Project name: 1f0n_sv5

Status: done

Started: 2025-02-19 06:50:56
Settings
Chain sequence(s) A: SRPGLPVEYLQVPSPSMGRDIKVQFQSGGNNSPAVYLLDGLRAQDDVNGWARNTPAFEWYYQSGLSIVMPVGGQSSFYSDWLKPACGKAGCQTYKWETFLTSELPQWLSANRAVKPTGSAAIGLSMAGSSAMILAAYHPQQFIYAGSLSALLDPSQGMGPAFIDAAMGDAGGYKAADMWGPSSDPAWERNDPTQQIPKLVANNTRLWVYCGNGTPNELGGANIPAEFLENFVRSSNLKFQDAYNAAGGHNAVFNFPPNGTHSWEYWGAQLNAMKGDLQSSLGAG
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                                          (00:03:53)
[INFO]       Auto_mut: Residue number 228 from chain A and a score of 2.019 (phenylalanine)        
                       selected for automated muatation                                            (00:03:55)
[INFO]       Auto_mut: Residue number 224 from chain A and a score of 1.774 (isoleucine) selected  
                       for automated muatation                                                     (00:03:55)
[INFO]       Auto_mut: Residue number 256 from chain A and a score of 1.397 (phenylalanine)        
                       selected for automated muatation                                            (00:03:55)
[INFO]       Auto_mut: Residue number 229 from chain A and a score of 1.395 (leucine) selected for 
                       automated muatation                                                         (00:03:55)
[INFO]       Auto_mut: Residue number 254 from chain A and a score of 1.356 (phenylalanine)        
                       selected for automated muatation                                            (00:03:55)
[INFO]       Auto_mut: Residue number 253 from chain A and a score of 1.037 (valine) selected for  
                       automated muatation                                                         (00:03:55)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into glutamic acid    (00:03:55)
[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 (00:03:55)
[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 (00:03:55)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into lysine           (00:05:02)
[INFO]       Auto_mut: Mutating residue number 228 from chain A (phenylalanine) into arginine      (00:05:02)
[INFO]       Auto_mut: Mutating residue number 228 from chain A (phenylalanine) into lysine        (00:05:07)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into aspartic acid    (00:06:15)
[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 (00:06:27)
[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 (00:06:34)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into arginine         (00:07:22)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (phenylalanine) into lysine        (00:07:32)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (phenylalanine) into arginine      (00:07:40)
[INFO]       Auto_mut: Mutating residue number 229 from chain A (leucine) into glutamic acid       (00:08:32)
[INFO]       Auto_mut: Mutating residue number 229 from chain A (leucine) into aspartic acid       (00:08:45)
[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 (00:08:50)
[INFO]       Auto_mut: Mutating residue number 229 from chain A (leucine) into lysine              (00:09:44)
[INFO]       Auto_mut: Mutating residue number 229 from chain A (leucine) into arginine            (00:09:52)
[INFO]       Auto_mut: Mutating residue number 254 from chain A (phenylalanine) into lysine        (00:09:56)
[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 (00:11:03)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (valine) into glutamic acid        (00:11:10)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (valine) into aspartic acid        (00:11:15)
[INFO]       Auto_mut: Mutating residue number 254 from chain A (phenylalanine) into arginine      (00:12:12)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (valine) into lysine               (00:12:20)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (valine) into arginine             (00:12:25)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 0.1087 kcal/mol, Difference in average    
                       score from the base case: -0.0251                                           (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       lysine: Energy difference: -0.2356 kcal/mol, Difference in average score    
                       from the base case: -0.0247                                                 (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 0.5538 kcal/mol, Difference in average    
                       score from the base case: -0.0250                                           (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       arginine: Energy difference: -0.1644 kcal/mol, Difference in average score  
