Project name: Paulla de Paiva Pinto Louzada

Status: done

Started: 2024-07-03 18:33:56
Settings
Chain sequence(s) A: KNNVVIVATGGTIAGAGASSTNSATYSAAKVPVDALIKAVPQVNDLANITGIQALQVASESITDKELLSLARQVNDLVKKPSVNGVVITHGTDTMEETAFFLNLVVHTDKPIVLVGSMRPSTALSADGPLNLYSAVALASSNEAKNKGVMVLMNDSIFAARDVTKGINIHTHAFVSQWGALGTLVEGKPYWFRSSVKKHTNNSEFNIEKIQGDALPGVQIVYGSDNMMPDAYQAFAKAGVKAIIHAGTGNGSMANYLVPEVRKLHDEQGLQIVRSSRVAQGFVLRNAEQPDDKYGWIAAHDLNPQKARLLMALALTKTNDAKEIQNMFWNY
input PDB
Selected Chain(s) A
Distance of aggregation 5 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                                          (00:04:34)
[INFO]       Auto_mut: Residue number 196 from chain A and a score of 1.693 (valine) selected for  
                       automated muatation                                                         (00:04:36)
[INFO]       Auto_mut: Residue number 192 from chain A and a score of 1.656 (phenylalanine)        
                       selected for automated muatation                                            (00:04:36)
[INFO]       Auto_mut: Residue number 130 from chain A and a score of 1.528 (leucine) selected for 
                       automated muatation                                                         (00:04:36)
[INFO]       Auto_mut: Residue number 124 from chain A and a score of 1.509 (leucine) selected for 
                       automated muatation                                                         (00:04:36)
[INFO]       Auto_mut: Residue number 222 from chain A and a score of 1.315 (tyrosine) selected    
                       for automated muatation                                                     (00:04:36)
[INFO]       Auto_mut: Residue number 278 from chain A and a score of 1.145 (valine) selected for  
                       automated muatation                                                         (00:04:36)
[INFO]       Auto_mut: Mutating residue number 196 from chain A (valine) into glutamic acid        (00:04:36)
[INFO]       Auto_mut: Mutating residue number 192 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 192 from chain A (phenylalanine) into glutamic acid (00:04:36)
[INFO]       Auto_mut: Mutating residue number 196 from chain A (valine) into aspartic acid        (00:04:36)
[INFO]       Auto_mut: Mutating residue number 196 from chain A (valine) into arginine             (00:06:37)
[INFO]       Auto_mut: Mutating residue number 196 from chain A (valine) into lysine               (00:06:44)
[INFO]       Auto_mut: Mutating residue number 192 from chain A (phenylalanine) into lysine        (00:06:47)
[INFO]       Auto_mut: Mutating residue number 192 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 192 from chain A (phenylalanine) into aspartic acid (00:08:46)
[INFO]       Auto_mut: Mutating residue number 130 from chain A (leucine) into glutamic acid       (00:08:56)
[INFO]       Auto_mut: Mutating residue number 130 from chain A (leucine) into aspartic acid       (00:09:08)
[INFO]       Auto_mut: Mutating residue number 192 from chain A (phenylalanine) into arginine      (00:10:42)
[INFO]       Auto_mut: Mutating residue number 130 from chain A (leucine) into lysine              (00:11:03)
[INFO]       Auto_mut: Mutating residue number 130 from chain A (leucine) into arginine            (00:11:09)
[INFO]       Auto_mut: Mutating residue number 124 from chain A (leucine) into glutamic acid       (00:12:57)
[INFO]       Auto_mut: Mutating residue number 124 from chain A (leucine) into aspartic acid       (00:13:14)
[INFO]       Auto_mut: Mutating residue number 222 from chain A (tyrosine) into glutamic acid      (00:13:21)
[INFO]       Auto_mut: Mutating residue number 124 from chain A (leucine) into lysine              (00:15:01)
[INFO]       Auto_mut: Mutating residue number 124 from chain A (leucine) into arginine            (00:15:17)
[INFO]       Auto_mut: Mutating residue number 222 from chain A (tyrosine) into lysine             (00:15:28)
[INFO]       Auto_mut: Mutating residue number 222 from chain A (tyrosine) into aspartic acid      (00:17:07)
[INFO]       Auto_mut: Mutating residue number 278 from chain A (valine) into glutamic acid        (00:17:35)
[INFO]       Auto_mut: Mutating residue number 278 from chain A (valine) into aspartic acid        (00:17:41)
