Project name: 1f0n_sv3best

Status: done

Started: 2025-02-17 23:38:49
Settings
Chain sequence(s) A: SRPGLPVETLQVPSPSMGRDIKVQFQSGGNNSPAVYLLDGLRAQDDYNGWDRNTPAFEWYYQSGLSIVMPVGGQSSFYSDWLKPACGKAGCQTYKWETFLTSELPQWLSANRAVKPTGSAAIGLSMAGSSAMILAAYHPQQFIYAGSLSALLDPSQGDGPALIDKAMGDAGGYKAADMWGPSSDPAWERNDPTQQIPKLVANNTRLWVYCGNGTPNELGGANKPAEDLENLVRSSNLKFQDAYNAAGGHNATFNLPPNGTHSWEYWGAQLNAMKGDLQSSLGAG
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                                          (00:04:16)
[INFO]       Auto_mut: Residue number 254 from chain A and a score of 0.662 (phenylalanine)        
                       selected for automated muatation                                            (00:04:18)
[INFO]       Auto_mut: Residue number 152 from chain A and a score of 0.274 (leucine) selected for 
                       automated muatation                                                         (00:04:18)
[INFO]       Auto_mut: Residue number 256 from chain A and a score of 0.231 (leucine) selected for 
                       automated muatation                                                         (00:04:18)
[INFO]       Auto_mut: Residue number 255 from chain A and a score of 0.169 (asparagine) selected  
                       for automated muatation                                                     (00:04:18)
[INFO]       Auto_mut: Residue number 92 from chain A and a score of 0.061 (cysteine) selected for 
                       automated muatation                                                         (00:04:18)
[INFO]       Auto_mut: Residue number 8 from chain A and a score of 0.013 (valine) selected for    
                       automated muatation                                                         (00:04:18)
[INFO]       Auto_mut: Mutating residue number 152 from chain A (leucine) into glutamic acid       (00:04:18)
[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 (00:04:18)
[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 (00:04:18)
[INFO]       Auto_mut: Mutating residue number 254 from chain A (phenylalanine) into arginine      (00:05:42)
[INFO]       Auto_mut: Mutating residue number 254 from chain A (phenylalanine) into lysine        (00:05:45)
[INFO]       Auto_mut: Mutating residue number 152 from chain A (leucine) into lysine              (00:06:14)
[INFO]       Auto_mut: Mutating residue number 152 from chain A (leucine) into aspartic acid       (00:07:09)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (leucine) into glutamic acid       (00:07:14)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (leucine) into aspartic acid       (00:08:28)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (leucine) into lysine              (00:08:43)
[INFO]       Auto_mut: Mutating residue number 152 from chain A (leucine) into arginine            (00:08:50)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (leucine) into arginine            (00:09:54)
[INFO]       Auto_mut: Mutating residue number 255 from chain A (asparagine) into glutamic acid    (00:10:08)
[INFO]       Auto_mut: Mutating residue number 255 from chain A (asparagine) into aspartic acid    (00:10:49)
[INFO]       Auto_mut: Mutating residue number 92 from chain A (cysteine) into glutamic acid       (00:11:22)
[INFO]       Auto_mut: Mutating residue number 255 from chain A (asparagine) into lysine           (00:11:51)
[INFO]       Auto_mut: Mutating residue number 255 from chain A (asparagine) into arginine         (00:12:23)
[INFO]       Auto_mut: Mutating residue number 92 from chain A (cysteine) into lysine              (00:12:45)
[INFO]       Auto_mut: Mutating residue number 92 from chain A (cysteine) into aspartic acid       (00:14:09)
[INFO]       Auto_mut: Mutating residue number 8 from chain A (valine) into glutamic acid          (00:14:18)
[INFO]       Auto_mut: Mutating residue number 8 from chain A (valine) into aspartic acid          (00:15:11)
[INFO]       Auto_mut: Mutating residue number 92 from chain A (cysteine) into arginine            (00:15:31)
[INFO]       Auto_mut: Mutating residue number 8 from chain A (valine) into lysine                 (00:15:47)
[INFO]       Auto_mut: Mutating residue number 8 from chain A (valine) into arginine               (00:16:40)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 1.5633 kcal/mol, Difference in average    
                       score from the base case: -0.0241                                           (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       lysine: Energy difference: 1.6401 kcal/mol, Difference in average score     
                       from the base case: -0.0279                                                 (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 2.0394 kcal/mol, Difference in average    
                       score from the base case: -0.0315                                           (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       arginine: Energy difference: 1.9619 kcal/mol, Difference in average score   
                       from the base case: -0.0257                                                 (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 152 from chain A (leucine) into glutamic  
