Project name: 1QTR

Status: done

Started: 2024-12-07 17:40:55
Settings
Chain sequence(s) A: LRGLYPPLAAYDSGWLDTGDGHRIYWELSGNPNGKPAVFIHGGPGGGISPHHRQLFDPERYKVLLFDQRGCGRSRPHASLDNNTTWHLVADIERLREMAGVEQWLVFGGSWGSTLALAYAQTHPERVSEMVLRGIFTLRKQRLHWYYQDGASRFFPEKWERVLSILSDDERKDVIAAYRQRLTSADPQVQLEAAKLWSVWEGETVTLLPSRESASFGEDDFALAFARIENHYFTHLGFLESDDQLLRNVPLIRHIPAVIVHGRYDMACQVQNAWDLAKAWPEAELHIVEGAGHSYDEPGILHQLMIATDRFAGK
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]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:03:04)
[INFO]       Auto_mut: Residue number 211 from chain A and a score of 1.665 (leucine) selected for 
                       automated muatation                                                         (00:03:06)
[INFO]       Auto_mut: Residue number 210 from chain A and a score of 1.436 (leucine) selected for 
                       automated muatation                                                         (00:03:06)
[INFO]       Auto_mut: Residue number 157 from chain A and a score of 0.837 (phenylalanine)        
                       selected for automated muatation                                            (00:03:06)
[INFO]       Auto_mut: Residue number 269 from chain A and a score of 0.703 (methionine) selected  
                       for automated muatation                                                     (00:03:06)
[INFO]       Auto_mut: Residue number 209 from chain A and a score of 0.602 (threonine) selected   
                       for automated muatation                                                     (00:03:06)
[INFO]       Auto_mut: Residue number 267 from chain A and a score of 0.469 (tyrosine) selected    
                       for automated muatation                                                     (00:03:06)
[INFO]       Auto_mut: Mutating residue number 211 from chain A (leucine) into glutamic acid       (00:03:06)
[INFO]       Auto_mut: Mutating residue number 211 from chain A (leucine) into aspartic acid       (00:03:06)
[INFO]       Auto_mut: Mutating residue number 210 from chain A (leucine) into glutamic acid       (00:03:06)
[INFO]       Auto_mut: Mutating residue number 211 from chain A (leucine) into arginine            (00:04:39)
[INFO]       Auto_mut: Mutating residue number 210 from chain A (leucine) into lysine              (00:04:40)
[INFO]       Auto_mut: Mutating residue number 211 from chain A (leucine) into lysine              (00:04:41)
[INFO]       Auto_mut: Mutating residue number 210 from chain A (leucine) into aspartic acid       (00:06:21)
[INFO]       Auto_mut: Mutating residue number 157 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 157 from chain A (phenylalanine) into glutamic acid (00:06:23)
[INFO]       Auto_mut: Mutating residue number 157 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 157 from chain A (phenylalanine) into aspartic acid (00:06:23)
[INFO]       Auto_mut: Mutating residue number 210 from chain A (leucine) into arginine            (00:07:52)
[INFO]       Auto_mut: Mutating residue number 157 from chain A (phenylalanine) into arginine      (00:07:57)
[INFO]       Auto_mut: Mutating residue number 157 from chain A (phenylalanine) into lysine        (00:07:58)
[INFO]       Auto_mut: Mutating residue number 269 from chain A (methionine) into glutamic acid    (00:09:27)
[INFO]       Auto_mut: Mutating residue number 269 from chain A (methionine) into aspartic acid    (00:09:31)
[INFO]       Auto_mut: Mutating residue number 209 from chain A (threonine) into glutamic acid     (00:09:34)
[INFO]       Auto_mut: Mutating residue number 269 from chain A (methionine) into lysine           (00:11:02)
[INFO]       Auto_mut: Mutating residue number 269 from chain A (methionine) into arginine         (00:11:03)
[INFO]       Auto_mut: Mutating residue number 209 from chain A (threonine) into lysine            (00:11:11)
[INFO]       Auto_mut: Mutating residue number 209 from chain A (threonine) into aspartic acid     (00:12:37)
[INFO]       Auto_mut: Mutating residue number 267 from chain A (tyrosine) into glutamic acid      (00:12:45)
[INFO]       Auto_mut: Mutating residue number 267 from chain A (tyrosine) into aspartic acid      (00:13:24)
