Project name: 1345e2ffa9998fa

Status: done

Started: 2024-06-18 12:26:11
Settings
Chain sequence(s) A: TSVWTKGVTPPANFTQGEDVFHAPYVANQGWYDITKTFNGKDDLLSGAATAGNMLHWWFDQNKDQIKRYLEEHPEKQKINFNGEQMFDVKEAIDTKNHQLDSKLFEYFKEKAFPYLKHLGVFPDHVIDMFINGYRLSLTNHGPTPVKEGSKDPRGGIFDAVFTRGDQSKLLTSRHDFKEKNLKEISDLIKKELTEGKALGLSHTYRINHVINLWGADFDSNGNLKAIYVTDSDSNASIGMKKYFVGVNSAGKVAISAKEIKEDNIGAQVLGLFTLSTGQDSWNQTN
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                                          (00:02:55)
[INFO]       Auto_mut: Residue number 255 from chain A and a score of 1.590 (tyrosine) selected    
                       for automated muatation                                                     (00:02:57)
[INFO]       Auto_mut: Residue number 260 from chain A and a score of 1.424 (isoleucine) selected  
                       for automated muatation                                                     (00:02:57)
[INFO]       Auto_mut: Residue number 300 from chain A and a score of 1.020 (valine) selected for  
                       automated muatation                                                         (00:02:57)
[INFO]       Auto_mut: Residue number 254 from chain A and a score of 0.892 (threonine) selected   
                       for automated muatation                                                     (00:02:57)
[INFO]       Auto_mut: Residue number 74 from chain A and a score of 0.659 (valine) selected for   
                       automated muatation                                                         (00:02:57)
[INFO]       Auto_mut: Residue number 320 from chain A and a score of 0.572 (alanine) selected for 
                       automated muatation                                                         (00:02:57)
[INFO]       Auto_mut: Mutating residue number 255 from chain A (tyrosine) into glutamic acid      (00:02:57)
[INFO]       Auto_mut: Mutating residue number 255 from chain A (tyrosine) into aspartic acid      (00:02:57)
[INFO]       Auto_mut: Mutating residue number 260 from chain A (isoleucine) into glutamic acid    (00:02:57)
[INFO]       Auto_mut: Mutating residue number 260 from chain A (isoleucine) into lysine           (00:04:18)
[INFO]       Auto_mut: Mutating residue number 255 from chain A (tyrosine) into lysine             (00:04:18)
[INFO]       Auto_mut: Mutating residue number 255 from chain A (tyrosine) into arginine           (00:04:18)
[INFO]       Auto_mut: Mutating residue number 260 from chain A (isoleucine) into aspartic acid    (00:05:44)
[INFO]       Auto_mut: Mutating residue number 300 from chain A (valine) into glutamic acid        (00:05:44)
[INFO]       Auto_mut: Mutating residue number 300 from chain A (valine) into aspartic acid        (00:05:48)
[INFO]       Auto_mut: Mutating residue number 260 from chain A (isoleucine) into arginine         (00:07:03)
[INFO]       Auto_mut: Mutating residue number 300 from chain A (valine) into lysine               (00:07:04)
[INFO]       Auto_mut: Mutating residue number 300 from chain A (valine) into arginine             (00:07:08)
[INFO]       Auto_mut: Mutating residue number 254 from chain A (threonine) into glutamic acid     (00:08:29)
[INFO]       Auto_mut: Mutating residue number 254 from chain A (threonine) into aspartic acid     (00:08:32)
[INFO]       Auto_mut: Mutating residue number 74 from chain A (valine) into glutamic acid         (00:08:33)
[INFO]       Auto_mut: Mutating residue number 254 from chain A (threonine) into lysine            (00:09:49)
[INFO]       Auto_mut: Mutating residue number 74 from chain A (valine) into lysine                (00:09:53)
[INFO]       Auto_mut: Mutating residue number 254 from chain A (threonine) into arginine          (00:10:05)
[INFO]       Auto_mut: Mutating residue number 74 from chain A (valine) into aspartic acid         (00:11:20)
[INFO]       Auto_mut: Mutating residue number 320 from chain A (alanine) into glutamic acid       (00:11:29)
[INFO]       Auto_mut: Mutating residue number 320 from chain A (alanine) into aspartic acid       (00:11:40)
[INFO]       Auto_mut: Mutating residue number 74 from chain A (valine) into arginine              (00:12:39)
