Project name: 1f0n_v4

Status: done

Started: 2025-02-18 07:11:58
Settings
Chain sequence(s) A: SRPGLPVEYLQVPSPSMGRDIKVQFQSGGNNSPAVYLLDGLRAQDDYNGWDINTPAFEWYYQSGLSIVMPVGGQSSFYSDWLSPACGKAGCQTYKWETFLTSELPQWLSANRAVKPTGSAAIGLSMAGSSAMILAAYHPQQFIYAGSLSALLDPSQGMGPSLIGAAMGDAGGYKAADMWGPSSDPAWERNDPTQQIPKLVANNTRLWVYCGNGTPNELGGANPAASALENLVRSSNLKFQDAYNAAGGHNAVFNFPPNGTHSWEYWGAQLNAMKGDLQSSLGAG
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                                          (00:03:29)
[INFO]       Auto_mut: Residue number 53 from chain A and a score of 1.546 (isoleucine) selected   
                       for automated muatation                                                     (00:03:30)
[INFO]       Auto_mut: Residue number 256 from chain A and a score of 1.348 (phenylalanine)        
                       selected for automated muatation                                            (00:03:30)
[INFO]       Auto_mut: Residue number 83 from chain A and a score of 1.234 (leucine) selected for  
                       automated muatation                                                         (00:03:30)
[INFO]       Auto_mut: Residue number 254 from chain A and a score of 1.225 (phenylalanine)        
                       selected for automated muatation                                            (00:03:30)
[INFO]       Auto_mut: Residue number 253 from chain A and a score of 0.995 (valine) selected for  
                       automated muatation                                                         (00:03:30)
[INFO]       Auto_mut: Residue number 255 from chain A and a score of 0.761 (asparagine) selected  
                       for automated muatation                                                     (00:03:30)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (isoleucine) into glutamic acid     (00:03:30)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (isoleucine) into aspartic acid     (00:03:30)
[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 (00:03:30)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (isoleucine) into arginine          (00:05:05)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (phenylalanine) into lysine        (00:05:13)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (isoleucine) into lysine            (00:05:15)
[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 (00:07:24)
[INFO]       Auto_mut: Mutating residue number 83 from chain A (leucine) into glutamic acid        (00:07:40)
[INFO]       Auto_mut: Mutating residue number 83 from chain A (leucine) into aspartic acid        (00:07:48)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (phenylalanine) into arginine      (00:09:36)
[INFO]       Auto_mut: Mutating residue number 83 from chain A (leucine) into lysine               (00:09:48)
[INFO]       Auto_mut: Mutating residue number 83 from chain A (leucine) into arginine             (00:10:02)
[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 (00:11:06)
[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 (00:11:28)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (valine) into glutamic acid        (00:11:32)
[INFO]       Auto_mut: Mutating residue number 254 from chain A (phenylalanine) into lysine        (00:12:44)
[INFO]       Auto_mut: Mutating residue number 254 from chain A (phenylalanine) into arginine      (00:13:21)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (valine) into lysine               (00:13:24)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (valine) into aspartic acid        (00:14:45)
[INFO]       Auto_mut: Mutating residue number 255 from chain A (asparagine) into glutamic acid    (00:15:36)
[INFO]       Auto_mut: Mutating residue number 255 from chain A (asparagine) into aspartic acid    (00:17:03)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (valine) into arginine             (00:17:12)
[INFO]       Auto_mut: Mutating residue number 255 from chain A (asparagine) into lysine           (00:20:18)
[INFO]       Auto_mut: Mutating residue number 255 from chain A (asparagine) into arginine         (00:21:08)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 0.5617 kcal/mol, Difference in average    
                       score from the base case: -0.0262                                           (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (isoleucine) into lysine: 
                       Energy difference: -1.1715 kcal/mol, Difference in average score from the   
                       base case: -0.0316                                                          (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 1.2072 kcal/mol, Difference in average    
                       score from the base case: -0.0349                                           (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (isoleucine) into         
                       arginine: Energy difference: -1.0741 kcal/mol, Difference in average score  