                       from the base case: -0.0260                                                 (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -1.0452 kcal/mol, Difference in average   
                       score from the base case: -0.0224                                           (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.3859 kcal/mol, Difference in average score    
                       from the base case: -0.0244                                                 (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: -0.0769 kcal/mol, Difference in average   
                       score from the base case: -0.0241                                           (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.4653 kcal/mol, Difference in average score  
                       from the base case: -0.0324                                                 (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: -1.7364 kcal/mol, Difference in average   
                       score from the base case: 0.0005                                            (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.3382 kcal/mol, Difference in average score     
                       from the base case: 0.0012                                                  (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: -0.7424 kcal/mol, Difference in average   
                       score from the base case: 0.0031                                            (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       arginine: Energy difference: -0.0800 kcal/mol, Difference in average score  
                       from the base case: -0.0115                                                 (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 229 from chain A (leucine) into glutamic  
                       acid: Energy difference: 1.4253 kcal/mol, Difference in average score from  
                       the base case: -0.0022                                                      (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 229 from chain A (leucine) into lysine:   
                       Energy difference: 0.4786 kcal/mol, Difference in average score from the    
                       base case: -0.0019                                                          (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 229 from chain A (leucine) into aspartic  
                       acid: Energy difference: 1.8011 kcal/mol, Difference in average score from  
                       the base case: -0.0013                                                      (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 229 from chain A (leucine) into arginine: 
                       Energy difference: -0.2554 kcal/mol, Difference in average score from the   
                       base case: 0.0008                                                           (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 1.5592 kcal/mol, Difference in average    
                       score from the base case: 0.0057                                            (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       lysine: Energy difference: 1.0055 kcal/mol, Difference in average score     
                       from the base case: 0.0013                                                  (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 1.6385 kcal/mol, Difference in average    
                       score from the base case: -0.0110                                           (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       arginine: Energy difference: 1.0873 kcal/mol, Difference in average score   
                       from the base case: -0.0070                                                 (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.2021 kcal/mol, Difference in average score from 
                       the base case: -0.0031                                                      (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (valine) into lysine:    
                       Energy difference: -0.7666 kcal/mol, Difference in average score from the   
                       base case: -0.0019                                                          (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.1266 kcal/mol, Difference in average score from 
                       the base case: -0.0002                                                      (00:14:08)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (valine) into arginine:  
                       Energy difference: -0.5169 kcal/mol, Difference in average score from the   
                       base case: -0.0076                                                          (00:14:08)
