Project name: abf6e03230febef

Status: done

Started: 2024-07-08 13:05:28
Settings
Chain sequence(s) A: REVESVDLPHCHLIKGIEAGSEDIDILPNGLAFFSVGLKFPGLHSFAPDKPGGILMMDLKEEKPRARELRISRGFDLASFNPHGISTFIDNDDTVYLFVVNHPEFKNTVEIFKFEEAENSLLHLKTVKHELLPSVNDITAVGPAHFYATNDHYFSDPFLKYLETYLNLHWANVVYYSPNEVKVVAEGFDSANGINISPDDKYIYVADILAHEIHVLEKHTNMNLTQLKVLELDTLVDNLSIDPSSGDIWVGCHPNGQKLFVYDPNNPPSSEVLRIQNILSEKPTVTTVYANNGSVLQGSSVASVYDGKLLIGTLYHRALYCEL
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                                          (00:02:18)
[INFO]       Auto_mut: Residue number 193 from chain A and a score of 2.343 (leucine) selected for 
                       automated muatation                                                         (00:02:20)
[INFO]       Auto_mut: Residue number 192 from chain A and a score of 2.243 (tyrosine) selected    
                       for automated muatation                                                     (00:02:20)
[INFO]       Auto_mut: Residue number 196 from chain A and a score of 2.201 (tyrosine) selected    
                       for automated muatation                                                     (00:02:20)
[INFO]       Auto_mut: Residue number 189 from chain A and a score of 2.196 (phenylalanine)        
                       selected for automated muatation                                            (00:02:20)
[INFO]       Auto_mut: Residue number 197 from chain A and a score of 1.869 (leucine) selected for 
                       automated muatation                                                         (00:02:20)
[INFO]       Auto_mut: Residue number 291 from chain A and a score of 1.845 (phenylalanine)        
                       selected for automated muatation                                            (00:02:20)
[INFO]       Auto_mut: Mutating residue number 193 from chain A (leucine) into glutamic acid       (00:02:20)
[INFO]       Auto_mut: Mutating residue number 193 from chain A (leucine) into aspartic acid       (00:02:20)
[INFO]       Auto_mut: Mutating residue number 192 from chain A (tyrosine) into glutamic acid      (00:02:20)
[INFO]       Auto_mut: Mutating residue number 193 from chain A (leucine) into lysine              (00:03:25)
[INFO]       Auto_mut: Mutating residue number 193 from chain A (leucine) into arginine            (00:03:25)
[INFO]       Auto_mut: Mutating residue number 192 from chain A (tyrosine) into lysine             (00:03:30)
[INFO]       Auto_mut: Mutating residue number 192 from chain A (tyrosine) into aspartic acid      (00:04:34)
[INFO]       Auto_mut: Mutating residue number 196 from chain A (tyrosine) into glutamic acid      (00:04:38)
[INFO]       Auto_mut: Mutating residue number 196 from chain A (tyrosine) into aspartic acid      (00:04:51)
[INFO]       Auto_mut: Mutating residue number 192 from chain A (tyrosine) into arginine           (00:05:42)
[INFO]       Auto_mut: Mutating residue number 196 from chain A (tyrosine) into lysine             (00:05:43)
[INFO]       Auto_mut: Mutating residue number 196 from chain A (tyrosine) into arginine           (00:05:55)
[INFO]       Auto_mut: Mutating residue number 189 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 189 from chain A (phenylalanine) into glutamic acid (00:06:57)
[INFO]       Auto_mut: Mutating residue number 189 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 189 from chain A (phenylalanine) into aspartic acid (00:07:00)
[INFO]       Auto_mut: Mutating residue number 197 from chain A (leucine) into glutamic acid       (00:07:04)
[INFO]       Auto_mut: Mutating residue number 189 from chain A (phenylalanine) into lysine        (00:08:04)
[INFO]       Auto_mut: Mutating residue number 189 from chain A (phenylalanine) into arginine      (00:08:08)
[INFO]       Auto_mut: Mutating residue number 197 from chain A (leucine) into lysine              (00:08:09)
[INFO]       Auto_mut: Mutating residue number 197 from chain A (leucine) into aspartic acid       (00:09:17)
[INFO]       Auto_mut: Mutating residue number 291 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 291 from chain A (phenylalanine) into glutamic acid (00:09:21)
[INFO]       Auto_mut: Mutating residue number 291 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 291 from chain A (phenylalanine) into aspartic acid (00:09:24)
