Project name: 946_en

Status: done

Started: 2024-06-13 14:30:02
Settings
Chain sequence(s) A: NFTLPPNFGKRPTDLELSVKLVEMLENIMLRDGCTLEESKIKKVLEKPKYINLALEAQFTIMPKTALELAKVFRLKNIEALAILVCGCSPTGNLSNIYSRRLKGDLNLSWVMTTCSTLCANERMPELLEKYSRGIYDGDLKDKVPYKGILISLELVTKPCTEGIELKSKRPQLLRKVMKELEEKVKELEEEVTRLSKENVGKSIMFAMTPKILKTSSLMPKLGYEKGLEISEKACLNGRCRRTVSMETGCRNVQLCSTILNVAFPPEVIGPLFFFPLLYMQNQKEEGDKIVKEYKEEEKKKE
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                                          (00:07:08)
[INFO]       Auto_mut: Residue number 206 from chain A and a score of 2.362 (phenylalanine)        
                       selected for automated muatation                                            (00:07:10)
[INFO]       Auto_mut: Residue number 262 from chain A and a score of 1.747 (valine) selected for  
                       automated muatation                                                         (00:07:10)
[INFO]       Auto_mut: Residue number 205 from chain A and a score of 1.710 (methionine) selected  
                       for automated muatation                                                     (00:07:10)
[INFO]       Auto_mut: Residue number 207 from chain A and a score of 1.523 (alanine) selected for 
                       automated muatation                                                         (00:07:10)
[INFO]       Auto_mut: Residue number 19 from chain A and a score of 1.350 (valine) selected for   
                       automated muatation                                                         (00:07:10)
[INFO]       Auto_mut: Residue number 2 from chain A and a score of 1.086 (phenylalanine) selected 
                       for automated muatation                                                     (00:07:10)
[INFO]       Auto_mut: Mutating residue number 262 from chain A (valine) into glutamic acid        (00:07:10)
[INFO]       Auto_mut: Mutating residue number 206 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 206 from chain A (phenylalanine) into glutamic acid (00:07:10)
[INFO]       Auto_mut: Mutating residue number 206 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 206 from chain A (phenylalanine) into aspartic acid (00:07:10)
[INFO]       Auto_mut: Mutating residue number 262 from chain A (valine) into lysine               (00:10:13)
[INFO]       Auto_mut: Mutating residue number 206 from chain A (phenylalanine) into arginine      (00:10:19)
[INFO]       Auto_mut: Mutating residue number 206 from chain A (phenylalanine) into lysine        (00:10:29)
[INFO]       Auto_mut: Mutating residue number 262 from chain A (valine) into aspartic acid        (00:13:38)
[INFO]       Auto_mut: Mutating residue number 205 from chain A (methionine) into glutamic acid    (00:13:40)
[INFO]       Auto_mut: Mutating residue number 205 from chain A (methionine) into aspartic acid    (00:13:57)
[INFO]       Auto_mut: Mutating residue number 262 from chain A (valine) into arginine             (00:16:43)
[INFO]       Auto_mut: Mutating residue number 205 from chain A (methionine) into lysine           (00:16:48)
[INFO]       Auto_mut: Mutating residue number 205 from chain A (methionine) into arginine         (00:17:07)
[INFO]       Auto_mut: Mutating residue number 207 from chain A (alanine) into glutamic acid       (00:19:57)
[INFO]       Auto_mut: Mutating residue number 207 from chain A (alanine) into aspartic acid       (00:20:06)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (valine) into glutamic acid         (00:20:28)
[INFO]       Auto_mut: Mutating residue number 207 from chain A (alanine) into lysine              (00:23:31)
[INFO]       Auto_mut: Mutating residue number 207 from chain A (alanine) into arginine            (00:23:37)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (valine) into lysine                (00:23:42)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (valine) into aspartic acid         (00:26:58)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (phenylalanine) into glutamic acid   (00:27:06)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (phenylalanine) into aspartic acid   (00:27:07)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (valine) into arginine              (00:30:17)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (phenylalanine) into arginine        (00:30:57)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (phenylalanine) into lysine          (00:31:01)