[INFO]       Auto_mut: Mutating residue number 222 from chain A (tyrosine) into arginine           (00:19:14)
[INFO]       Auto_mut: Mutating residue number 278 from chain A (valine) into lysine               (00:19:46)
[INFO]       Auto_mut: Mutating residue number 278 from chain A (valine) into arginine             (00:19:51)
[INFO]       Auto_mut: Effect of mutation residue number 196 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.2459 kcal/mol, Difference in average score from 
                       the base case: -0.0122                                                      (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 196 from chain A (valine) into lysine:    
                       Energy difference: -0.3541 kcal/mol, Difference in average score from the   
                       base case: -0.0117                                                          (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 196 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.2898 kcal/mol, Difference in average score from 
                       the base case: -0.0085                                                      (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 196 from chain A (valine) into arginine:  
                       Energy difference: -0.6620 kcal/mol, Difference in average score from the   
                       base case: -0.0121                                                          (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 192 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 1.1645 kcal/mol, Difference in average    
                       score from the base case: -0.0081                                           (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 192 from chain A (phenylalanine) into     
                       lysine: Energy difference: 1.3427 kcal/mol, Difference in average score     
                       from the base case: -0.0110                                                 (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 192 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 1.3956 kcal/mol, Difference in average    
                       score from the base case: -0.0076                                           (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 192 from chain A (phenylalanine) into     
                       arginine: Energy difference: 1.4384 kcal/mol, Difference in average score   
                       from the base case: -0.0111                                                 (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 130 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.3315 kcal/mol, Difference in average score from  
                       the base case: -0.0068                                                      (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 130 from chain A (leucine) into lysine:   
                       Energy difference: 0.1077 kcal/mol, Difference in average score from the    
                       base case: -0.0094                                                          (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 130 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.7223 kcal/mol, Difference in average score from  
                       the base case: -0.0081                                                      (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 130 from chain A (leucine) into arginine: 
                       Energy difference: 0.1555 kcal/mol, Difference in average score from the    
                       base case: -0.0070                                                          (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 124 from chain A (leucine) into glutamic  
                       acid: Energy difference: -0.5974 kcal/mol, Difference in average score from 
                       the base case: -0.0054                                                      (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 124 from chain A (leucine) into lysine:   
                       Energy difference: 0.1103 kcal/mol, Difference in average score from the    
                       base case: -0.0080                                                          (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 124 from chain A (leucine) into aspartic  