[INFO]       Auto_mut: Mutating residue number 209 from chain A (threonine) into arginine          (00:14:10)
[INFO]       Auto_mut: Mutating residue number 267 from chain A (tyrosine) into lysine             (00:14:29)
[INFO]       Auto_mut: Mutating residue number 267 from chain A (tyrosine) into arginine           (00:15:07)
[INFO]       Auto_mut: Effect of mutation residue number 211 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.5396 kcal/mol, Difference in average score from  
                       the base case: -0.0445                                                      (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 211 from chain A (leucine) into lysine:   
                       Energy difference: 0.0077 kcal/mol, Difference in average score from the    
                       base case: -0.0469                                                          (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 211 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.9012 kcal/mol, Difference in average score from  
                       the base case: -0.0423                                                      (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 211 from chain A (leucine) into arginine: 
                       Energy difference: 0.0109 kcal/mol, Difference in average score from the    
                       base case: -0.0412                                                          (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 210 from chain A (leucine) into glutamic  
                       acid: Energy difference: 1.4115 kcal/mol, Difference in average score from  
                       the base case: -0.0424                                                      (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 210 from chain A (leucine) into lysine:   
                       Energy difference: -0.2354 kcal/mol, Difference in average score from the   
                       base case: -0.0393                                                          (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 210 from chain A (leucine) into aspartic  
                       acid: Energy difference: 1.2778 kcal/mol, Difference in average score from  
                       the base case: -0.0438                                                      (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 210 from chain A (leucine) into arginine: 
                       Energy difference: -0.0728 kcal/mol, Difference in average score from the   
                       base case: -0.0413                                                          (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 157 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 0.6358 kcal/mol, Difference in average    
                       score from the base case: -0.0507                                           (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 157 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.3507 kcal/mol, Difference in average score     
                       from the base case: -0.0498                                                 (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 157 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 1.1254 kcal/mol, Difference in average    
                       score from the base case: -0.0501                                           (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 157 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.5512 kcal/mol, Difference in average score   
                       from the base case: -0.0565                                                 (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 269 from chain A (methionine) into        
                       glutamic acid: Energy difference: 2.6837 kcal/mol, Difference in average    
                       score from the base case: -0.0169                                           (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 269 from chain A (methionine) into        
                       lysine: Energy difference: 1.1013 kcal/mol, Difference in average score     
                       from the base case: -0.0199                                                 (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 269 from chain A (methionine) into        