[INFO]       Auto_mut: Effect of mutation residue number 206 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 0.3263 kcal/mol, Difference in average    
                       score from the base case: -0.0529                                           (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 206 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.0536 kcal/mol, Difference in average score     
                       from the base case: -0.0468                                                 (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 206 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 0.8974 kcal/mol, Difference in average    
                       score from the base case: -0.0449                                           (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 206 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.3731 kcal/mol, Difference in average score   
                       from the base case: -0.0492                                                 (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 262 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.7828 kcal/mol, Difference in average score from  
                       the base case: -0.0355                                                      (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 262 from chain A (valine) into lysine:    
                       Energy difference: -0.1658 kcal/mol, Difference in average score from the   
                       base case: -0.0344                                                          (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 262 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.9050 kcal/mol, Difference in average score from  
                       the base case: -0.0356                                                      (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 262 from chain A (valine) into arginine:  
                       Energy difference: 0.1444 kcal/mol, Difference in average score from the    
                       base case: -0.0377                                                          (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 205 from chain A (methionine) into        
                       glutamic acid: Energy difference: 0.2443 kcal/mol, Difference in average    
                       score from the base case: -0.0346                                           (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 205 from chain A (methionine) into        
                       lysine: Energy difference: 0.4806 kcal/mol, Difference in average score     
                       from the base case: -0.0316                                                 (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 205 from chain A (methionine) into        
                       aspartic acid: Energy difference: 0.6681 kcal/mol, Difference in average    
                       score from the base case: -0.0300                                           (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 205 from chain A (methionine) into        
                       arginine: Energy difference: 0.7142 kcal/mol, Difference in average score   
                       from the base case: -0.0338                                                 (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 207 from chain A (alanine) into glutamic  
                       acid: Energy difference: 2.4365 kcal/mol, Difference in average score from  
                       the base case: -0.0062                                                      (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 207 from chain A (alanine) into lysine:   
                       Energy difference: 0.7626 kcal/mol, Difference in average score from the    
