Project name: 1357911

Status: done

Started: 2024-07-09 06:13:30
Settings
Chain sequence(s) A: AMFMVKNGNGTACIMANFSAAFSVNYDTKSGPKNMTFDLPSDATVVLNRSSCGKENTSDPSLVIAFGRGHTLTLNFTRNATRYSVQLMSFVYNLSDTHLFPNASSKEIKTVESITDIRADIDKKYRCVSGTQVHMNNVTVTLHDATIQAYLSNSSFSRGETRCEQDRPSPTTAPPAPPSPSPSPVPKSPSVDKYNVSGTNGTCLLASMGLQLNLTYERKDNTTVTRLLNINPNKTSASGSCGAHLVTLELHSEGTTVLLFQFGMNASSSRFFLQGIQLNTILPDARDPAFKAANGSLRALQATVGNSYKCNAEEHVRVTKAF
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                                          (00:03:09)
[INFO]       Auto_mut: Residue number 322 from chain A and a score of 1.406 (phenylalanine)        
                       selected for automated muatation                                            (00:03:11)
[INFO]       Auto_mut: Residue number 185 from chain A and a score of 0.909 (valine) selected for  
                       automated muatation                                                         (00:03:11)
[INFO]       Auto_mut: Residue number 191 from chain A and a score of 0.757 (valine) selected for  
                       automated muatation                                                         (00:03:11)
[INFO]       Auto_mut: Residue number 304 from chain A and a score of 0.715 (valine) selected for  
                       automated muatation                                                         (00:03:11)
[INFO]       Auto_mut: Residue number 205 from chain A and a score of 0.667 (leucine) selected for 
                       automated muatation                                                         (00:03:11)
[INFO]       Auto_mut: Residue number 281 from chain A and a score of 0.577 (isoleucine) selected  
                       for automated muatation                                                     (00:03:11)
[INFO]       Auto_mut: Mutating residue number 322 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 322 from chain A (phenylalanine) into glutamic acid (00:03:11)
[INFO]       Auto_mut: Mutating residue number 322 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 322 from chain A (phenylalanine) into aspartic acid (00:03:11)
[INFO]       Auto_mut: Mutating residue number 185 from chain A (valine) into glutamic acid        (00:03:11)
[INFO]       Auto_mut: Mutating residue number 185 from chain A (valine) into lysine               (00:04:39)
[INFO]       Auto_mut: Mutating residue number 322 from chain A (phenylalanine) into arginine      (00:04:51)
[INFO]       Auto_mut: Mutating residue number 322 from chain A (phenylalanine) into lysine        (00:04:54)
[INFO]       Auto_mut: Mutating residue number 185 from chain A (valine) into aspartic acid        (00:06:36)
[INFO]       Auto_mut: Mutating residue number 191 from chain A (valine) into glutamic acid        (00:06:41)
[INFO]       Auto_mut: Mutating residue number 191 from chain A (valine) into aspartic acid        (00:06:45)
[INFO]       Auto_mut: Mutating residue number 185 from chain A (valine) into arginine             (00:08:07)
[INFO]       Auto_mut: Mutating residue number 191 from chain A (valine) into lysine               (00:08:13)
[INFO]       Auto_mut: Mutating residue number 191 from chain A (valine) into arginine             (00:08:16)
[INFO]       Auto_mut: Mutating residue number 304 from chain A (valine) into glutamic acid        (00:09:44)
[INFO]       Auto_mut: Mutating residue number 304 from chain A (valine) into aspartic acid        (00:09:45)
[INFO]       Auto_mut: Mutating residue number 205 from chain A (leucine) into glutamic acid       (00:09:53)
[INFO]       Auto_mut: Mutating residue number 304 from chain A (valine) into arginine             (00:11:19)
[INFO]       Auto_mut: Mutating residue number 304 from chain A (valine) into lysine               (00:11:21)
[INFO]       Auto_mut: Mutating residue number 205 from chain A (leucine) into lysine              (00:11:37)
[INFO]       Auto_mut: Mutating residue number 205 from chain A (leucine) into aspartic acid       (00:12:56)
[INFO]       Auto_mut: Mutating residue number 281 from chain A (isoleucine) into glutamic acid    (00:13:05)
[INFO]       Auto_mut: Mutating residue number 281 from chain A (isoleucine) into aspartic acid    (00:13:16)