                       aspartic acid: Energy difference: 3.0198 kcal/mol, Difference in average    
                       score from the base case: -0.0159                                           (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 269 from chain A (methionine) into        
                       arginine: Energy difference: 1.5642 kcal/mol, Difference in average score   
                       from the base case: -0.0244                                                 (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 209 from chain A (threonine) into         
                       glutamic acid: Energy difference: 1.8345 kcal/mol, Difference in average    
                       score from the base case: -0.0205                                           (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 209 from chain A (threonine) into lysine: 
                       Energy difference: -0.0474 kcal/mol, Difference in average score from the   
                       base case: -0.0174                                                          (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 209 from chain A (threonine) into         
                       aspartic acid: Energy difference: 3.3473 kcal/mol, Difference in average    
                       score from the base case: -0.0154                                           (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 209 from chain A (threonine) into         
                       arginine: Energy difference: -1.5366 kcal/mol, Difference in average score  
                       from the base case: -0.0104                                                 (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 267 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 0.5528 kcal/mol, Difference in average score from  
                       the base case: -0.0476                                                      (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 267 from chain A (tyrosine) into lysine:  
                       Energy difference: 0.1471 kcal/mol, Difference in average score from the    
                       base case: -0.0615                                                          (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 267 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 0.6601 kcal/mol, Difference in average score from  
                       the base case: -0.0548                                                      (00:17:04)
[INFO]       Auto_mut: Effect of mutation residue number 267 from chain A (tyrosine) into          
                       arginine: Energy difference: 0.6012 kcal/mol, Difference in average score   
                       from the base case: -0.0672                                                 (00:17:04)
[INFO]       Main:     Simulation completed successfully.                                          (00:17:11)
Show buried residues
Minimal score value
-3.9096
Maximal score value
1.6648
Average score
-0.8347
Total score value
-262.0912
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
4 L A 0.0191
5 R A -1.4709
6 G A -0.8841
7 L A -0.3888
8 Y A -0.1274
9 P A -0.2806
10 P A -0.3312
11 L A 0.1280
12 A A 0.1166
13 A A -0.1254
14 Y A -0.0076
15 D A -0.9634
16 S A -0.4361
17 G A -0.6298
18 W A -0.9751
19 L A -1.4868
20 D A -3.2865
21 T A -2.4474
22 G A -2.2924
23 D A -3.1941
24 G A -2.8194
25 H A 0.0000
26 R A -3.5379
27 I A 0.0000
28 Y A 0.0000
29 W A -0.3790
30 E A 0.0000
31 L A 0.0000
32 S A 0.0000
33 G A -1.5342
34 N A -2.0485
35 P A -1.6533
36 N A -2.1796
37 G A -2.2840
38 K A -1.8291
39 P A -1.4124
40 A A 0.0000
41 V A 0.0000
42 F A 0.0000
43 I A 0.0000
44 H A 0.0000
45 G A -0.1207
46 G A -0.1592
47 P A 0.0000
48 G A 0.0000
49 G A -0.0666
50 G A -0.4104
51 I A -0.3832
52 S A -0.4811
53 P A -0.6443
54 H A -1.0545
55 H A -0.5871
56 R A -0.5848
57 Q A 0.0000
58 L A 0.0000
59 F A 0.0000
60 D A -1.6382
61 P A -1.7931
62 E A -3.2072
63 R A -3.4651
64 Y A 0.0000
65 K A -1.5592
66 V A 0.0000
67 L A 0.0000
68 L A 0.0000
69 F A 0.0000
70 D A 0.0000
71 Q A 0.0000
72 R A 0.0000
73 G A 0.0000
74 C A 0.0000
75 G A -1.7841
76 R A -2.5934
77 S A 0.0000
78 R A -3.3453
79 P A -2.1822