                       base case: -0.0033                                                          (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 207 from chain A (alanine) into aspartic  
                       acid: Energy difference: 2.8886 kcal/mol, Difference in average score from  
                       the base case: -0.0005                                                      (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 207 from chain A (alanine) into arginine: 
                       Energy difference: -0.3675 kcal/mol, Difference in average score from the   
                       base case: -0.0068                                                          (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (valine) into glutamic    
                       acid: Energy difference: -0.2017 kcal/mol, Difference in average score from 
                       the base case: -0.0304                                                      (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (valine) into lysine:     
                       Energy difference: -0.7770 kcal/mol, Difference in average score from the   
                       base case: -0.0409                                                          (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (valine) into aspartic    
                       acid: Energy difference: 0.1552 kcal/mol, Difference in average score from  
                       the base case: -0.0425                                                      (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (valine) into arginine:   
                       Energy difference: -0.7778 kcal/mol, Difference in average score from the   
                       base case: -0.0470                                                          (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (phenylalanine) into       
                       glutamic acid: Energy difference: 2.0572 kcal/mol, Difference in average    
                       score from the base case: -0.0292                                           (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (phenylalanine) into       
                       lysine: Energy difference: 1.6040 kcal/mol, Difference in average score     
                       from the base case: -0.0334                                                 (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (phenylalanine) into       
                       aspartic acid: Energy difference: 2.6806 kcal/mol, Difference in average    
                       score from the base case: -0.0243                                           (00:34:46)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (phenylalanine) into       
                       arginine: Energy difference: 1.6573 kcal/mol, Difference in average score   
                       from the base case: -0.0357                                                 (00:34:46)
[INFO]       Main:     Simulation completed successfully.                                          (00:34:52)
Show buried residues
Minimal score value
-5.7552
Maximal score value
2.3618
Average score
-1.1624
Total score value
-351.0309
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 N A -0.4315
2 F A 1.0862
3 T A 0.5801
4 L A 0.0079
5 P A -0.2008
6 P A -1.0569
7 N A -2.2569
8 F A 0.0000
9 G A -1.4148
10 K A -2.3392
11 R A -1.5698
12 P A -0.9147
13 T A -0.8258
14 D A -0.8189
15 L A 0.6753
16 E A -0.5946
17 L A 0.0000
18 S A 0.8841
19 V A 1.3496
20 K A -0.4795
21 L A 0.0000
22 V A 0.3078
23 E A -0.8018
24 M A 0.0000
25 L A 0.0000
26 E A -1.3614
27 N A 0.0000
28 I A 0.0000
29 M A 0.0000
30 L A -0.5614
31 R A -1.0985
32 D A -0.2570
33 G A 0.0000
34 C A 0.0000
35 T A -0.3547
36 L A 0.0000
37 E A -1.9462
38 E A -2.6999
39 S A -2.2478
40 K A -2.5618
41 I A -2.2716
42 K A -3.4030
43 K A -3.5273
44 V A 0.0000
45 L A -1.7265
46 E A -3.1365
47 K A -3.0392
48 P A -2.1003
49 K A -2.5221
50 Y A -1.4433
51 I A -1.2551
52 N A -2.1092
53 L A 0.0000
54 A A 0.0000
55 L A -0.8353
56 E A -1.4286
57 A A 0.0000
58 Q A 0.0000
59 F A 0.0000
60 T A -0.7386
61 I A -0.6018
62 M A 0.0000
63 P A 0.0000
64 K A -1.8139
65 T A 0.0000