[INFO]       Auto_mut: Mutating residue number 205 from chain A (leucine) into arginine            (00:14:34)
[INFO]       Auto_mut: Mutating residue number 281 from chain A (isoleucine) into lysine           (00:14:38)
[INFO]       Auto_mut: Mutating residue number 281 from chain A (isoleucine) into arginine         (00:14:47)
[INFO]       Auto_mut: Effect of mutation residue number 322 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 0.1360 kcal/mol, Difference in average    
                       score from the base case: -0.0306                                           (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 322 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.1021 kcal/mol, Difference in average score     
                       from the base case: -0.0262                                                 (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 322 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 0.1293 kcal/mol, Difference in average    
                       score from the base case: -0.0304                                           (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 322 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.1911 kcal/mol, Difference in average score   
                       from the base case: -0.0307                                                 (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 185 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.7664 kcal/mol, Difference in average score from 
                       the base case: -0.0390                                                      (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 185 from chain A (valine) into lysine:    
                       Energy difference: -0.3276 kcal/mol, Difference in average score from the   
                       base case: -0.0248                                                          (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 185 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.0626 kcal/mol, Difference in average score from 
                       the base case: -0.0386                                                      (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 185 from chain A (valine) into arginine:  
                       Energy difference: -0.2812 kcal/mol, Difference in average score from the   
                       base case: -0.0392                                                          (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 191 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.3365 kcal/mol, Difference in average score from 
                       the base case: -0.0550                                                      (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 191 from chain A (valine) into lysine:    
                       Energy difference: -0.2566 kcal/mol, Difference in average score from the   
                       base case: -0.0507                                                          (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 191 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.0101 kcal/mol, Difference in average score from  
                       the base case: -0.0546                                                      (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 191 from chain A (valine) into arginine:  
                       Energy difference: -0.6864 kcal/mol, Difference in average score from the   
                       base case: -0.0535                                                          (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 304 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.0064 kcal/mol, Difference in average score from  
                       the base case: -0.0557                                                      (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 304 from chain A (valine) into lysine:    
                       Energy difference: -0.2826 kcal/mol, Difference in average score from the   
                       base case: -0.0550                                                          (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 304 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.3154 kcal/mol, Difference in average score from  