                       acid: Energy difference: -0.7169 kcal/mol, Difference in average score from 
                       the base case: -0.0054                                                      (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 124 from chain A (leucine) into arginine: 
                       Energy difference: 0.3229 kcal/mol, Difference in average score from the    
                       base case: -0.0072                                                          (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 222 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 0.6574 kcal/mol, Difference in average score from  
                       the base case: -0.0030                                                      (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 222 from chain A (tyrosine) into lysine:  
                       Energy difference: 0.3282 kcal/mol, Difference in average score from the    
                       base case: -0.0055                                                          (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 222 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 0.8252 kcal/mol, Difference in average score from  
                       the base case: -0.0026                                                      (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 222 from chain A (tyrosine) into          
                       arginine: Energy difference: 0.6180 kcal/mol, Difference in average score   
                       from the base case: -0.0053                                                 (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 278 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.0865 kcal/mol, Difference in average score from  
                       the base case: -0.0064                                                      (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 278 from chain A (valine) into lysine:    
                       Energy difference: -0.0593 kcal/mol, Difference in average score from the   
                       base case: -0.0061                                                          (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 278 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.0056 kcal/mol, Difference in average score from 
                       the base case: -0.0066                                                      (00:22:07)
[INFO]       Auto_mut: Effect of mutation residue number 278 from chain A (valine) into arginine:  
                       Energy difference: 0.2208 kcal/mol, Difference in average score from the    
                       base case: -0.0064                                                          (00:22:07)
[INFO]       Main:     Simulation completed successfully.                                          (00:22:17)
Show buried residues
Minimal score value
-2.367
Maximal score value
1.6932
Average score
-0.3028
Total score value
-100.2181
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 K A -1.7415
2 N A -0.6166
3 N A -0.5342
4 V A 0.0000
5 V A 0.0000
6 I A 0.0000
7 V A 0.0000
8 A A 0.0000
9 T A 0.0000
10 G A 0.0000
11 G A 0.0000
12 T A 0.0000
13 I A 0.0000
14 A A 0.0000
15 G A 0.0000
16 A A 0.0000
17 G A -0.2268
18 A A 0.0134
19 S A -0.0550
20 S A -0.2367
21 T A -0.3312
22 N A -1.2854
23 S A 0.0000
24 A A 0.0535
25 T A 0.0733
26 Y A 0.4606
27 S A -0.0614
28 A A -0.0027
29 A A -0.2557
30 K A -1.6388
31 V A -0.0457
32 P A -0.1181
33 V A 0.0000
34 D A -1.7807
35 A A -0.2844
36 L A 0.0000
37 I A 0.0000
38 K A -1.6894
39 A A -0.2494
40 V A 0.0000
41 P A -0.4384
42 Q A -1.1683
43 V A 0.0000
44 N A -1.0135
45 D A -1.8633
46 L A -0.0571
47 A A 0.0000
48 N A -0.6910
49 I A 0.1737
50 T A -0.0323
51 G A -0.0482
52 I A 0.4133
53 Q A -0.3691
54 A A -0.0337
55 L A 0.1305
56 Q A -0.2588
57 V A 0.2542
58 A A 0.0778
59 S A 0.0000
60 E A -1.8587
61 S A -0.4979
62 I A 0.2003
63 T A -0.1334
64 D A -0.9152
65 K A -1.8443
66 E A -0.5272
67 L A 0.0000
68 L A 0.0000
69 S A -0.1614
70 L A 0.0000
71 A A 0.0000
72 R A -0.7501
73 Q A -0.4905
74 V A 0.0000
75 N A -0.6600
76 D A -1.8373
77 L A 0.0000
78 V A 0.0000
79 K A -1.8838
80 K A -1.3565
81 P A -0.4809
82 S A -0.2588
83 V A 0.0000
84 N A -0.4375
85 G A 0.0000
86 V A 0.0000
87 V A 0.0000
88 I A 0.0000