[INFO]       Auto_mut: Mutating residue number 320 from chain A (alanine) into lysine              (00:12:48)
[INFO]       Auto_mut: Mutating residue number 320 from chain A (alanine) into arginine            (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 255 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 2.2887 kcal/mol, Difference in average score from  
                       the base case: -0.0345                                                      (00:14:19)
[INFO]       Auto_mut: Effect of mutation residue number 255 from chain A (tyrosine) into lysine:  
                       Energy difference: 1.5970 kcal/mol, Difference in average score from the    
                       base case: -0.0330                                                          (00:14:19)
[INFO]       Auto_mut: Effect of mutation residue number 255 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 2.7597 kcal/mol, Difference in average score from  
                       the base case: -0.0348                                                      (00:14:19)
[INFO]       Auto_mut: Effect of mutation residue number 255 from chain A (tyrosine) into          
                       arginine: Energy difference: 1.6897 kcal/mol, Difference in average score   
                       from the base case: -0.0278                                                 (00:14:19)
[INFO]       Auto_mut: Effect of mutation residue number 260 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -2.6892 kcal/mol, Difference in average   
                       score from the base case: -0.0342                                           (00:14:19)
[INFO]       Auto_mut: Effect of mutation residue number 260 from chain A (isoleucine) into        
                       lysine: Energy difference: -2.9423 kcal/mol, Difference in average score    
                       from the base case: -0.0330                                                 (00:14:19)
[INFO]       Auto_mut: Effect of mutation residue number 260 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: -2.5298 kcal/mol, Difference in average   
                       score from the base case: -0.0339                                           (00:14:19)
[INFO]       Auto_mut: Effect of mutation residue number 260 from chain A (isoleucine) into        
                       arginine: Energy difference: -2.6820 kcal/mol, Difference in average score  
                       from the base case: -0.0347                                                 (00:14:19)
[INFO]       Auto_mut: Effect of mutation residue number 300 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.0179 kcal/mol, Difference in average score from 
                       the base case: -0.0406                                                      (00:14:19)
[INFO]       Auto_mut: Effect of mutation residue number 300 from chain A (valine) into lysine:    
                       Energy difference: -0.6131 kcal/mol, Difference in average score from the   
                       base case: -0.0283                                                          (00:14:19)
[INFO]       Auto_mut: Effect of mutation residue number 300 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.8978 kcal/mol, Difference in average score from  
                       the base case: -0.0390                                                      (00:14:19)
[INFO]       Auto_mut: Effect of mutation residue number 300 from chain A (valine) into arginine:  
                       Energy difference: -0.3798 kcal/mol, Difference in average score from the   
                       base case: -0.0313                                                          (00:14:19)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (threonine) into         
                       glutamic acid: Energy difference: -0.9705 kcal/mol, Difference in average   
                       score from the base case: -0.0034                                           (00:14:19)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (threonine) into lysine: 
                       Energy difference: -1.5003 kcal/mol, Difference in average score from the   
