Project name: 1AZW

Status: done

Started: 2024-12-07 17:41:34
Settings
Chain sequence(s) A: MRTLYPEITPYQQGSLKVDDRHTLYFEQCGNPHGKPVVMLHGGPGGGCNDKMRRFHDPAKYRIVLFDQRGSGRSTPHADLVDNTTWDLVADIERLRTHLGVDRWQVFGGSWGSTLALAYAQTHPQQVTELVLRGIFLLRRFELEWFYQEGASRLFPDAWEHYLNAIPPVERADLMSAFHRRLTSDDEATRLAAAKAWSVWEGATSFLHVDEDFVTGHEDAHFALAFARIENHYFVNGGFFEVEDQLLRDAHRIADIPGVIVHGRYDVVCPLQSAWDLHKAWPKAQLQISPASGHSAFEPENVDALVRATDGFA
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                                          (00:03:04)
[INFO]       Auto_mut: Residue number 169 from chain A and a score of 1.114 (valine) selected for  
                       automated muatation                                                         (00:03:06)
[INFO]       Auto_mut: Residue number 206 from chain A and a score of 0.746 (phenylalanine)        
                       selected for automated muatation                                            (00:03:06)
[INFO]       Auto_mut: Residue number 207 from chain A and a score of 0.630 (leucine) selected for 
                       automated muatation                                                         (00:03:06)
[INFO]       Auto_mut: Residue number 265 from chain A and a score of 0.587 (tyrosine) selected    
                       for automated muatation                                                     (00:03:06)
[INFO]       Auto_mut: Residue number 81 from chain A and a score of 0.496 (valine) selected for   
                       automated muatation                                                         (00:03:06)
[INFO]       Auto_mut: Residue number 11 from chain A and a score of 0.422 (tyrosine) selected for 
                       automated muatation                                                         (00:03:06)
[INFO]       Auto_mut: Mutating residue number 169 from chain A (valine) into glutamic acid        (00:03:06)
[INFO]       Auto_mut: Mutating residue number 169 from chain A (valine) into aspartic acid        (00:03:06)
[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 (00:03:06)
[INFO]       Auto_mut: Mutating residue number 169 from chain A (valine) into arginine             (00:04:28)
[INFO]       Auto_mut: Mutating residue number 169 from chain A (valine) into lysine               (00:04:29)
[INFO]       Auto_mut: Mutating residue number 206 from chain A (phenylalanine) into lysine        (00:04:37)
[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 (00:05:57)
[INFO]       Auto_mut: Mutating residue number 207 from chain A (leucine) into glutamic acid       (00:05:57)
[INFO]       Auto_mut: Mutating residue number 207 from chain A (leucine) into aspartic acid       (00:06:37)
[INFO]       Auto_mut: Mutating residue number 207 from chain A (leucine) into lysine              (00:07:19)
[INFO]       Auto_mut: Mutating residue number 206 from chain A (phenylalanine) into arginine      (00:07:22)
[INFO]       Auto_mut: Mutating residue number 207 from chain A (leucine) into arginine            (00:08:01)
[INFO]       Auto_mut: Mutating residue number 265 from chain A (tyrosine) into glutamic acid      (00:08:51)
[INFO]       Auto_mut: Mutating residue number 265 from chain A (tyrosine) into aspartic acid      (00:08:52)
[INFO]       Auto_mut: Mutating residue number 81 from chain A (valine) into glutamic acid         (00:09:32)
[INFO]       Auto_mut: Mutating residue number 265 from chain A (tyrosine) into arginine           (00:10:16)
[INFO]       Auto_mut: Mutating residue number 265 from chain A (tyrosine) into lysine             (00:10:19)
[INFO]       Auto_mut: Mutating residue number 81 from chain A (valine) into lysine                (00:11:02)
[INFO]       Auto_mut: Mutating residue number 81 from chain A (valine) into aspartic acid         (00:11:53)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (tyrosine) into glutamic acid       (00:11:58)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (tyrosine) into aspartic acid       (00:12:35)
[INFO]       Auto_mut: Mutating residue number 81 from chain A (valine) into arginine              (00:13:20)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (tyrosine) into lysine              (00:13:26)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (tyrosine) into arginine            (00:14:02)
