Project name: V208T [mutate: VA208T]

Status: done

submitted: 2017-05-19 15:03:52, status changed: 2017-05-19 17:49:28
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Chain sequence(s) A: MRSGSHHHHHHRSDITSLYKKAGSAAAPFTMENLYFQSYQGNSDCYFGNGSAYRGTHSLTESGASCLPWNSMILIGKVYTAQNPSAQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTWEYCDVPSCSTCGLRQYSQPQFRIKGGLFADIASHPWQAAIFAKHRRSPGERFLCGGILISSCWILSAAHCFQERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQLKSDSSRCAQESSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKEAHVRLYPSSRCTSQHLLNRTVTDNMLCAGDTRSGGPQANLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQKDVPGVYTKVTNYLDWIRDNMRP
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues VA208T
Energy difference between WD and mutated (by FoldX) 0.414011 kcal/mol
Show buried residues

Minimal score value
-2.4017
Maximal score value
2.151
Average score
-0.2737
Total score value
-107.289

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 0.7278
2 R A -1.6886
3 S A -0.4974
4 G A 0.0000
5 S A -0.3975
6 H A -1.2225
7 H A -1.3341
8 H A -1.2113
9 H A -1.3351
10 H A -1.3513
11 H A -1.5206
12 R A -2.0587
13 S A -0.5187
14 D A -0.1799
15 I A 0.4925
16 T A 0.0305
17 S A -0.2193
18 L A 0.0000
19 Y A 0.2606
20 K A 0.0000
21 K A -1.3332
22 A A -0.2876
23 G A -0.4625
24 S A -0.1207
25 A A 0.0000
26 A A 0.2466
27 A A 0.2113
28 P A 0.0000
29 F A 1.9356
30 T A 0.4001
31 M A 0.7657
32 E A -1.4726
33 N A -0.5579
34 L A 0.2641
35 Y A 0.3269
36 F A 0.2228
37 Q A -0.7325
38 S A -0.3138
39 Y A 0.0839
40 Q A -0.4179
41 G A -0.4246
42 N A -1.3020
43 S A -0.3989
44 D A -0.6585
45 C A 0.5019
46 Y A 1.7145
47 F A 2.1510
48 G A 0.2849
49 N A -0.1325
50 G A 0.0000
51 S A -0.0455
52 A A 0.0311
53 Y A -0.2061
54 R A -1.8211
55 G A -0.4170
56 T A -0.2134
57 H A -1.0392
58 S A -0.1763
59 L A 1.2633
60 T A 0.1451
61 E A -0.2163
62 S A -0.3323
63 G A -0.4973
64 A A -0.0509
65 S A -0.1038
66 C A 0.0000
67 L A 0.0000
68 P A -0.2549
69 W A 0.0000
70 N A -1.3116
71 S A -0.1724
72 M A 1.4478
73 I A 2.0647
74 L A 0.0000
75 I A 0.9018
76 G A -0.2288
77 K A -0.5854
78 V A 1.1908
79 Y A 0.5743
80 T A 0.0030
81 A A -0.1722
82 Q A -1.2872
83 N A -0.7652
84 P A 0.0000
85 S A -0.0265
86 A A -0.0375
87 Q A -0.3009
88 A A 0.0000
89 L A 0.2575
90 G A 0.0000
91 L A 1.2717
92 G A -0.4492
93 K A -1.7999
94 H A -0.6698
95 N A -0.3460
96 Y A 0.0000
97 C A 0.0659
98 R A 0.0000
99 N A 0.0000
100 P A 0.0000
101 D A -0.6228
102 G A -0.6418
103 D A -0.4961
104 A A 0.0000
105 K A 0.0000
106 P A 0.0000
107 W A 0.0000
108 C A 0.0000
109 H A 0.0000
110 V A 0.4082
111 L A 0.0737
112 K A -1.8656
113 N A -2.0782
114 R A -2.3751
115 R A -2.0961