                       from the base case: -0.0011                                                 (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: -0.5090 kcal/mol, Difference in average   
                       score from the base case: -0.0302                                           (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       lysine: Energy difference: -0.1116 kcal/mol, Difference in average score    
                       from the base case: -0.0282                                                 (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: -0.7879 kcal/mol, Difference in average   
                       score from the base case: -0.0253                                           (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       arginine: Energy difference: -0.0527 kcal/mol, Difference in average score  
                       from the base case: -0.0320                                                 (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 83 from chain A (leucine) into glutamic   
                       acid: Energy difference: 1.5031 kcal/mol, Difference in average score from  
                       the base case: -0.0412                                                      (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 83 from chain A (leucine) into lysine:    
                       Energy difference: -0.1656 kcal/mol, Difference in average score from the   
                       base case: -0.0281                                                          (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 83 from chain A (leucine) into aspartic   
                       acid: Energy difference: 1.4792 kcal/mol, Difference in average score from  
                       the base case: -0.0438                                                      (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 83 from chain A (leucine) into arginine:  
                       Energy difference: -0.2934 kcal/mol, Difference in average score from the   
                       base case: -0.0294                                                          (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 2.5677 kcal/mol, Difference in average    
                       score from the base case: -0.0114                                           (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       lysine: Energy difference: 2.6120 kcal/mol, Difference in average score     
                       from the base case: -0.0129                                                 (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 3.0586 kcal/mol, Difference in average    
                       score from the base case: -0.0264                                           (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       arginine: Energy difference: 2.2820 kcal/mol, Difference in average score   
                       from the base case: -0.0167                                                 (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.0068 kcal/mol, Difference in average score from 
                       the base case: -0.0343                                                      (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (valine) into lysine:    
                       Energy difference: -1.0057 kcal/mol, Difference in average score from the   
                       base case: -0.0233                                                          (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.0553 kcal/mol, Difference in average score from 
                       the base case: -0.0248                                                      (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (valine) into arginine:  
                       Energy difference: -0.8766 kcal/mol, Difference in average score from the   
                       base case: -0.0271                                                          (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 255 from chain A (asparagine) into        
                       glutamic acid: Energy difference: -0.8918 kcal/mol, Difference in average   
                       score from the base case: -0.0039                                           (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 255 from chain A (asparagine) into        
                       lysine: Energy difference: -1.4399 kcal/mol, Difference in average score    
                       from the base case: -0.0099                                                 (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 255 from chain A (asparagine) into        
                       aspartic acid: Energy difference: -0.6382 kcal/mol, Difference in average   
                       score from the base case: -0.0001                                           (00:28:12)
[INFO]       Auto_mut: Effect of mutation residue number 255 from chain A (asparagine) into        