[INFO]       Auto_mut: Effect of mutation residue number 169 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.3939 kcal/mol, Difference in average score from 
                       the base case: -0.0330                                                      (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 169 from chain A (valine) into lysine:    
                       Energy difference: -0.9775 kcal/mol, Difference in average score from the   
                       base case: -0.0310                                                          (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 169 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.0448 kcal/mol, Difference in average score from  
                       the base case: -0.0351                                                      (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 169 from chain A (valine) into arginine:  
                       Energy difference: -0.5819 kcal/mol, Difference in average score from the   
                       base case: -0.0371                                                          (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 206 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 4.4854 kcal/mol, Difference in average    
                       score from the base case: -0.0025                                           (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 206 from chain A (phenylalanine) into     
                       lysine: Energy difference: 1.1673 kcal/mol, Difference in average score     
                       from the base case: -0.0041                                                 (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 206 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 5.2804 kcal/mol, Difference in average    
                       score from the base case: -0.0075                                           (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 206 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.8755 kcal/mol, Difference in average score   
                       from the base case: -0.0042                                                 (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 207 from chain A (leucine) into glutamic  
                       acid: Energy difference: 1.6433 kcal/mol, Difference in average score from  
                       the base case: -0.0149                                                      (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 207 from chain A (leucine) into lysine:   
                       Energy difference: 0.2685 kcal/mol, Difference in average score from the    
                       base case: -0.0191                                                          (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 207 from chain A (leucine) into aspartic  
                       acid: Energy difference: 1.8167 kcal/mol, Difference in average score from  
                       the base case: -0.0166                                                      (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 207 from chain A (leucine) into arginine: 
                       Energy difference: 0.1144 kcal/mol, Difference in average score from the    
                       base case: -0.0194                                                          (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 265 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 1.0106 kcal/mol, Difference in average score from  
                       the base case: -0.0204                                                      (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 265 from chain A (tyrosine) into lysine:  
                       Energy difference: 0.5108 kcal/mol, Difference in average score from the    
                       base case: -0.0218                                                          (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 265 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 1.0357 kcal/mol, Difference in average score from  