[INFO]       Auto_mut: Mutating residue number 197 from chain A (leucine) into arginine            (00:10:21)
[INFO]       Auto_mut: Mutating residue number 291 from chain A (phenylalanine) into lysine        (00:10:25)
[INFO]       Auto_mut: Mutating residue number 291 from chain A (phenylalanine) into arginine      (00:10:27)
[INFO]       Auto_mut: Effect of mutation residue number 193 from chain A (leucine) into glutamic  
                       acid: Energy difference: 1.7651 kcal/mol, Difference in average score from  
                       the base case: -0.0163                                                      (00:11:42)
[INFO]       Auto_mut: Effect of mutation residue number 193 from chain A (leucine) into lysine:   
                       Energy difference: 1.3025 kcal/mol, Difference in average score from the    
                       base case: -0.0199                                                          (00:11:42)
[INFO]       Auto_mut: Effect of mutation residue number 193 from chain A (leucine) into aspartic  
                       acid: Energy difference: 3.0495 kcal/mol, Difference in average score from  
                       the base case: -0.0134                                                      (00:11:42)
[INFO]       Auto_mut: Effect of mutation residue number 193 from chain A (leucine) into arginine: 
                       Energy difference: 1.3563 kcal/mol, Difference in average score from the    
                       base case: -0.0236                                                          (00:11:42)
[INFO]       Auto_mut: Effect of mutation residue number 192 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 0.6943 kcal/mol, Difference in average score from  
                       the base case: -0.0427                                                      (00:11:42)
[INFO]       Auto_mut: Effect of mutation residue number 192 from chain A (tyrosine) into lysine:  
                       Energy difference: 0.4095 kcal/mol, Difference in average score from the    
                       base case: -0.0433                                                          (00:11:42)
[INFO]       Auto_mut: Effect of mutation residue number 192 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 1.0255 kcal/mol, Difference in average score from  
                       the base case: -0.0439                                                      (00:11:42)
[INFO]       Auto_mut: Effect of mutation residue number 192 from chain A (tyrosine) into          
                       arginine: Energy difference: 0.7215 kcal/mol, Difference in average score   
                       from the base case: -0.0438                                                 (00:11:42)
[INFO]       Auto_mut: Effect of mutation residue number 196 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 0.3323 kcal/mol, Difference in average score from  
                       the base case: -0.0377                                                      (00:11:43)
[INFO]       Auto_mut: Effect of mutation residue number 196 from chain A (tyrosine) into lysine:  
                       Energy difference: -0.2974 kcal/mol, Difference in average score from the   
                       base case: -0.0380                                                          (00:11:43)
[INFO]       Auto_mut: Effect of mutation residue number 196 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 0.9141 kcal/mol, Difference in average score from  
                       the base case: -0.0353                                                      (00:11:43)
[INFO]       Auto_mut: Effect of mutation residue number 196 from chain A (tyrosine) into          
                       arginine: Energy difference: -0.1574 kcal/mol, Difference in average score  
                       from the base case: -0.0386                                                 (00:11:43)
[INFO]       Auto_mut: Effect of mutation residue number 189 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 0.6371 kcal/mol, Difference in average    
                       score from the base case: -0.0467                                           (00:11:43)
[INFO]       Auto_mut: Effect of mutation residue number 189 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.5857 kcal/mol, Difference in average score     