                       the base case: -0.0564                                                      (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 304 from chain A (valine) into arginine:  
                       Energy difference: -0.1078 kcal/mol, Difference in average score from the   
                       base case: -0.0567                                                          (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 205 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.7243 kcal/mol, Difference in average score from  
                       the base case: -0.0385                                                      (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 205 from chain A (leucine) into lysine:   
                       Energy difference: 0.3627 kcal/mol, Difference in average score from the    
                       base case: -0.0377                                                          (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 205 from chain A (leucine) into aspartic  
                       acid: Energy difference: 1.0578 kcal/mol, Difference in average score from  
                       the base case: -0.0329                                                      (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 205 from chain A (leucine) into arginine: 
                       Energy difference: 0.4961 kcal/mol, Difference in average score from the    
                       base case: -0.0383                                                          (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 281 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 1.0064 kcal/mol, Difference in average    
                       score from the base case: -0.0387                                           (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 281 from chain A (isoleucine) into        
                       lysine: Energy difference: 0.3207 kcal/mol, Difference in average score     
                       from the base case: -0.0373                                                 (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 281 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 2.1575 kcal/mol, Difference in average    
                       score from the base case: -0.0382                                           (00:16:31)
[INFO]       Auto_mut: Effect of mutation residue number 281 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.7000 kcal/mol, Difference in average score   
                       from the base case: -0.0384                                                 (00:16:31)
[INFO]       Main:     Simulation completed successfully.                                          (00:16:40)
Show buried residues
Minimal score value
-4.9819
Maximal score value
1.4064
Average score
-0.9938
Total score value
-320.0059
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 A A -0.2436
2 M A 0.3377
3 F A 0.0000
4 M A 0.2624
5 V A 0.0000
6 K A -1.7636
7 N A -2.1009
8 G A -1.7370
9 N A -2.0437
10 G A -1.6417
11 T A -1.5233
12 A A 0.0000
13 C A -0.5498
14 I A 0.0000
15 M A 0.0000
16 A A 0.0000
17 N A -0.6767
18 F A 0.0000
19 S A -1.1271
20 A A 0.0000
21 A A -0.9747
22 F A 0.0000
23 S A -0.8759
24 V A 0.0000
25 N A -2.6956
26 Y A 0.0000
27 D A -3.2705
28 T A 0.0000
29 K A -2.7100
30 S A -1.8436
31 G A -1.7592
32 P A -2.6852
33 K A -3.5144
34 N A -2.7545
35 M A -0.9898
36 T A -0.6248
37 F A -0.6024
38 D A -1.7336
39 L A -1.1434
40 P A -1.2933
41 S A -1.2808
42 D A -1.9811
43 A A -0.9080
44 T A -0.1465
45 V A 0.4228
46 V A 0.0660
47 L A 0.3456
48 N A -1.3458
49 R A -1.9146
50 S A 0.0000
51 S A -1.3565
52 C A -1.2891
53 G A 0.0000
54 K A -3.3414
55 E A -3.5367
56 N A -2.8719
57 T A -2.1199
58 S A -2.1606
59 D A -2.5009
60 P A 0.0000
61 S A -0.8293
62 L A 0.0000
63 V A 0.0000
64 I A 0.0000
65 A A -0.5089
66 F A 0.0000
67 G A -1.8348
68 R A -2.3609
69 G A -1.0284
70 H A 0.0000
71 T A -0.2166
72 L A 0.0000
73 T A -0.4351
74 L A 0.0000
75 N A -0.6523
76 F A 0.0000
77 T A -1.6922
78 R A -2.4133
79 N A -2.1047
80 A A -1.1129
81 T A -1.4927
82 R A -2.8112
83 Y A 0.0000
84 S A -2.0893
85 V A 0.0000
86 Q A -1.1028
87 L A -0.2693
88 M A 0.0000