[INFO]       Main:     Simulation completed successfully.                                          (00:14:15)
Show buried residues
Minimal score value
-3.2321
Maximal score value
2.019
Average score
-0.5688
Total score value
-161.5457
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 -1.2859
3 R A -2.1430
4 P A -1.3685
5 G A -1.0101
6 L A -0.5424
7 P A -0.1037
8 V A 0.1525
9 E A -0.2295
10 Y A 0.0999
11 L A 0.0000
12 Q A -1.3762
13 V A 0.0000
14 P A -1.2938
15 S A 0.0000
16 P A -0.9410
17 S A -0.7049
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 -1.4803
24 V A 0.0000
25 Q A -0.1797
26 F A 0.0000
27 Q A 0.0000
28 S A -0.8029
29 G A -1.1326
30 G A -1.5884
31 N A -2.3561
32 N A -2.5036
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 -0.6789
42 L A -1.1513
43 R A -2.5608
44 A A 0.0000
45 Q A -2.5994
46 D A -3.2321
47 D A -2.6252
48 V A -1.4163
49 N A 0.0000
50 G A 0.0000
51 W A 0.0000
52 A A 0.0000
53 R A -1.9106
54 N A -1.4624
55 T A 0.0000
56 P A -0.9798
57 A A 0.0000
58 F A 0.0000
59 E A -0.7290
60 W A -0.2986
61 Y A 0.0000
62 Y A -0.0691
63 Q A -1.0897
64 S A 0.0000
65 G A -1.0224
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 -1.8023
74 G A -1.1663
75 Q A -1.5753
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 -0.6809
82 W A 0.0000
83 L A -0.0369
84 K A -1.6954
85 P A -1.1079
86 A A 0.0000
87 C A -0.5558
88 G A -1.1007
89 K A -1.8149
90 A A -0.7905
91 G A -0.4599
92 C A 0.1530
93 Q A -0.7057
94 T A -0.7518
95 Y A 0.0000
96 K A -0.8446
97 W A 0.0000
98 E A 0.0000
99 T A -0.4284
100 F A 0.0000
101 L A 0.0000
102 T A -0.3975
103 S A -0.6525
104 E A -0.8115
105 L A 0.0000
106 P A 0.0000
107 Q A -1.4868
108 W A -0.6051
109 L A 0.0000
110 S A -1.3893
111 A A -0.7798
112 N A -1.0332
113 R A -1.5641
114 A A -1.7452
115 V A 0.0000
116 K A -2.2054
117 P A -1.3574
118 T A -1.0166
119 G A -0.6424
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 -0.0854
127 M A -0.1050
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 -0.1419
139 H A -0.5317
140 P A -0.9914
141 Q A -1.3911
142 Q A -0.9901
143 F A 0.0000
144 I A -0.4516
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 0.2807
153 L A 0.0000
154 D A -1.1254
155 P A 0.0000
156 S A -1.3203
157 Q A -1.5535
158 G A -0.5506
159 M A 0.5333
160 G A -0.0083
161 P A -0.2640
162 A A 0.1023
163 F A 0.6064
164 I A 0.0000
165 D A -1.3186
166 A A -0.9407
167 A A -1.1439
168 M A 0.0000
169 G A -1.8862
170 D A -2.5631
171 A A 0.0000
172 G A -1.7322
173 G A -1.7682
174 Y A 0.0000
175 K A -2.4080
176 A A 0.0000
177 A A -1.1416
178 D A -1.2130
179 M A 0.0000
180 W A 0.0000
181 G A 0.0000
182 P A -0.8348
183 S A -0.9767
184 S A -0.8622
185 D A -1.1673
186 P A -1.1240
187 A A -0.8308
188 W A 0.0000
189 E A -1.9633
190 R A -1.3958
191 N A 0.0000
192 D A 0.0000
193 P A 0.0000
194 T A -1.2199
195 Q A -1.5830
196 Q A 0.0000
197 I A 0.0000
198 P A -1.0718
199 K A -1.4587
200 L A 0.0000
201 V A -1.3331
202 A A -0.9492
203 N A -1.5213
204 N A -1.7348
205 T A 0.0000
206 R A -1.3513
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 -0.4199
214 G A 0.0000
215 T A -0.7359
216 P A -1.6080
217 N A -2.1599
218 E A -2.2121
219 L A -1.0933
220 G A -1.1759
221 G A -0.8559
222 A A -0.6619
223 N A -0.0130
224 I A 1.7740
225 P A 0.8736
226 A A 0.0000
227 E A 0.4521
228 F A 2.0190
229 L A 1.3948
230 E A 0.0000
231 N A -0.4575
232 F A 0.8772
233 V A 0.0000
234 R A -0.4718
235 S A -0.7407
236 S A -0.8866
237 N A 0.0000
238 L A -0.6886
239 K A -2.4023
240 F A 0.0000
241 Q A 0.0000
242 D A -2.6746
243 A A -1.8151
244 Y A 0.0000
245 N A -2.3557
246 A A -1.2572
247 A A -0.9141
248 G A -1.1349
249 G A -1.7521
250 H A -1.6687
251 N A -1.2898
252 A A -0.2830
253 V A 1.0368
254 F A 1.3563
255 N A 0.9051
256 F A 1.3972
257 P A 0.3354
258 P A -0.3807
259 N A -0.8385
260 G A 0.0000
261 T A 0.0000
262 H A -0.1579
263 S A -0.5280
264 W A -0.6089
265 E A -0.9854
266 Y A 0.0000
267 W A 0.0000
268 G A 0.0000
269 A A -0.3407
270 Q A 0.0000
271 L A 0.0000
272 N A -0.7033
273 A A -0.7223
274 M A 0.0000
275 K A -1.4259
276 G A -1.7211
277 D A -2.2175
278 L A 0.0000
279 Q A -1.4394
280 S A -1.2942
281 S A -0.9750
282 L A -0.6185
283 G A -0.8682
284 A A -1.0197
285 G A -0.8985
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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 -1.0452 -0.0224 View CSV PDB
IR224A -0.4653 -0.0324 View CSV PDB
FK228A -0.2356 -0.0247 View CSV PDB
FR228A -0.1644 -0.026 View CSV PDB
VR253A -0.5169 -0.0076 View CSV PDB
FR256A -0.08 -0.0115 View CSV PDB
VK253A -0.7666 -0.0019 View CSV PDB
FD254A 1.6385 -0.011 View CSV PDB
FR254A 1.0873 -0.007 View CSV PDB
LK229A 0.4786 -0.0019 View CSV PDB
LE229A 1.4253 -0.0022 View CSV PDB
FE256A -1.7364 0.0005 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018