 A A -0.9480
203 N A -1.5318
204 N A -1.7274
205 T A 0.0000
206 R A -1.4011
207 L A 0.0000
208 W A 0.0000
209 V A 0.0000
210 Y A 0.7318
211 C A 0.0000
212 G A 0.0000
213 N A -0.7972
214 G A 0.0000
215 T A -1.0492
216 P A -1.6295
217 N A -2.1720
218 E A -2.2636
219 L A -1.3685
220 G A -1.4389
221 G A -1.3258
222 A A -1.1699
223 N A -1.4419
224 A A -0.8149
225 G A -0.9717
226 A A 0.0000
227 S A -0.9877
228 A A -0.7440
229 A A -0.4829
230 E A 0.0000
231 N A -1.4522
232 A A -0.5080
233 V A -0.0473
234 R A 0.0000
235 S A -0.4978
236 S A -0.6066
237 N A 0.0000
238 L A -0.0157
239 K A -2.0510
240 F A 0.0000
241 Q A 0.0000
242 D A -2.5350
243 A A -1.7352
244 Y A 0.0000
245 N A -2.3520
246 A A -1.2579
247 A A -0.9152
248 G A -1.1334
249 G A -1.7478
250 H A -1.7331
251 N A -1.4086
252 A A -0.5990
253 V A 0.4607
254 F A 1.0513
255 N A 0.7772
256 F A 1.3954
257 P A 0.2920
258 P A -0.4107
259 N A -0.7596
260 G A 0.0000
261 T A 0.0000
262 H A -0.8664
263 S A -0.8778
264 W A -0.7258
265 E A -1.7979
266 Y A 0.0000
267 W A 0.0000
268 G A 0.0000
269 A A -0.5176
270 Q A 0.0000
271 L A 0.0000
272 N A -0.6922
273 A A -0.6421
274 M A 0.0000
275 K A -1.2708
276 G A -1.4962
277 D A -1.8200
278 L A 0.0000
279 Q A -1.2931
280 S A -1.1404
281 S A -0.8453
282 L A -0.5474
283 G A -0.8181
284 A A -0.9722
285 G A -0.9001
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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
VK53A -0.8729 -0.0238 View CSV PDB
VR53A -0.7016 -0.0252 View CSV PDB
FE256A -0.4933 -0.0255 View CSV PDB
FD256A -0.7739 -0.0193 View CSV PDB
VR253A -1.2788 -0.0075 View CSV PDB
NR255A -0.5242 -0.0074 View CSV PDB
VK253A -0.2864 -0.0053 View CSV PDB
NK255A -0.978 -0.0022 View CSV PDB
FR254A 2.5167 -0.0136 View CSV PDB
FD254A 3.3537 -0.0171 View CSV PDB
YE210A -7.3831 0.0023 View CSV PDB
YD210A -7.4231 0.0046 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018