89 S A 0.0000
90 F A 0.0000
91 V A 0.1684
92 Y A 0.0000
93 N A -0.7514
94 L A -1.4112
95 S A -1.4246
96 D A 0.0000
97 T A -1.2121
98 H A -1.3539
99 L A -0.6369
100 F A 0.0000
101 P A -1.1370
102 N A -2.4650
103 A A -2.3823
104 S A -2.1110
105 S A -1.9546
106 K A -2.4225
107 E A -1.9147
108 I A 0.3022
109 K A -0.5211
110 T A -0.6299
111 V A 0.0000
112 E A -1.8089
113 S A -0.7213
114 I A 0.2929
115 T A -1.1360
116 D A -2.4020
117 I A 0.0000
118 R A -3.3680
119 A A 0.0000
120 D A -2.7603
121 I A -2.1622
122 D A -2.7936
123 K A -2.9549
124 K A -2.2589
125 Y A 0.0000
126 R A -1.9302
127 C A 0.0000
128 V A 0.2267
129 S A -0.7026
130 G A 0.0000
131 T A 0.0000
132 Q A -1.7577
133 V A 0.0000
134 H A -1.9205
135 M A 0.0000
136 N A -2.3381
137 N A -1.6790
138 V A 0.0000
139 T A -1.1402
140 V A 0.0000
141 T A -1.0422
142 L A 0.0000
143 H A -1.2254
144 D A -1.3105
145 A A 0.0000
146 T A -0.8530
147 I A 0.0000
148 Q A 0.0000
149 A A 0.0000
150 Y A -0.2450
151 L A 0.0000
152 S A -1.0493
153 N A -1.5743
154 S A -1.0203
155 S A -0.7458
156 F A -0.9776
157 S A -1.8911
158 R A -2.4386
159 G A -2.2800
160 E A -2.4969
161 T A -2.5030
162 R A -3.2247
163 C A 0.0000
164 E A -3.2695
165 Q A -2.3577
166 D A -2.2572
167 R A -3.3337
168 P A -1.7281
169 S A -1.2957
170 P A -0.7321
171 T A -0.3540
172 T A -0.2696
173 A A -0.2100
174 P A -0.3889
175 P A -0.4391
176 A A -0.3439
177 P A -0.5234
178 P A -0.5906
179 S A -0.6049
180 P A -0.6343
181 S A -0.6358
182 P A -0.2774
183 S A -0.1440
184 P A -0.0035
185 V A 0.9094
186 P A -0.3259
187 K A -1.5340
188 S A -1.0827
189 P A -0.7982
190 S A -0.3885
191 V A 0.7570
192 D A -1.0514
193 K A -1.7163
194 Y A 0.0000
195 N A -1.1730
196 V A 0.0000
197 S A -0.7894
198 G A -0.8680
199 T A -0.8838
200 N A -1.4916
201 G A -1.0104
202 T A -0.4858
203 C A -0.0458
204 L A 0.0000
205 L A 0.6673
206 A A -0.2327
207 S A -0.6758
208 M A 0.0090
209 G A -0.3085
210 L A -0.5893
211 Q A -1.1247
212 L A -0.5298
213 N A -1.4291
214 L A 0.0000
215 T A -0.9708
216 Y A 0.0000
217 E A -4.0910
218 R A -4.5217
219 K A -4.9819
220 D A -4.1512
221 N A -3.7558
222 T A -2.4769
223 T A -1.8168
224 V A -0.7427
225 T A -0.6211
226 R A -0.5932
227 L A -0.3134
228 L A -0.3425
229 N A -1.1337
230 I A 0.0000
231 N A -2.3758
232 P A -2.1796
233 N A -2.7254
234 K A -3.2531
235 T A -2.3047
236 S A -1.3804
237 A A -0.9291
238 S A -0.9041
239 G A -0.8474
240 S A -0.3983
241 C A -0.3317
242 G A -0.2840
243 A A -0.2576
244 H A -0.6834
245 L A 0.0160
246 V A 0.0000
247 T A -0.2021
248 L A 0.0000
249 E A -0.7618
250 L A 0.0000
251 H A -1.4143
252 S A -2.2457
253 E A -3.0434
254 G A -1.3995
255 T A -0.4852
256 T A -0.5835
257 V A -0.4822
258 L A 0.0000
259 L A -0.2488
260 F A 0.0000
261 Q A -0.3545
262 F A 0.0000
263 G A 0.0000
264 M A -0.2971
265 N A -0.7373
266 A A -0.4187
267 S A -0.5402
268 S A -0.6072
269 S A -0.2530
270 R A -0.8446
271 F A -0.3429
272 F A -0.3161
273 L A 0.0000
274 Q A -0.7435
275 G A 0.0000
276 I A -0.3791
277 Q A -0.7739
278 L A 0.0000
279 N A -0.6402
280 T A 0.0000
281 I A 0.5766
282 L A 0.0000
283 P A -1.0605
284 D A -2.3070
285 A A 0.0000
286 R A -4.9817
287 D A -3.3947
288 P A -1.8709
289 A A -0.7566
290 F A 0.0000
291 K A -1.1513
292 A A 0.0000
293 A A -0.8197
294 N A -0.8789
295 G A -0.8547
296 S A -0.4398
297 L A -0.7282
298 R A -1.4086
299 A A -0.6710
300 L A -0.4561
301 Q A -1.0230
302 A A -0.6165
303 T A -0.2468
304 V A 0.7152
305 G A -0.3910
306 N A -1.3185
307 S A -0.7040
308 Y A -0.7370
309 K A -1.7813
310 C A -1.2980
311 N A -1.9311
312 A A -1.8584
313 E A -2.7459
314 E A -2.5016
315 H A -2.2564
316 V A -1.1139
317 R A -1.8201
318 V A -1.0310
319 T A -0.9390
320 K A -1.2209
321 A A -0.1361
322 F A 1.4064
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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
VR191A -0.6864 -0.0535 View CSV PDB
VE185A -0.7664 -0.039 View CSV PDB
VE191A -0.3365 -0.055 View CSV PDB
VK304A -0.2826 -0.055 View CSV PDB
VR304A -0.1078 -0.0567 View CSV PDB
VR185A -0.2812 -0.0392 View CSV PDB
FK322A 0.1021 -0.0262 View CSV PDB
FD322A 0.1293 -0.0304 View CSV PDB
IK281A 0.3207 -0.0373 View CSV PDB
LK205A 0.3627 -0.0377 View CSV PDB
LR205A 0.4961 -0.0383 View CSV PDB
IR281A 0.7 -0.0384 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018