                       acid: Energy difference: 3.1142 kcal/mol, Difference in average score from  
                       the base case: 0.0075                                                       (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 152 from chain A (leucine) into lysine:   
                       Energy difference: 1.9669 kcal/mol, Difference in average score from the    
                       base case: 0.0122                                                           (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 152 from chain A (leucine) into aspartic  
                       acid: Energy difference: 3.9007 kcal/mol, Difference in average score from  
                       the base case: 0.0048                                                       (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 152 from chain A (leucine) into arginine: 
                       Energy difference: -0.2584 kcal/mol, Difference in average score from the   
                       base case: 0.0063                                                           (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (leucine) into glutamic  
                       acid: Energy difference: 1.4701 kcal/mol, Difference in average score from  
                       the base case: -0.0113                                                      (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (leucine) into lysine:   
                       Energy difference: 2.4282 kcal/mol, Difference in average score from the    
                       base case: -0.0156                                                          (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (leucine) into aspartic  
                       acid: Energy difference: 1.5774 kcal/mol, Difference in average score from  
                       the base case: -0.0119                                                      (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (leucine) into arginine: 
                       Energy difference: 0.9354 kcal/mol, Difference in average score from the    
                       base case: -0.0262                                                          (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 255 from chain A (asparagine) into        
                       glutamic acid: Energy difference: 0.1407 kcal/mol, Difference in average    
                       score from the base case: -0.0081                                           (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 255 from chain A (asparagine) into        
                       lysine: Energy difference: -0.8179 kcal/mol, Difference in average score    
                       from the base case: -0.0094                                                 (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 255 from chain A (asparagine) into        
                       aspartic acid: Energy difference: 0.3295 kcal/mol, Difference in average    
                       score from the base case: -0.0074                                           (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 255 from chain A (asparagine) into        
                       arginine: Energy difference: -0.0323 kcal/mol, Difference in average score  
                       from the base case: -0.0194                                                 (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 92 from chain A (cysteine) into glutamic  
                       acid: Energy difference: 1.8022 kcal/mol, Difference in average score from  
                       the base case: -0.0358                                                      (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 92 from chain A (cysteine) into lysine:   
                       Energy difference: 1.6815 kcal/mol, Difference in average score from the    
                       base case: -0.0329                                                          (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 92 from chain A (cysteine) into aspartic  
                       acid: Energy difference: 2.1368 kcal/mol, Difference in average score from  
                       the base case: -0.0334                                                      (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 92 from chain A (cysteine) into arginine: 
                       Energy difference: 1.7047 kcal/mol, Difference in average score from the    
                       base case: -0.0362                                                          (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain A (valine) into glutamic     
                       acid: Energy difference: 1.8773 kcal/mol, Difference in average score from  
                       the base case: -0.0230                                                      (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain A (valine) into lysine:      
                       Energy difference: 0.6684 kcal/mol, Difference in average score from the    
                       base case: -0.0209                                                          (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain A (valine) into aspartic     
                       acid: Energy difference: 3.1332 kcal/mol, Difference in average score from  