                       arginine: Energy difference: -1.6576 kcal/mol, Difference in average score  
                       from the base case: -0.0131                                                 (00:28:12)
[INFO]       Main:     Simulation completed successfully.                                          (00:28:19)
Show buried residues
Minimal score value
-3.2289
Maximal score value
1.5456
Average score
-0.5476
Total score value
-155.515
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 -1.9150
4 P A -1.2519
5 G A -0.9393
6 L A -0.4599
7 P A -0.0557
8 V A 0.2535
9 E A -0.2452
10 Y A 0.0274
11 L A 0.0000
12 Q A -1.4203
13 V A 0.0000
14 P A -1.3146
15 S A 0.0000
16 P A -0.9597
17 S A -0.7343
18 M A 0.0000
19 G A -1.3571
20 R A -1.8822
21 D A -2.1846
22 I A 0.0000
23 K A -1.4294
24 V A 0.0000
25 Q A 0.0000
26 F A 0.0000
27 Q A 0.0000
28 S A -0.7852
29 G A -1.0964
30 G A -1.5515
31 N A -2.2958
32 N A -2.3732
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 -1.1906
43 R A -2.6606
44 A A 0.0000
45 Q A -2.8884
46 D A -3.2289
47 D A -2.3531
48 Y A -0.3728
49 N A 0.0000
50 G A -0.0639
51 W A 0.0000
52 D A 0.5352
53 I A 1.5456
54 N A -0.3478
55 T A 0.0000
56 P A -0.4948
57 A A 0.0000
58 F A 0.0000
59 E A -0.6763
60 W A -0.2742
61 Y A 0.0000
62 Y A -0.0478
63 Q A -1.0851
64 S A 0.0000
65 G A -1.0203
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 -1.8164
74 G A 0.0000
75 Q A -1.6412
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 -0.4546
82 W A 0.0000
83 L A 1.2338
84 S A 0.1746
85 P A -0.2668
86 A A 0.0000
87 C A -0.5354
88 G A -1.2858
89 K A -1.9292
90 A A -0.8627
91 G A -0.5697
92 C A 0.0418
93 Q A -0.5847
94 T A -0.4650
95 Y A 0.0000
96 K A -0.7309
97 W A 0.0000
98 E A -0.5732
99 T A -0.5424
100 F A 0.0000
101 L A 0.0000
102 T A -0.4652
103 S A -0.6862
104 E A -0.8442
105 L A 0.0000
106 P A 0.0000
107 Q A -1.4499
108 W A -0.6151
109 L A 0.0000
110 S A -1.2921
111 A A -0.7383
112 N A -1.0213
113 R A -1.5125
114 A A -1.6548
115 V A 0.0000
116 K A -1.8545
117 P A -1.1913
118 T A -0.9090
119 G A -0.5721
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 -0.1080
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 -0.3239
139 H A -0.6127
140 P A -1.0241
141 Q A -1.4081
142 Q A -0.9672
143 F A 0.0000
144 I A -0.4241
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 0.3164
153 L A 0.0000
154 D A -1.0655
155 P A 0.0000
156 S A -1.3653
157 Q A -1.5336
158 G A -0.5910
159 M A 0.4935
160 G A 0.0000
161 P A -0.2200
162 S A 0.0365
163 L A 0.5188
164 I A 0.0000
165 G A -0.7026
166 A A -0.7236
167 A A -1.0278
168 M A 0.0000
169 G A -1.8473
170 D A -2.5280
171 A A 0.0000
172 G A -1.8520
173 G A -1.8730
174 Y A 0.0000
175 K A -2.0850
176 A A -1.0320
177 A A -0.6396
178 D A -0.3891
179 M A 0.0000
180 W A 0.0000
181 G A 0.0000
182 P A -0.8343
183 S A -0.9133
184 S A -0.8409
185 D A -1.1826
186 P A -1.2209
187 A A -0.9335
188 W A 0.0000
189 E A -2.1509
190 R A -1.8504
191 N A 0.0000
192 D A 0.0000
193 P A 0.0000
194 T A -1.2345
195 Q A -1.6269
196 Q A 0.0000
197 I A 0.0000
198 P A -1.0606
199 K A -1.4661
200 L A 0.0000
201 V A -1.3209
202 A A -0.9442
203 N A -1.5164
204 N A -1.7117
205 T A 0.0000
206 R A -1.1637
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 -0.7155
214 G A 0.0000
215 T A -1.0661
216 P A -1.5846
217 N A -2.1948
218 E A -2.2603
219 L A -1.3636
220 G A -1.3549
221 G A -1.1426
222 A A -0.9273
223 N A -0.9518
224 P A -0.5362
225 A A -0.2700
226 A A 0.0000
227 S A -0.5209
228 A A -0.1462
229 L A 0.3858
230 E A 0.0000
231 N A -1.0043
232 L A 0.1496
233 V A 0.0000
234 R A 0.0000
235 S A -0.4549
236 S A -0.6204
237 N A 0.0000
238 L A -0.0635
239 K A -2.0717
240 F A 0.0000
241 Q A 0.0000
242 D A -2.5402
243 A A -1.7375
244 Y A 0.0000
245 N A -2.3586
246 A A -1.2581
247 A A -0.9155
248 G A -1.1384
249 G A -1.7476
250 H A -1.6747
251 N A -1.3037
252 A A -0.3423
253 V A 0.9951
254 F A 1.2253
255 N A 0.7606
256 F A 1.3484
257 P A 0.2187
258 P A -0.4686
259 N A -0.8601
260 G A 0.0000
261 T A 0.0000
262 H A -0.5636
263 S A -0.6545
264 W A -0.6462
265 E A -1.7751
266 Y A 0.0000
267 W A 0.0000
268 G A 0.0000
269 A A -0.5186
270 Q A 0.0000
271 L A 0.0000
272 N A -0.7231
273 A A -0.5674
274 M A 0.0000
275 K A -1.1054
276 G A -1.2240
277 D A -1.1717
278 L A 0.0000
279 Q A -1.1025
280 S A -0.9436
281 S A -0.6635
282 L A -0.4490
283 G A -0.7517
284 A A -0.9098
285 G A -0.8995
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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
IK53A -1.1715 -0.0316 View CSV PDB
VR253A -0.8766 -0.0271 View CSV PDB
VK253A -1.0057 -0.0233 View CSV PDB
FD256A -0.7879 -0.0253 View CSV PDB
FE256A -0.509 -0.0302 View CSV PDB
NR255A -1.6576 -0.0131 View CSV PDB
LR83A -0.2934 -0.0294 View CSV PDB
NK255A -1.4399 -0.0099 View CSV PDB
LK83A -0.1656 -0.0281 View CSV PDB
IR53A -1.0741 -0.0011 View CSV PDB
FD254A 3.0586 -0.0264 View CSV PDB
FR254A 2.282 -0.0167 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018