80 H A -1.7039
81 A A -0.9657
82 S A -1.1974
83 L A -1.0144
84 D A -2.3864
85 N A -2.0701
86 N A 0.0000
87 T A -0.4348
88 T A 0.0000
89 W A 0.1829
90 H A -0.5593
91 L A 0.0000
92 V A 0.0000
93 A A -0.5024
94 D A 0.0000
95 I A 0.0000
96 E A -1.6610
97 R A -2.4063
98 L A 0.0000
99 R A 0.0000
100 E A -2.8418
101 M A -1.0567
102 A A -1.1094
103 G A -1.7418
104 V A 0.0000
105 E A -3.2315
106 Q A -2.9306
107 W A 0.0000
108 L A 0.0000
109 V A 0.0000
110 F A 0.0000
111 G A 0.0000
112 G A 0.0000
113 S A 0.0000
114 W A 0.0000
115 G A 0.0000
116 S A 0.0000
117 T A 0.0000
118 L A 0.0000
119 A A 0.0000
120 L A 0.0000
121 A A 0.0000
122 Y A 0.0000
123 A A 0.0000
124 Q A 0.0000
125 T A -0.3122
126 H A -0.9844
127 P A -1.3517
128 E A -2.6477
129 R A -2.3835
130 V A 0.0000
131 S A -1.1129
132 E A 0.0000
133 M A 0.0000
134 V A 0.0000
135 L A 0.0000
136 R A -0.1254
137 G A 0.0000
138 I A 0.0000
139 F A 0.0000
140 T A 0.0000
141 L A 0.0000
142 R A -1.6930
143 K A -2.1655
144 Q A -2.2909
145 R A 0.0000
146 L A 0.0000
147 H A -2.0169
148 W A -1.5261
149 Y A 0.0000
150 Y A 0.0000
151 Q A -2.0835
152 D A -2.8403
153 G A 0.0000
154 A A 0.0000
155 S A -1.3722
156 R A -1.4910
157 F A 0.8365
158 F A -0.4768
159 P A -1.8229
160 E A -2.9522
161 K A -2.3393
162 W A 0.0000
163 E A -3.3741
164 R A -3.0853
165 V A 0.0000
166 L A -1.5581
167 S A -1.3328
168 I A -0.7895
169 L A 0.0000
170 S A -2.1341
171 D A -3.6254
172 D A -3.8840
173 E A -3.1829
174 R A -3.4449
175 K A -3.9096
176 D A -3.1563
177 V A 0.0000
178 I A -0.8384
179 A A -1.0672
180 A A 0.0000
181 Y A 0.0000
182 R A -1.0024
183 Q A -1.4039
184 R A -1.4110
185 L A 0.0000
186 T A -0.7902
187 S A -0.9792
188 A A -0.8331
189 D A -1.4807
190 P A -1.4152
191 Q A -1.7581
192 V A -1.0578
193 Q A -1.3576
194 L A -1.7310
195 E A -2.0481
196 A A 0.0000
197 A A 0.0000
198 K A -1.5062
199 L A -0.6938
200 W A 0.0000
201 S A 0.0000
202 V A -0.1551
203 W A 0.0000
204 E A -0.1392
205 G A 0.0000
206 E A -0.7883
207 T A 0.0000
208 V A 0.4195
209 T A 0.6018
210 L A 1.4358
211 L A 1.6648
212 P A -0.2009
213 S A -1.4073
214 R A -2.9771
215 E A -2.8918
216 S A 0.0000
217 A A -1.4371
218 S A -1.3220
219 F A -0.8903
220 G A -1.3817
221 E A -2.5637
222 D A -2.7863
223 D A -2.5646
224 F A -1.3217
225 A A 0.0000
226 L A -1.2362
227 A A 0.0000
228 F A 0.0000
229 A A 0.0000
230 R A -0.1742
231 I A 0.0000
232 E A 0.0000
233 N A 0.0000
234 H A 0.0000
235 Y A 0.0000
236 F A 0.0000
237 T A -0.1384
238 H A -0.4501
239 L A -0.4899
240 G A 0.0000
241 F A -0.1829
242 L A 0.0000
243 E A -2.1259
244 S A -1.8748
245 D A -2.2659
246 D A -2.4129
247 Q A -1.9905
248 L A 0.0000
249 L A -1.5452
250 R A -2.2730
251 N A -1.2621
252 V A 0.0000
253 P A -0.7140
254 L A -0.0114
255 I A 0.0000
256 R A -1.8127
257 H A -1.7226
258 I A 0.0000
259 P A -1.1660
260 A A 0.0000
261 V A 0.0000
262 I A 0.0000
263 V A 0.0000
264 H A 0.0000
265 G A 0.0000
266 R A -0.8771
267 Y A 0.4690
268 D A 0.0000
269 M A 0.7025
270 A A 0.0000
271 C A 0.0000
272 Q A -0.4664
273 V A -0.2856
274 Q A -1.1265
275 N A 0.0000
276 A A 0.0000
277 W A -0.2012
278 D A -0.8257
279 L A 0.0000
280 A A -1.3914
281 K A -1.8049
282 A A -1.5127
283 W A 0.0000
284 P A -2.0711
285 E A -2.9503
286 A A -2.3293
287 E A -2.1837
288 L A -0.8877
289 H A -0.5173
290 I A -0.1568
291 V A -0.7845
292 E A -1.9227
293 G A -1.1087
294 A A 0.0000
295 G A 0.0000
296 H A 0.0000
297 S A -0.3290
298 Y A -0.6517
299 D A -1.4967
300 E A -0.6826
301 P A -1.2300
302 G A -1.2190
303 I A 0.0000
304 L A 0.0000
305 H A -0.9034
306 Q A -0.2473
307 L A 0.0000
308 M A 0.0000
309 I A 0.3134
310 A A 0.0000
311 T A 0.0000
312 D A -1.4255
313 R A -2.1935
314 F A 0.0000
315 A A -1.9411
316 G A -2.3274
317 K A -2.5370
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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
LK210A -0.2354 -0.0393 View CSV PDB
LR210A -0.0728 -0.0413 View CSV PDB
TR209A -1.5366 -0.0104 View CSV PDB
TK209A -0.0474 -0.0174 View CSV PDB
LK211A 0.0077 -0.0469 View CSV PDB
LR211A 0.0109 -0.0412 View CSV PDB
YK267A 0.1471 -0.0615 View CSV PDB
FK157A 0.3507 -0.0498 View CSV PDB
YR267A 0.6012 -0.0672 View CSV PDB
FR157A 0.5512 -0.0565 View CSV PDB
MK269A 1.1013 -0.0199 View CSV PDB
MR269A 1.5642 -0.0244 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018