                       the base case: -0.0231                                                      (00:18:09)
[INFO]       Auto_mut: Effect of mutation residue number 8 from chain A (valine) into arginine:    
                       Energy difference: 0.4521 kcal/mol, Difference in average score from the    
                       base case: -0.0164                                                          (00:18:09)
[INFO]       Main:     Simulation completed successfully.                                          (00:18:16)
Show buried residues
Minimal score value
-3.4178
Maximal score value
0.6621
Average score
-0.7513
Total score value
-213.3799
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 -1.1758
3 R A -1.9295
4 P A -1.2658
5 G A -0.9534
6 L A -0.4865
7 P A -0.1030
8 V A 0.0135
9 E A -0.6573
10 T A -0.7710
11 L A 0.0000
12 Q A -1.9472
13 V A 0.0000
14 P A -1.4974
15 S A 0.0000
16 P A -0.9935
17 S A -0.7674
18 M A 0.0000
19 G A -1.4125
20 R A -2.0445
21 D A -2.2149
22 I A 0.0000
23 K A -1.8197
24 V A 0.0000
25 Q A 0.0000
26 F A 0.0000
27 Q A 0.0000
28 S A -0.7816
29 G A -1.1130
30 G A -1.5520
31 N A -2.3036
32 N A -2.4237
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 -0.7377
42 L A -1.1959
43 R A -2.6671
44 A A 0.0000
45 Q A -3.0121
46 D A -3.4178
47 D A -2.7863
48 Y A -1.5119
49 N A 0.0000
50 G A -1.2756
51 W A 0.0000
52 D A -1.0993
53 R A -1.7239
54 N A -1.3006
55 T A 0.0000
56 P A -0.9535
57 A A 0.0000
58 F A 0.0000
59 E A -0.6805
60 W A -0.2717
61 Y A 0.0000
62 Y A -0.0501
63 Q A -1.0809
64 S A 0.0000
65 G A -1.0148
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 -1.9333
74 G A -1.2247
75 Q A -1.6468
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 -0.7796
82 W A 0.0000
83 L A -0.0074
84 K A -1.6638
85 P A -1.1118
86 A A 0.0000
87 C A -0.6928
88 G A -1.1687
89 K A -1.9036
90 A A -0.8468
91 G A -0.5459
92 C A 0.0615
93 Q A -0.7620
94 T A -0.7980
95 Y A 0.0000
96 K A -0.9262
97 W A 0.0000
98 E A -0.6570
99 T A -0.5925
100 F A 0.0000
101 L A 0.0000
102 T A -0.5149
103 S A -0.7812
104 E A -1.0163
105 L A 0.0000
106 P A 0.0000
107 Q A -1.6483
108 W A -0.9585
109 L A 0.0000
110 S A -1.4858
111 A A -0.9844
112 N A -1.4084
113 R A -1.6454
114 A A -1.7701
115 V A 0.0000
116 K A -2.0169
117 P A -1.2852
118 T A -0.9553
119 G A -0.6089
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 -0.0727
127 M A -0.0836
128 A A 0.0000
129 G A 0.0000
130 S A 0.0132
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 -0.4503
139 H A -0.6258
140 P A -1.0335
141 Q A -1.4060
142 Q A -0.9824
143 F A 0.0000
144 I A -0.4255
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 0.2741
153 L A 0.0000
154 D A -1.4154
155 P A 0.0000
156 S A -1.9253
157 Q A -2.2645
158 G A -1.9825
159 D A -2.3615
160 G A -1.6569
161 P A 0.0000
162 A A -1.3106
163 L A -1.0070
164 I A 0.0000
165 D A -2.0301
166 K A -2.5443
167 A A -1.9121
168 M A 0.0000
169 G A -2.3623
170 D A -2.9457
171 A A 0.0000
172 G A -1.7476
173 G A -1.9834
174 Y A 0.0000
175 K A -2.1791
176 A A 0.0000
177 A A -0.9280
178 D A -1.1089
179 M A 0.0000
180 W A 0.0000
181 G A 0.0000
182 P A -0.7885
183 S A -1.2108
184 S A -0.8507
185 D A -1.2872
186 P A -1.4129
187 A A -1.2454
188 W A 0.0000
189 E A -2.5096
190 R A -2.5435
191 N A 0.0000
192 D A 0.0000
193 P A 0.0000
194 T A -1.3404
195 Q A -1.7974
196 Q A 0.0000
197 I A 0.0000
198 P A -1.0770
199 K A -1.5009
200 L A 0.0000
201 V A -1.3270
202 A A -0.9545
203 N A -1.5299
204 N A -1.7170
205 T A 0.0000
206 R A -1.3274
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 -1.0863
214 G A 0.0000
215 T A -1.4639
216 P A -1.4931
217 N A -2.1173
218 E A -2.1754
219 L A -0.9449
220 G A -1.0354
221 G A -1.1512
222 A A -1.3415
223 N A -2.0866
224 K A -2.8069
225 P A -2.0726
226 A A 0.0000
227 E A -2.4188
228 D A -2.6039
229 L A -0.9048
230 E A 0.0000
231 N A -1.6573
232 L A -0.1136
233 V A 0.0000
234 R A -0.5652
235 S A -0.6289
236 S A -0.7764
237 N A 0.0000
238 L A -0.5366
239 K A -2.2196
240 F A 0.0000
241 Q A -1.4733
242 D A -2.6302
243 A A -1.7904
244 Y A 0.0000
245 N A -2.3838
246 A A -1.2757
247 A A -0.9269
248 G A -1.1368
249 G A -1.7624
250 H A -1.8257
251 N A -1.5228
252 A A -0.8643
253 T A -0.1458
254 F A 0.6621
255 N A 0.1694
256 L A 0.2309
257 P A -0.1910
258 P A -0.6268
259 N A -0.9596
260 G A 0.0000
261 T A 0.0000
262 H A -0.9808
263 S A -0.2593
264 W A -0.1667
265 E A -0.6709
266 Y A 0.0000
267 W A 0.0000
268 G A 0.0000
269 A A -0.2630
270 Q A 0.0000
271 L A 0.0000
272 N A -0.7642
273 A A -0.5712
274 M A 0.0000
275 K A -1.0936
276 G A -1.1711
277 D A -1.1571
278 L A 0.0000
279 Q A -1.0450
280 S A -0.8909
281 S A -0.6194
282 L A -0.4222
283 G A -0.7299
284 A A -0.8897
285 G A -0.8953
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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
NK255A -0.8179 -0.0094 View CSV PDB
NR255A -0.0323 -0.0194 View CSV PDB
VR8A 0.4521 -0.0164 View CSV PDB
VK8A 0.6684 -0.0209 View CSV PDB
LR256A 0.9354 -0.0262 View CSV PDB
CR92A 1.7047 -0.0362 View CSV PDB
CE92A 1.8022 -0.0358 View CSV PDB
FK254A 1.6401 -0.0279 View CSV PDB
FD254A 2.0394 -0.0315 View CSV PDB
LE256A 1.4701 -0.0113 View CSV PDB
LR152A -0.2584 0.0063 View CSV PDB
LD152A 3.9007 0.0048 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018