                       base case: 0.0113                                                           (00:14:19)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (threonine) into         
                       aspartic acid: Energy difference: 1.1603 kcal/mol, Difference in average    
                       score from the base case: -0.0008                                           (00:14:20)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (threonine) into         
                       arginine: Energy difference: -1.1496 kcal/mol, Difference in average score  
                       from the base case: 0.0064                                                  (00:14:20)
[INFO]       Auto_mut: Effect of mutation residue number 74 from chain A (valine) into glutamic    
                       acid: Energy difference: 0.2977 kcal/mol, Difference in average score from  
                       the base case: -0.0265                                                      (00:14:20)
[INFO]       Auto_mut: Effect of mutation residue number 74 from chain A (valine) into lysine:     
                       Energy difference: 0.0386 kcal/mol, Difference in average score from the    
                       base case: -0.0125                                                          (00:14:20)
[INFO]       Auto_mut: Effect of mutation residue number 74 from chain A (valine) into aspartic    
                       acid: Energy difference: 0.3779 kcal/mol, Difference in average score from  
                       the base case: -0.0304                                                      (00:14:20)
[INFO]       Auto_mut: Effect of mutation residue number 74 from chain A (valine) into arginine:   
                       Energy difference: -0.2648 kcal/mol, Difference in average score from the   
                       base case: -0.0286                                                          (00:14:20)
[INFO]       Auto_mut: Effect of mutation residue number 320 from chain A (alanine) into glutamic  
                       acid: Energy difference: -0.4076 kcal/mol, Difference in average score from 
                       the base case: -0.0040                                                      (00:14:20)
[INFO]       Auto_mut: Effect of mutation residue number 320 from chain A (alanine) into lysine:   
                       Energy difference: -0.6359 kcal/mol, Difference in average score from the   
                       base case: -0.0010                                                          (00:14:20)
[INFO]       Auto_mut: Effect of mutation residue number 320 from chain A (alanine) into aspartic  
                       acid: Energy difference: -0.2094 kcal/mol, Difference in average score from 
                       the base case: -0.0016                                                      (00:14:20)
[INFO]       Auto_mut: Effect of mutation residue number 320 from chain A (alanine) into arginine: 
                       Energy difference: -0.4673 kcal/mol, Difference in average score from the   
                       base case: -0.0159                                                          (00:14:20)
[INFO]       Main:     Simulation completed successfully.                                          (00:14:26)
Show buried residues
Minimal score value
-4.2339
Maximal score value
1.5901
Average score
-0.888
Total score value
-253.9769
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
49 T A -0.6608
50 S A -0.4834
51 V A -0.3462
52 W A -0.2394
53 T A 0.0000
54 K A -1.4220
55 G A -1.0609
56 V A 0.0000
57 T A -0.6454
58 P A -0.3054
59 P A -0.1125
60 A A -0.2453
61 N A -0.3920
62 F A -0.2161
63 T A -0.6555
64 Q A -1.6844
65 G A -1.8936
66 E A -2.9151
67 D A -3.0807
68 V A 0.0000
69 F A -0.8072
70 H A -0.3765
71 A A 0.0000
72 P A 0.2123
73 Y A 0.3675
74 V A 0.6589
75 A A -0.4301
76 N A -1.3236
77 Q A -0.9136
78 G A -0.9371
79 W A 0.0000
80 Y A 0.0000
81 D A 0.0000
82 I A 0.0000
83 T A 0.0000
84 K A 0.0000
85 T A -0.1189
86 F A 0.4977
87 N A -0.6641
88 G A -0.6864
89 K A -0.9723
90 D A 0.0000
91 D A -0.7332
92 L A -0.2678
93 L A 0.0000
94 S A 0.0000
95 G A 0.0000
96 A A 0.0000
97 A A 0.0000
98 T A 0.0000
99 A A 0.0000
100 G A 0.0000
101 N A 0.0000