                       from the base case: -0.0441                                                 (00:11:43)
[INFO]       Auto_mut: Effect of mutation residue number 189 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 0.9877 kcal/mol, Difference in average    
                       score from the base case: -0.0458                                           (00:11:43)
[INFO]       Auto_mut: Effect of mutation residue number 189 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.9025 kcal/mol, Difference in average score   
                       from the base case: -0.0522                                                 (00:11:43)
[INFO]       Auto_mut: Effect of mutation residue number 197 from chain A (leucine) into glutamic  
                       acid: Energy difference: 1.1365 kcal/mol, Difference in average score from  
                       the base case: -0.0404                                                      (00:11:43)
[INFO]       Auto_mut: Effect of mutation residue number 197 from chain A (leucine) into lysine:   
                       Energy difference: 0.1814 kcal/mol, Difference in average score from the    
                       base case: -0.0405                                                          (00:11:43)
[INFO]       Auto_mut: Effect of mutation residue number 197 from chain A (leucine) into aspartic  
                       acid: Energy difference: 1.5236 kcal/mol, Difference in average score from  
                       the base case: -0.0392                                                      (00:11:43)
[INFO]       Auto_mut: Effect of mutation residue number 197 from chain A (leucine) into arginine: 
                       Energy difference: 0.3113 kcal/mol, Difference in average score from the    
                       base case: -0.0462                                                          (00:11:43)
[INFO]       Auto_mut: Effect of mutation residue number 291 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 0.7054 kcal/mol, Difference in average    
                       score from the base case: -0.0400                                           (00:11:43)
[INFO]       Auto_mut: Effect of mutation residue number 291 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.3107 kcal/mol, Difference in average score     
                       from the base case: -0.0451                                                 (00:11:43)
[INFO]       Auto_mut: Effect of mutation residue number 291 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 1.7749 kcal/mol, Difference in average    
                       score from the base case: -0.0436                                           (00:11:43)
[INFO]       Auto_mut: Effect of mutation residue number 291 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.4679 kcal/mol, Difference in average score   
                       from the base case: -0.0443                                                 (00:11:43)
[INFO]       Main:     Simulation completed successfully.                                          (00:11:48)
Show buried residues
Minimal score value
-4.1769
Maximal score value
2.3428
Average score
-0.6345
Total score value
-204.9427
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
32 R A -3.0889
33 E A -3.2999
34 V A -2.2916
35 E A -2.5743
36 S A -1.7759
37 V A -0.9927
38 D A -1.8169
39 L A -0.6291
40 P A -0.9200
41 H A -1.3222
42 C A -0.7932
43 H A -1.1348
44 L A -0.7781
45 I A 0.0000
46 K A -2.9662
47 G A -2.6996
48 I A 0.0000
49 E A -2.1878
50 A A -1.1410
51 G A 0.0000
52 S A 0.0000
53 E A 0.0000
54 D A 0.0000
55 I A 0.0000
56 D A -0.2090
57 I A -0.0835
58 L A 0.0000
59 P A -0.6432
60 N A -1.4368
61 G A 0.0000
62 L A -0.7428
63 A A 0.0000
64 F A 0.0000
65 F A 0.0000
66 S A 0.0000
67 V A -0.5905
68 G A -0.8285
69 L A 0.0000
70 K A -1.1190
71 F A -0.2321
72 P A 0.2054
73 G A 0.3161
74 L A 0.6422
75 H A 0.3329
76 S A -0.2761
77 F A 0.0218
78 A A -1.1885
79 P A -1.6258
80 D A -2.6413
81 K A -2.7608
82 P A -1.4433
83 G A -0.7972
84 G A -0.6933
85 I A 0.0000
86 L A 0.0000
87 M A 0.0000
88 M A 0.0000
89 D A -2.3565
90 L A 0.0000
91 K A -3.5733
92 E A -4.1769
93 E A -4.0107
94 K A -3.7811
95 P A -3.4784
96 R A -3.7024
97 A A -2.6326
98 R A -3.5775
99 E A -3.3078
100 L A 0.0000
101 R A -2.9342
102 I A -1.3085
103 S A -1.1852
104 R A -2.2436
105 G A -1.5538
106 F A -0.9392