66 A A 0.0000
67 L A -1.3774
68 E A -2.4129
69 L A 0.0000
70 A A 0.0000
71 K A -2.2033
72 V A -0.0558
73 F A -1.2427
74 R A -2.5806
75 L A -1.9108
76 K A -2.5671
77 N A -1.9047
78 I A -0.4847
79 E A 0.0000
80 A A 0.0000
81 L A 0.0000
82 A A 0.0000
83 I A 0.0000
84 L A 0.0000
85 V A 0.0000
86 C A 0.0000
87 G A 0.0000
88 C A 0.0000
89 S A 0.0000
90 P A 0.0000
91 T A 0.0000
92 G A 0.0000
93 N A 0.1339
94 L A 0.3839
95 S A 0.0000
96 N A 0.0000
97 I A 0.5865
98 Y A 0.0000
99 S A 0.0000
100 R A -2.5651
101 R A -2.2153
102 L A 0.0000
103 K A -3.3107
104 G A 0.0000
105 D A -2.2417
106 L A -1.2108
107 N A -1.1800
108 L A 0.0000
109 S A 0.0000
110 W A -0.3209
111 V A 0.0000
112 M A 0.0000
113 T A 0.1939
114 T A 0.0000
115 C A 0.0000
116 S A 0.0000
117 T A 0.2732
118 L A 0.4818
119 C A -0.3745
120 A A 0.0000
121 N A -1.7744
122 E A -2.8081
123 R A -2.7184
124 M A 0.0000
125 P A -2.3100
126 E A -3.3397
127 L A 0.0000
128 L A 0.0000
129 E A -3.0746
130 K A -2.3669
131 Y A -1.7279
132 S A 0.0000
133 R A -3.1715
134 G A -1.9851
135 I A -1.5444
136 Y A -2.0419
137 D A -2.7726
138 G A -2.6457
139 D A -3.6894
140 L A 0.0000
141 K A -3.6198
142 D A -3.4603
143 K A -2.6037
144 V A 0.0000
145 P A -1.2552
146 Y A -1.2333
147 K A -0.9913
148 G A -0.0057
149 I A 0.0000
150 L A 0.1583
151 I A 0.8342
152 S A 0.0000
153 L A 0.0000
154 E A -1.6342
155 L A -0.7949
156 V A 0.0000
157 T A -1.4588
158 K A -2.4607
159 P A 0.0000
160 C A -1.2956
161 T A -1.7417
162 E A -2.6959
163 G A 0.0000
164 I A -1.9256
165 E A -3.4757
166 L A -2.4461
167 K A -2.7822
168 S A -2.8977
169 K A -3.2892
170 R A -3.2876
171 P A -2.6882
172 Q A -2.3518
173 L A -1.4793
174 L A 0.0000
175 R A -3.2951
176 K A -3.3745
177 V A -2.5356
178 M A -2.9974
179 K A -4.6788
180 E A -4.5926
181 L A 0.0000
182 E A -4.6747
183 E A -5.0838
184 K A -4.4345
185 V A 0.0000
186 K A -4.8716
187 E A -4.7338
188 L A 0.0000
189 E A -3.8311
190 E A -3.9594
191 E A -3.2258
192 V A 0.0000
193 T A -2.4701
194 R A -2.9234
195 L A 0.0000
196 S A 0.0000
197 K A -3.2582
198 E A -3.2388
199 N A 0.0000
200 V A 0.0000
201 G A -2.1141
202 K A -1.4502
203 S A 0.4146
204 I A 0.9128
205 M A 1.7095
206 F A 2.3618
207 A A 1.5232
208 M A 0.0000
209 T A 0.3060
210 P A -0.4712
211 K A -1.2444
212 I A 0.0000
213 L A -0.2438
214 K A -1.5471
215 T A 0.0000
216 S A 0.0000
217 S A -0.9026
218 L A -0.2598
219 M A 0.0000
220 P A 0.0000
221 K A -1.2711
222 L A -0.6750
223 G A 0.0000
224 Y A 0.0000
225 E A -2.4836
226 K A -2.0780
227 G A 0.0000
228 L A -2.1000
229 E A -3.1350
230 I A -2.1358
231 S A 0.0000
232 E A -2.8430
233 K A -2.5098
234 A A -1.5024
235 C A -0.8849
236 L A 0.0000
237 N A -2.3404
238 G A -2.5480
239 R A -3.4303
240 C A 0.0000
241 R A -2.3456
242 R A -1.8900
243 T A 0.0000
244 V A 0.0000
245 S A 0.0000
246 M A 0.0000
247 E A 0.0000
248 T A 0.0000
249 G A 0.0000
250 C A 0.0000
251 R A 0.0000
252 N A 0.0000
253 V A 0.0000
254 Q A -0.0548
255 L A 0.0000
256 C A 0.0000
257 S A 0.0000
258 T A 0.0000
259 I A 0.0000
260 L A 0.0000
261 N A 0.7163
262 V A 1.7466
263 A A 0.5185
264 F A 0.0000
265 P A -0.2117
266 P A -0.7639
267 E A -1.3732
268 V A 0.5449
269 I A 0.0000
270 G A 0.0000
271 P A 0.0000
272 L A 0.0000
273 F A 0.0000
274 F A 0.0000
275 F A 0.0000
276 P A 0.0000
277 L A 0.5192
278 L A 0.2840
279 Y A 0.0000
280 M A -0.5668
281 Q A -1.7069
282 N A -1.7274
283 Q A 0.0000
284 K A -2.5024
285 E A -3.1467
286 E A -2.7040
287 G A 0.0000
288 D A -2.8902
289 K A -3.4606
290 I A -2.4913
291 V A -3.3550
292 K A -4.4009
293 E A -4.4810
294 Y A -3.9908
295 K A -5.3407
296 E A -5.7552
297 E A -5.5949
298 E A -5.0993
299 K A -5.4854
300 K A -5.2854
301 K A -4.7317
302 E A -4.0692
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
VR19A -0.7778 -0.047 View CSV PDB
VK19A -0.777 -0.0409 View CSV PDB
VK262A -0.1658 -0.0344 View CSV PDB
AR207A -0.3675 -0.0068 View CSV PDB
FK206A 0.0536 -0.0468 View CSV PDB
VR262A 0.1444 -0.0377 View CSV PDB
FE206A 0.3263 -0.0529 View CSV PDB
ME205A 0.2443 -0.0346 View CSV PDB
MK205A 0.4806 -0.0316 View CSV PDB
FR2A 1.6573 -0.0357 View CSV PDB
FK2A 1.604 -0.0334 View CSV PDB
AK207A 0.7626 -0.0033 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018