102 M A 0.0000
103 L A 0.0000
104 H A 0.0000
105 W A 0.0000
106 W A 0.0000
107 F A 0.0000
108 D A -1.3803
109 Q A -1.5425
110 N A 0.0000
111 K A -3.1860
112 D A -3.6603
113 Q A -3.4706
114 I A 0.0000
115 K A -3.8694
116 R A -4.2339
117 Y A 0.0000
118 L A 0.0000
119 E A -3.6137
120 E A -2.8670
121 H A -2.3405
122 P A -2.4826
123 E A -2.8790
124 K A -2.2142
125 Q A -2.1167
126 K A -2.3202
127 I A 0.0000
128 N A -3.0694
129 F A -1.8881
130 N A -2.2689
131 G A -2.4201
132 E A -3.2098
133 Q A -2.9213
134 M A -1.8377
135 F A 0.0000
136 D A -1.7710
137 V A 0.0000
138 K A -2.0177
139 E A -2.2851
140 A A 0.0000
141 I A -1.6516
142 D A -2.5589
143 T A -2.1408
144 K A -1.8444
145 N A -1.4384
146 H A -1.7314
147 Q A -0.8102
148 L A -0.5217
149 D A -2.0934
150 S A 0.0000
151 K A -2.2522
152 L A 0.0000
153 F A 0.0000
154 E A -2.0366
155 Y A 0.0000
156 F A 0.0000
157 K A 0.0000
158 E A -1.1965
159 K A -1.3118
160 A A 0.0000
161 F A 0.0000
162 P A -0.6750
163 Y A -0.4014
164 L A -0.0286
167 K A -1.5907
168 H A -1.5760
169 L A -0.0771
170 G A -0.0600
171 V A 0.0000
172 F A 0.1457
173 P A 0.0000
174 D A 0.0000
175 H A 0.0000
176 V A 0.0000
177 I A 0.0000
178 D A 0.0000
179 M A 0.0000
180 F A 0.0000
181 I A 0.0000
182 N A 0.0000
183 G A 0.0000
184 Y A 0.0000
185 R A -2.4370
186 L A 0.0000
187 S A -0.4347
188 L A 0.4764
189 T A -0.1546
190 N A -0.8414
191 H A -1.1653
192 G A -0.9183
193 P A -0.6316
194 T A -0.7631
195 P A -1.0092
196 V A -1.2488
197 K A -2.9083
198 E A -3.2889
199 G A -2.6106
200 S A -2.1797
201 K A -2.7031
202 D A 0.0000
203 P A -1.1970
204 R A -1.0790
205 G A -0.9053
206 G A 0.0000
207 I A 0.0000
208 F A 0.0000
209 D A -0.5549
210 A A -0.3671
211 V A -0.6025
212 F A 0.0000
213 T A -1.2546
214 R A -2.3730
215 G A -2.4454
216 D A -2.0241
217 Q A -1.7871
218 S A -1.1239
219 K A -0.8667
220 L A -0.4699
221 L A 0.0000
222 T A 0.0000
223 S A -0.2906
224 R A -0.8686
225 H A -1.3832
226 D A -2.7570
227 F A 0.0000
228 K A -3.7348
229 E A -3.8756
230 K A -4.0341
231 N A -3.2942
232 L A -1.9334
233 K A -3.1933
234 E A -2.8883
235 I A 0.0000
236 S A 0.0000
237 D A -2.5083
238 L A -1.5451
239 I A 0.0000
240 K A -2.1881
241 K A -2.6185
242 E A 0.0000
243 L A 0.0000
244 T A -1.8204
245 E A -2.6328
246 G A -1.6507
247 K A -1.2220
248 A A 0.0000
249 L A 0.0000
250 G A 0.0000
251 L A 0.0000
252 S A 0.0000
253 H A 0.0000
254 T A 0.8921
255 Y A 1.5901
259 R A -0.7528
260 I A 1.4242
261 N A 0.4637
262 H A 0.0000
263 V A 0.0000
264 I A 0.0000
265 N A 0.0000
266 L A 0.0000
267 W A 0.0000
268 G A 0.0000
269 A A 0.0000
270 D A -0.8943
271 F A 0.0000
272 D A -1.4406
273 S A -1.2667
274 N A -1.9452
275 G A -1.9990
276 N A -2.1193
277 L A 0.0000
278 K A -1.4606
279 A A 0.0000
280 I A 0.0000
281 Y A 0.0000
282 V A 0.0000
283 T A 0.0000
284 D A 0.0000
285 S A 0.0000
286 D A -0.6332
287 S A -0.8202
288 N A -1.2583
289 A A -0.5795
290 S A -0.5000
291 I A -0.1196
292 G A 0.0000
293 M A 0.0000
294 K A 0.0000
295 K A -0.4612
296 Y A -0.5432
297 F A -0.7862
298 V A 0.0000
299 G A 0.1581
300 V A 1.0198
301 N A 0.0000
302 S A -0.7720
303 A A -0.2464
304 G A -0.5208
305 K A -1.3897
306 V A 0.0000
307 A A 0.0000
308 I A 0.0000
309 S A -0.6061
310 A A -1.3808
311 K A -2.6265
312 E A -3.0086
313 I A -1.5643
314 K A -2.8260
315 E A -3.1895
316 D A -2.9751
317 N A -1.9527
318 I A -0.2278
319 G A -0.2501
320 A A 0.5715
321 Q A -0.1319
322 V A 0.0000
323 L A -1.4584
324 G A 0.0000
325 L A 0.0000
326 F A 0.0000
327 T A 0.0000
328 L A 0.0000
329 S A -0.6332
330 T A 0.0000
331 G A -1.2743
332 Q A -2.2762
333 D A -2.7990
334 S A -2.1567
335 W A 0.0000
336 N A -3.0051
337 Q A -2.3260
338 T A -1.6598
339 N A -2.3817
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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
IK260A -2.9423 -0.033 View CSV PDB
IR260A -2.682 -0.0347 View CSV PDB
VK300A -0.6131 -0.0283 View CSV PDB
VR300A -0.3798 -0.0313 View CSV PDB
VR74A -0.2648 -0.0286 View CSV PDB
AR320A -0.4673 -0.0159 View CSV PDB
TE254A -0.9705 -0.0034 View CSV PDB
AE320A -0.4076 -0.004 View CSV PDB
VK74A 0.0386 -0.0125 View CSV PDB
YK255A 1.597 -0.033 View CSV PDB
YR255A 1.6897 -0.0278 View CSV PDB
TD254A 1.1603 -0.0008 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018