116 L A -0.0382
117 T A 0.1705
118 W A 0.6266
119 E A -0.2129
120 Y A 0.0844
121 C A 0.0000
122 D A -1.7894
123 V A 0.0000
124 P A -0.1062
125 S A 0.0000
126 C A 0.2325
127 S A 0.0000
128 T A -0.0206
129 C A 0.0000
130 G A -0.4382
131 L A -0.3010
132 R A -2.1280
133 Q A -1.6832
134 Y A 0.0000
135 S A -0.2150
136 Q A -0.5036
137 P A -0.3245
138 Q A 0.0000
139 F A 0.2122
140 R A -1.3749
141 I A 1.4439
142 K A -1.0368
143 G A 0.0000
144 G A -0.4000
145 L A 0.6341
146 F A 2.0111
147 A A 0.0245
148 D A -1.7197
149 I A 0.0190
150 A A 0.1040
151 S A -0.0732
152 H A -0.0914
153 P A 0.0000
154 W A 0.0000
155 Q A 0.0000
156 A A 0.0000
157 A A 0.0000
158 I A 0.0000
159 F A 0.0000
160 A A -0.0898
161 K A -0.8599
162 H A -1.4529
163 R A -2.2619
164 R A -1.6317
165 S A -0.3867
166 P A -0.4240
167 G A -0.6126
168 E A -0.9257
169 R A -1.3621
170 F A 0.2305
171 L A 0.0000
172 C A 0.0000
173 G A 0.0000
174 G A 0.0000
175 I A 0.0000
176 L A 0.0000
177 I A 0.0000
178 S A -0.1024
179 S A -0.0691
180 C A 0.0000
181 W A 0.0000
182 I A 0.0000
183 L A 0.0000
184 S A 0.0000
185 A A 0.0000
186 A A 0.0000
187 H A -0.4110
188 C A 0.0000
189 F A -0.0014
190 Q A -1.5189
191 E A -2.1684
192 R A -0.9891
193 F A 0.1086
194 P A -0.2399
195 P A -0.3636
196 H A -0.5104
197 H A -0.3818
198 L A 0.0000
199 T A -0.0112
200 V A 0.0000
201 I A 0.0000
202 L A 0.0000
203 G A -0.1421
204 R A -0.2819
205 T A -0.0162
206 Y A -0.0768
207 R A -1.3749
208 T A -0.1160 mutated: VA208T
209 V A 0.8655
210 P A -0.2412
211 G A -0.4876
212 E A -1.9722
213 E A -1.1411
214 E A -0.6774
215 Q A -1.0341
216 K A -1.8177
217 F A 0.0000
218 E A -1.2248
219 V A 0.0000
220 E A -0.7467
221 K A -1.6944
222 Y A 0.1884
223 I A 1.0193
224 V A 1.2374
225 H A -0.1668
226 K A -0.5845
227 E A -0.1536
228 F A 1.0991
229 D A -2.0644
230 D A -2.4017
231 D A -2.0696
232 T A -0.5122
233 Y A 0.0000
234 D A 0.0000
235 N A 0.0000
236 D A 0.0000
237 I A 0.0000
238 A A 0.0000
239 L A 0.0000
240 L A 0.0000
241 Q A -0.1214
242 L A -0.0957
243 K A -1.6651
244 S A -0.4392
245 D A -0.2978
246 S A 0.0000
247 S A -0.4864
248 R A -2.0197
249 C A 0.0000
250 A A -0.4096
251 Q A -1.7249
252 E A -2.0553
253 S A -0.5196
254 S A 0.1217
255 V A 0.8404
256 V A 0.0000
257 R A -0.6050
258 T A -0.1458
259 V A 0.0000
260 C A 0.5878
261 L A 0.0000
262 P A -0.0642
263 P A -0.2057
264 A A 0.0000
265 D A -1.7894
266 L A 0.0000
267 Q A -0.9772
268 L A 0.8312
269 P A -0.3269
270 D A -1.7644
271 W A 0.0111
272 T A -0.0263
273 E A -0.4797
274 C A 0.0000
275 E A 0.0000
276 L A 0.0000
277 S A 0.0000
278 G A 0.0000
279 Y A 0.0000
280 G A 0.0000
281 K A -1.0576
282 H A -0.7157
283 E A -1.8504
284 A A -0.0079