                       the base case: -0.0197                                                      (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 265 from chain A (tyrosine) into          
                       arginine: Energy difference: 0.5474 kcal/mol, Difference in average score   
                       from the base case: -0.0150                                                 (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 81 from chain A (valine) into glutamic    
                       acid: Energy difference: 0.1221 kcal/mol, Difference in average score from  
                       the base case: -0.0283                                                      (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 81 from chain A (valine) into lysine:     
                       Energy difference: -0.1145 kcal/mol, Difference in average score from the   
                       base case: -0.0281                                                          (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 81 from chain A (valine) into aspartic    
                       acid: Energy difference: 0.2951 kcal/mol, Difference in average score from  
                       the base case: -0.0322                                                      (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 81 from chain A (valine) into arginine:   
                       Energy difference: 0.0677 kcal/mol, Difference in average score from the    
                       base case: -0.0314                                                          (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 1.1457 kcal/mol, Difference in average score from  
                       the base case: -0.0326                                                      (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (tyrosine) into lysine:   
                       Energy difference: 0.8609 kcal/mol, Difference in average score from the    
                       base case: -0.0306                                                          (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 1.4959 kcal/mol, Difference in average score from  
                       the base case: -0.0345                                                      (00:15:31)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (tyrosine) into arginine: 
                       Energy difference: 0.8986 kcal/mol, Difference in average score from the    
                       base case: -0.0313                                                          (00:15:31)
[INFO]       Main:     Simulation completed successfully.                                          (00:15:37)
Show buried residues
Minimal score value
-3.3954
Maximal score value
1.1137
Average score
-0.7022
Total score value
-219.7769
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 M A -0.0344
2 R A -1.3385
3 T A -0.7272
4 L A -0.6206
5 Y A -0.6306
6 P A -1.1093
7 E A -2.2322
8 I A -0.9426
9 T A -0.6054
10 P A -0.1641
11 Y A 0.4220
12 Q A -0.5366
13 Q A -1.2031
14 G A -0.7316
15 S A -0.9074
16 L A -1.0664
17 K A -2.5512
18 V A 0.0000
19 D A -2.6423
20 D A -3.0296
21 R A -2.6376
22 H A 0.0000
23 T A -1.6404
24 L A 0.0000
25 Y A -0.8037
26 F A -0.4077
27 E A 0.0000
28 Q A 0.0000
29 C A 0.0000
30 G A -0.7638
31 N A -1.3222
32 P A -1.0982
33 H A -1.6188
34 G A -1.6177
35 K A -1.3150
36 P A -1.2264
37 V A 0.0000
38 V A 0.0000
39 M A 0.0000
40 L A 0.0000
41 H A 0.0000
42 G A -0.1592
43 G A -0.1761
44 P A 0.0000
45 G A 0.0000
46 G A -0.2653
47 G A -0.6787
48 C A -1.2080
49 N A -2.1094
50 D A -2.9687
51 K A -2.2661
52 M A -1.3662
53 R A -1.4802
54 R A -1.1705
55 F A 0.0000
56 H A 0.0000
57 D A -0.9611
58 P A -0.8667
59 A A -1.1522
60 K A -2.0549
61 Y A 0.0000
62 R A -1.2448
63 I A 0.0000
64 V A 0.0000
65 L A 0.0000
66 F A 0.0000
67 D A 0.0000
68 Q A 0.0000
69 R A 0.0000
70 G A 0.0000
71 S A 0.0000
72 G A -1.3615
73 R A -1.9797
74 S A 0.0000
75 T A -1.1163
76 P A -0.6243
77 H A -0.8271
78 A A -0.1185
79 D A -0.1833
80 L A 0.2916
81 V A 0.4959