107 D A -1.4807
108 L A 0.0155
109 A A -0.4411
110 S A -0.7422
111 F A 0.0000
112 N A 0.0000
113 P A 0.0000
114 H A 0.0000
115 G A 0.0000
116 I A 0.0000
117 S A 0.0000
118 T A 0.2811
119 F A 0.3589
120 I A -0.1743
121 D A -1.5630
122 N A -2.6257
123 D A -3.2188
124 D A -2.8392
125 T A -1.7400
126 V A 0.0000
127 Y A -0.0302
128 L A 0.0000
129 F A 0.0000
130 V A 0.0000
131 V A 0.0000
132 N A 0.0000
133 H A 0.0000
134 P A -1.3225
135 E A -1.9469
136 F A -0.9354
137 K A -2.1839
138 N A -1.6673
139 T A 0.0000
140 V A 0.0000
141 E A 0.0000
142 I A 0.0000
143 F A 0.0000
144 K A -0.7096
145 F A 0.0000
146 E A -2.6937
147 E A -2.8030
148 A A -1.9602
149 E A -2.9543
150 N A -2.8676
151 S A -2.3370
152 L A 0.0000
153 L A -0.2081
154 H A -0.1696
155 L A 0.3232
156 K A -0.7139
157 T A -0.7010
158 V A 0.0000
159 K A -2.5315
160 H A -1.9465
161 E A -2.2030
162 L A -0.6530
163 L A 0.0000
164 P A -0.8627
165 S A 0.0000
166 V A 0.0000
167 N A 0.0000
168 D A 0.0000
169 I A 0.0000
170 T A 0.0000
171 A A 0.0000
172 V A 0.1739
173 G A 0.0000
174 P A -0.1350
175 A A -0.1317
176 H A -0.4223
177 F A 0.0000
178 Y A 0.0000
179 A A 0.0000
180 T A 0.0000
181 N A 0.0000
182 D A 0.0000
183 H A 0.5531
184 Y A 1.2582
185 F A 1.0515
186 S A -0.1826
187 D A -0.1603
188 P A 0.7934
189 F A 2.1957
190 L A 1.8310
191 K A 1.5865
192 Y A 2.2432
193 L A 2.3428
194 E A 0.0000
195 T A 1.2241
196 Y A 2.2010
197 L A 1.8695
198 N A 0.1490
199 L A 0.4689
200 H A -0.6002
201 W A 0.1361
202 A A 0.0000
203 N A -0.6791
204 V A 0.0000
205 V A 0.0000
206 Y A 0.0000
207 Y A 0.0000
208 S A 0.0000
209 P A -1.2400
210 N A -2.0680
211 E A -2.1364
212 V A -1.0211
213 K A -0.4448
214 V A 0.1247
215 V A 0.0000
216 A A -1.1583
217 E A -1.9288
218 G A -1.3461
219 F A 0.0000
220 D A -0.8267
221 S A 0.0000
222 A A 0.0000
223 N A 0.0000
224 G A 0.0000
225 I A 0.0000
226 N A -0.2731
227 I A -0.8872
228 S A -1.5674
229 P A -1.8820
230 D A -2.9959
231 D A -3.0560
232 K A -2.7380
233 Y A -1.3994
234 I A 0.0000
235 Y A 0.0000
236 V A 0.0000
237 A A 0.0000
238 D A 0.0000
239 I A 0.1698
240 L A 0.0453
241 A A -0.5772
242 H A -1.0935
243 E A -1.0857
244 I A 0.0000
245 H A 0.0000
246 V A 0.0000
247 L A 0.0000
248 E A -1.5232
249 K A -1.7836
250 H A -1.5601
251 T A -1.2060
252 N A -1.6355
253 M A -1.1249
254 N A -1.2035
255 L A 0.0000
256 T A -1.0512
257 Q A -1.3842
258 L A -0.6018
259 K A -1.6183
260 V A -0.5147
261 L A -0.8620
262 E A -2.2311
263 L A -1.5184
264 D A -2.4224
265 T A 0.0000
266 L A 0.0000
267 V A 0.0000
268 D A 0.0000
269 N A 0.0000
270 L A 0.0000
271 S A -0.1075
272 I A -0.1307
273 D A -0.3383
274 P A -0.7659
275 S A -0.5140
276 S A -0.7203
277 G A -0.9481
278 D A 0.0000
279 I A 0.0000
280 W A 0.0000
281 V A 0.0000
282 G A 0.0000
283 C A 0.0000
284 H A 0.0000
285 P A 0.0000
286 N A -1.3944
287 G A 0.0000
288 Q A -0.6072
289 K A -0.2146
290 L A 0.0000
291 F A 1.8452
292 V A 1.7745
293 Y A 0.3098
294 D A -1.2150
295 P A -1.4307
296 N A -2.2831
297 N A -2.3257
298 P A -1.3483
299 P A 0.0000
300 S A 0.0000
301 S A 0.0000
302 E A -0.4789
303 V A 0.0000
304 L A 0.0000
305 R A -0.4246
306 I A 0.0000
307 Q A -1.0690
308 N A -1.6216
309 I A 0.0000
310 L A -0.1120
311 S A -1.6134
312 E A -2.8200
313 K A -2.6062
314 P A -1.4423
315 T A -0.8690
316 V A 0.1243
317 T A 0.1047
318 T A 0.1027
319 V A 0.1050
320 Y A 0.0000
321 A A 0.0000
322 N A 0.0000
323 N A -2.0293
324 G A 0.0000
325 S A -0.5171
326 V A 0.2792
327 L A 0.0000
328 Q A 0.0000
329 G A 0.0000
330 S A 0.0000
331 S A 0.0000
332 V A 0.0000
333 A A 0.0000
334 S A 0.0000
335 V A -0.0750
336 Y A -1.0490
337 D A -1.9401
338 G A -0.8557
339 K A -0.5869
340 L A 0.0000
341 L A 0.0000
342 I A 0.0000
343 G A 0.0000
344 T A 0.0000
345 L A 0.0000
346 Y A 0.0000
347 H A -0.6101
348 R A -1.2861
349 A A 0.0000
350 L A 0.0000
351 Y A -0.5023
352 C A 0.0000
353 E A -0.4802
354 L A 0.8189
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
YK196A -0.2974 -0.038 View CSV PDB
YR196A -0.1574 -0.0386 View CSV PDB
LK197A 0.1814 -0.0405 View CSV PDB
LR197A 0.3113 -0.0462 View CSV PDB
FK291A 0.3107 -0.0451 View CSV PDB
YK192A 0.4095 -0.0433 View CSV PDB
FR291A 0.4679 -0.0443 View CSV PDB
FK189A 0.5857 -0.0441 View CSV PDB
FE189A 0.6371 -0.0467 View CSV PDB
YE192A 0.6943 -0.0427 View CSV PDB
LR193A 1.3563 -0.0236 View CSV PDB
LK193A 1.3025 -0.0199 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018