285 L A 1.5226
286 S A 0.0884
287 P A -0.0831
288 F A 0.0000
289 Y A 0.0000
290 S A -0.1203
291 E A -0.5023
292 R A -0.5428
293 L A 0.0072
294 K A -0.3479
295 E A 0.0000
296 A A 0.0000
297 H A 0.0000
298 V A 0.0000
299 R A -0.5187
300 L A 0.2948
301 Y A 0.0000
302 P A -0.1587
303 S A -0.2746
304 S A -0.3930
305 R A -0.7896
306 C A 0.0000
307 T A -0.1372
308 S A -0.2255
309 Q A 0.0000
310 H A -0.7791
311 L A 0.0000
312 L A 0.0555
313 N A -1.3711
314 R A -1.0548
315 T A -0.1085
316 V A 0.0000
317 T A -0.0652
318 D A -0.2197
319 N A -0.1711
320 M A 0.1895
321 L A 0.2619
322 C A 0.0000
323 A A 0.0000
324 G A 0.0000
325 D A -0.3076
326 T A 0.0000
327 R A -0.8961
328 S A -0.4570
329 G A -0.7490
330 G A -0.5277
331 P A -0.6139
332 Q A -1.2762
333 A A -0.2597
334 N A -0.1859
335 L A 1.4653
336 H A 0.0000
337 D A -0.3991
338 A A 0.0000
339 C A 0.0000
340 Q A -1.0471
341 G A -0.2570
342 D A 0.0000
343 S A 0.0000
344 G A 0.0000
345 G A 0.0000
346 P A 0.0000
347 L A 0.0000
348 V A 0.0000
349 C A 0.0000
350 L A 0.1433
351 N A -0.5095
352 D A -1.9117
353 G A -1.0212
354 R A -1.4251
355 M A 0.0000
356 T A 0.0000
357 L A 0.0000
358 V A 0.0000
359 G A 0.0000
360 I A 0.0000
361 I A 0.0000
362 S A 0.0000
363 W A 0.0000
364 G A -0.0815
365 L A 0.4130
366 G A -0.3892
367 C A 0.0872
368 G A -0.6297
369 Q A -1.1857
370 K A -1.9158
371 D A -0.6835
372 V A 0.1556
373 P A 0.0000
374 G A 0.0000
375 V A 0.0000
376 Y A 0.0000
377 T A 0.0000
378 K A 0.0000
379 V A 0.0000
380 T A 0.0000
381 N A 0.0000
382 Y A 0.1985
383 L A 0.4282
384 D A 0.0000
385 W A 0.2090
386 I A -0.0269
387 R A -1.7124
388 D A -1.2712
389 N A -0.6228
390 M A 0.6424
391 R A -1.7085
392 P A -0.6079

Above is the comparison between the input structure and the most aggregation prone model (predicted in the flexibility simulations, download both models in the PDB file format , download table with rmsd values ). The picture presents the most aggregation prone model (in blue) superimposed on the input structure (in red). The plot shows rmsd profile (distances between residues of the superimposed structures).

Dynamic mode uses CABS-flex simulations of protein structure fluctuations. The structure fluctuations may have impact on the size and extent of aggregation "hot-spots" on the protein surface. The dynamic mode uses the following pipeline: (1) based on the input structure, CABS-flex predicts a set of different models reflecting protein dynamics in solution; (2) for each of these models A3D score is calculated; (3) finally, the most aggregation prone model (the model with the highest A3D score, -0.2737 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015