89 T A 0.0000
90 H A 0.0000
91 G A 0.0000
92 T A 0.0000
93 D A -1.7908
94 T A -0.3323
95 M A 0.0000
96 E A 0.0000
97 E A 0.0000
98 T A 0.0000
99 A A 0.0000
100 F A 0.0000
101 F A 0.0000
102 L A 0.0000
103 N A 0.0000
104 L A 0.0000
105 V A 0.0000
106 V A 0.0000
107 H A -0.5160
108 T A -0.3948
109 D A -1.9790
110 K A -0.7144
111 P A 0.0000
112 I A 0.0000
113 V A 0.0000
114 L A 0.0000
115 V A 0.0000
116 G A 0.0000
117 S A 0.0000
118 M A 0.0000
119 R A -0.3287
120 P A 0.0000
121 S A -0.0836
122 T A -0.0915
123 A A 0.0000
124 L A 1.5090
125 S A 0.0702
126 A A -0.0275
127 D A 0.0000
128 G A 0.0000
129 P A 0.1767
130 L A 1.5280
131 N A 0.0000
132 L A 0.0000
133 Y A 0.3786
134 S A 0.0000
135 A A 0.0000
136 V A 0.0000
137 A A 0.0000
138 L A 0.0000
139 A A 0.0000
140 S A 0.0000
141 S A -0.2570
142 N A -1.5794
143 E A -1.9041
144 A A 0.0000
145 K A -1.4691
146 N A -1.7372
147 K A -0.5021
148 G A 0.0000
149 V A 0.0000
150 M A 0.0000
151 V A 0.0000
152 L A 0.0000
153 M A 0.0000
154 N A -0.9497
155 D A -0.9181
156 S A -0.1802
157 I A 0.0000
158 F A 0.0000
159 A A 0.0000
160 A A 0.0000
161 R A 0.0000
162 D A -0.2383
163 V A 0.0000
164 T A -0.0808
165 K A -0.4549
166 G A -0.4020
167 I A 0.4261
168 N A -0.9461
169 I A 0.6844
170 H A -0.4185
171 T A -0.2353
172 H A -0.5817
173 A A 0.0000
174 F A 0.0000
175 V A 0.7876
176 S A 0.0140
177 Q A -0.2823
178 W A 0.3777
179 G A -0.0841
180 A A -0.0156
181 L A 0.0000
182 G A 0.0000
183 T A -0.0244
184 L A 0.0000
185 V A 0.3302
186 E A -1.7227
187 G A -0.7253
188 K A -1.3235
189 P A -0.1633
190 Y A 0.5891
191 W A 0.7275
192 F A 1.6557
193 R A -1.5295
194 S A -0.5591
195 S A 0.2373
196 V A 1.6932
197 K A -0.1526
198 K A -0.6957
199 H A -0.2261
200 T A 0.0000
201 N A -1.5439
202 N A -1.4988
203 S A 0.0000
204 E A -0.9841
205 F A 0.0000
206 N A -0.1740
207 I A 0.0000
208 E A -1.9789
209 K A -1.2187
210 I A 0.0000
211 Q A -1.2827
212 G A -1.0113
213 D A -1.8673
214 A A -0.2620
215 L A 0.1634
216 P A -0.0431
217 G A -0.1644
218 V A 0.0000
219 Q A -0.5327
220 I A 0.2741
221 V A 0.0000
222 Y A 1.3153
223 G A 0.0000
224 S A -0.4509
225 D A -2.0338
226 N A -1.5632
227 M A 0.0909
228 M A 1.0627
229 P A -0.2066
230 D A -1.8004
231 A A -0.2977
232 Y A 0.0000
233 Q A -1.1218
234 A A -0.1245
235 F A 0.3418
236 A A -0.2464
237 K A -1.6877
238 A A -0.3028
239 G A -0.4199
240 V A -0.1737
241 K A -1.2961
242 A A 0.0000
243 I A 0.0000
244 I A 0.0000
245 H A 0.0000
246 A A 0.0000
247 G A 0.0000
248 T A -0.0652
249 G A -0.5118
250 N A -1.3236
251 G A 0.0000
252 S A -0.0333
253 M A 0.0000
254 A A -0.2234
255 N A -1.0975
256 Y A 0.7260
257 L A 0.0000
258 V A 0.0000
259 P A -0.3764
260 E A -0.8575
261 V A 0.0000
262 R A -0.9580
263 K A -1.4324
264 L A 0.0000
265 H A -0.5281
266 D A -2.2763
267 E A -2.3670
268 Q A -1.6139
269 G A -0.7016
270 L A 0.0000
271 Q A -0.1161
272 I A 0.0000
273 V A 0.0000
274 R A 0.0000
275 S A 0.0000
276 S A 0.0000
277 R A -1.5767
278 V A 1.1445
279 A A 0.0940
280 Q A -1.2453
281 G A -0.3869
282 F A 0.7121
283 V A 0.0000
284 L A 1.0547
285 R A -0.3749
286 N A -1.3094
287 A A -0.3710
288 E A -1.1295
289 Q A -0.3824
290 P A -0.2632
291 D A 0.0000
292 D A -2.1041
293 K A -1.9966
294 Y A -0.1456
295 G A -0.0807
296 W A 0.0000
297 I A 0.0000
298 A A 0.0000
299 A A 0.0000
300 H A -0.1049
301 D A -0.1240
302 L A 0.0000
303 N A -0.2257
304 P A 0.0000
305 Q A -0.2446
306 K A 0.0000
307 A A 0.0000
308 R A -0.5800
309 L A 0.0000
310 L A 0.0000
311 M A 0.0000
312 A A 0.0000
313 L A 0.0000
314 A A 0.0000
315 L A 0.0000
316 T A -0.3018
317 K A -1.4624
318 T A -0.5015
319 N A -1.5470
320 D A -1.6828
321 A A -0.5518
322 K A -2.0286
323 E A -2.1872
324 I A 0.0000
325 Q A 0.0000
326 N A -0.7245
327 M A 0.0000
328 F A 0.0000
329 W A 0.3862
330 N A -0.3789
331 Y A 0.0000
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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
VR196A -0.662 -0.0121 View CSV PDB
VK196A -0.3541 -0.0117 View CSV PDB
LD124A -0.7169 -0.0054 View CSV PDB
LE124A -0.5974 -0.0054 View CSV PDB
VK278A -0.0593 -0.0061 View CSV PDB
VD278A -0.0056 -0.0066 View CSV PDB
LK130A 0.1077 -0.0094 View CSV PDB
LR130A 0.1555 -0.007 View CSV PDB
YK222A 0.3282 -0.0055 View CSV PDB
YR222A 0.618 -0.0053 View CSV PDB
FK192A 1.3427 -0.011 View CSV PDB
FR192A 1.4384 -0.0111 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018