82 D A -1.3060
83 N A 0.0000
84 T A -0.2445
85 T A 0.0000
86 W A 0.1141
87 D A -0.6720
88 L A 0.0000
89 V A 0.0000
90 A A -0.4029
91 D A 0.0000
92 I A 0.0000
93 E A -1.0795
94 R A -1.6849
95 L A 0.0000
96 R A -1.6147
97 T A -1.6321
98 H A -1.4434
99 L A -0.9725
100 G A -1.4352
101 V A 0.0000
102 D A -2.7195
103 R A -2.5747
104 W A 0.0000
105 Q A 0.0000
106 V A 0.0000
107 F A 0.0000
108 G A 0.0000
109 G A 0.0000
110 S A -0.1189
111 W A 0.0000
112 G A 0.0000
113 S A 0.0000
114 T A 0.0000
115 L A 0.0000
116 A A 0.0000
117 L A 0.0000
118 A A 0.0000
119 Y A 0.0000
120 A A 0.0000
121 Q A 0.0000
122 T A -0.6291
123 H A -1.1245
124 P A -1.6141
125 Q A -2.0784
126 Q A -1.9492
127 V A 0.0000
128 T A -0.9725
129 E A 0.0000
130 L A 0.0000
131 V A 0.0000
132 L A 0.0000
133 R A -0.2212
134 G A 0.0000
135 I A 0.0000
136 F A 0.0000
137 L A 0.0000
138 L A 0.0000
139 R A -1.1771
140 R A -1.0739
141 F A 0.0128
142 E A 0.0000
143 L A 0.0000
144 E A -1.6094
145 W A -0.7947
146 F A 0.0000
147 Y A 0.0000
148 Q A -1.7071
149 E A -2.3725
150 G A 0.0000
151 A A 0.0000
152 S A 0.0000
153 R A -2.1495
154 L A -0.5652
155 F A -0.9878
156 P A -1.9666
157 D A -2.6419
158 A A -1.5833
159 W A 0.0000
160 E A -2.9754
161 H A -2.2868
162 Y A 0.0000
163 L A -1.4027
164 N A -1.9968
165 A A -1.0982
166 I A 0.0000
167 P A -0.1880
168 P A 0.0700
169 V A 1.1137
170 E A -0.2624
171 R A -0.8907
172 A A -0.7553
173 D A -1.6692
174 L A 0.0000
175 M A 0.0000
176 S A -1.0159
177 A A 0.0000
178 F A 0.0000
179 H A -1.1802
180 R A -2.1340
181 R A -1.9782
182 L A 0.0000
183 T A -1.7633
184 S A -2.4886
185 D A -3.3298
186 D A -3.3954
187 E A -3.0682
188 A A -1.5491
189 T A -1.6806
190 R A -1.9205
191 L A -0.8764
192 A A -0.4045
193 A A 0.0000
194 A A 0.0000
195 K A -1.0368
196 A A 0.0000
197 W A 0.0000
198 S A 0.0000
199 V A 0.0000
200 W A 0.0000
201 E A -0.0463
202 G A 0.0000
203 A A -0.2748
204 T A 0.0000
205 S A 0.0000
206 F A 0.7456
207 L A 0.6301
208 H A -0.3298
209 V A 0.2333
210 D A -1.4568
211 E A -2.6202
212 D A -2.4909
213 F A -1.0368
214 V A -1.1287
215 T A -1.7478
216 G A -1.5814
217 H A 0.0000
218 E A -1.7787
219 D A -2.1753
220 A A -1.2712
221 H A -1.3633
222 F A -0.8122
223 A A 0.0000
224 L A -0.6316
225 A A 0.0000
226 F A 0.0000
227 A A 0.0000
228 R A -0.3067
229 I A 0.0000
230 E A 0.0000
231 N A 0.0000
232 H A -0.2311
233 Y A 0.0000
234 F A 0.0000
235 V A -0.0865
236 N A -0.4749
237 G A -0.8102
238 G A 0.0000
239 F A -0.1192
240 F A -0.9533
241 E A -1.8225
242 V A -1.4517
243 E A -2.4605
244 D A -2.5176
245 Q A -1.8063
246 L A 0.0000
247 L A -1.4282
248 R A -2.0865
249 D A -1.8093
250 A A 0.0000
251 H A -2.3973
252 R A -3.0197
253 I A 0.0000
254 A A -2.2405
255 D A -2.6562
256 I A 0.0000
257 P A -1.1088
258 G A 0.0000
259 V A 0.0000
260 I A 0.0000
261 V A 0.0000
262 H A 0.0000
263 G A 0.0000
264 R A -1.2132
265 Y A 0.5866
266 D A 0.0000
267 V A 0.0000
268 V A 0.0000
269 C A 0.0000
270 P A -0.2021
271 L A 0.0000
272 Q A -0.6455
273 S A 0.0000
274 A A 0.0000
275 W A -0.0074
276 D A -0.6310
277 L A 0.0000
278 H A -1.4451
279 K A -1.9309
280 A A -1.4394
281 W A 0.0000
282 P A -2.0472
283 K A -2.6856
284 A A 0.0000
285 Q A -1.6160
286 L A -0.9021
287 Q A -0.9125
288 I A -0.3178
289 S A 0.0000
290 P A -0.6093
291 A A -0.1529
292 S A 0.0000
293 G A 0.0000
294 H A 0.0000
295 S A 0.0000
296 A A 0.0000
297 F A 0.2422
298 E A 0.0000
299 P A -0.3842
300 E A -0.6746
301 N A 0.0000
302 V A 0.0000
303 D A -1.0360
304 A A -1.0323
305 L A 0.0000
306 V A 0.0000
307 R A -2.2787
308 A A 0.0000
309 T A 0.0000
310 D A -1.4607
311 G A -1.0183
312 F A -0.4412
313 A A -0.7888
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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
VK169A -0.9775 -0.031 View CSV PDB
VR169A -0.5819 -0.0371 View CSV PDB
VK81A -0.1145 -0.0281 View CSV PDB
VR81A 0.0677 -0.0314 View CSV PDB
LR207A 0.1144 -0.0194 View CSV PDB
LK207A 0.2685 -0.0191 View CSV PDB
YK265A 0.5108 -0.0218 View CSV PDB
YK11A 0.8609 -0.0306 View CSV PDB
YR11A 0.8986 -0.0313 View CSV PDB
YR265A 0.5474 -0.015 View CSV PDB
FR206A 0.8755 -0.0042 View CSV PDB
FK206A 1.1673 -0.0041 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018