Project name: V208H [mutate: VA208H]

Status: done

submitted: 2017-05-19 15:01:27, status changed: 2017-05-19 17:50:01
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Chain sequence(s) A: MRSGSHHHHHHRSDITSLYKKAGSAAAPFTMENLYFQSYQGNSDCYFGNGSAYRGTHSLTESGASCLPWNSMILIGKVYTAQNPSAQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTWEYCDVPSCSTCGLRQYSQPQFRIKGGLFADIASHPWQAAIFAKHRRSPGERFLCGGILISSCWILSAAHCFQERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQLKSDSSRCAQESSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKEAHVRLYPSSRCTSQHLLNRTVTDNMLCAGDTRSGGPQANLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQKDVPGVYTKVTNYLDWIRDNMRP
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues VA208H
Energy difference between WD and mutated (by FoldX) -0.400457 kcal/mol
Show buried residues

Minimal score value
-2.4016
Maximal score value
2.2192
Average score
-0.2688
Total score value
-105.387

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 0.7141
2 R A -1.6771
3 S A -0.5628
4 G A -0.4186
5 S A -0.3475
6 H A -0.5291
7 H A -1.2258
8 H A -1.3605
9 H A -1.3196
10 H A -1.0247
11 H A -0.7524
12 R A -1.9024
13 S A -0.5826
14 D A -0.1606
15 I A 0.2527
16 T A -0.0079
17 S A -0.0718
18 L A 0.8175
19 Y A 0.2882
20 K A 0.0000
21 K A -1.6942
22 A A -0.3824
23 G A -0.4649
24 S A -0.3090
25 A A 0.0098
26 A A 0.0620
27 A A 0.0192
28 P A 0.0000
29 F A 1.9337
30 T A 0.4660
31 M A 0.4121
32 E A -1.9324
33 N A -1.2771
34 L A 1.4973
35 Y A 1.7372
36 F A 0.9097
37 Q A -1.0774
38 S A -0.4195
39 Y A 0.0120
40 Q A -0.6323
41 G A -0.5208
42 N A 0.0000
43 S A -0.0665
44 D A -0.3068
45 C A 0.7859
46 Y A 1.7340
47 F A 1.9373
48 G A 0.0000
49 N A -0.7640
50 G A 0.0000
51 S A 0.0000
52 A A 0.0166
53 Y A -0.0997
54 R A -1.6041
55 G A -0.4083
56 T A -0.2494
57 H A -0.7999
58 S A -0.1462
59 L A 0.6361
60 T A -0.1544
61 E A -1.5249
62 S A -0.5676
63 G A -0.4960
64 A A -0.0617
65 S A -0.1935
66 C A 0.1080
67 L A 0.2716
68 P A -0.1211
69 W A 0.4118
70 N A -0.7538
71 S A 0.1506
72 M A 1.4215
73 I A 2.2192
74 L A 0.4772
75 I A 0.3943
76 G A -0.0595
77 K A -0.7067
78 V A 0.2904
79 Y A 1.2186
80 T A -0.0981
81 A A -0.2311
82 Q A -1.2016
83 N A 0.0000
84 P A -0.2615
85 S A -0.0798
86 A A 0.0530
87 Q A -0.2572
88 A A 0.0000
89 L A 0.0000
90 G A 0.0104
91 L A 0.3891
92 G A -0.4461
93 K A -1.7676
94 H A -0.5342
95 N A -0.2583
96 Y A 0.0000
97 C A 0.1238
98 R A 0.0000
99 N A 0.0000
100 P A 0.0000
101 D A -0.8633
102 G A -0.6360
103 D A -0.2602
104 A A 0.0000
105 K A 0.0000
106 P A -0.0045
107 W A 0.1129
108 C A 0.0000
109 H A 0.0000
110 V A 0.4737
111 L A 0.1168
112 K A -2.0530
113 N A -1.8999
114 R A -2.4016
115 R A -2.3053
116 L A -0.1355
117 T A 0.0463
118 W A 0.1575
119 E A -0.2446
120 Y A 0.0000
121 C A 0.0000
122 D A -1.2687
123 V A 0.0000
124 P A -0.0385
125 S A -0.0408
126 C A 0.0000
127 S A 0.0000
128 T A 0.0000
129 C A 0.0000
130 G A -0.4160
131 L A -0.1534
132 R A -2.1256
133 Q A -0.8902
134 Y A 0.0000
135 S A -0.2537
136 Q A -1.2387
137 P A -0.4991
138 Q A -0.1675
139 F A 1.2570
140 R A -1.2568
141 I A 0.9351
142 K A -0.2070
143 G A -0.5734
144 G A -0.4671
145 L A 0.6851
146 F A 1.9980
147 A A 0.0736
148 D A -1.3817
149 I A 0.2152
150 A A 0.0633
151 S A -0.1721
152 H A -0.1009
153 P A 0.0000
154 W A 0.0000
155 Q A -0.1707
156 A A 0.0000
157 A A 0.0000
158 I A 0.0000
159 F A 0.1901
160 A A 0.0000
161 K A -1.0049
162 H A -0.9177
163 R A -1.9736
164 R A -0.8228
165 S A -0.3839
166 P A -0.3511
167 G A -0.8486
168 E A -2.0029
169 R A -0.8275
170 F A 0.0000
171 L A 0.2171
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 0.0000
179 S A -0.0500
180 C A 0.1000
181 W A 0.1407
182 I A 0.0000
183 L A 0.0000
184 S A 0.0000
185 A A 0.0000
186 A A -0.0854
187 H A -0.4627
188 C A 0.0177
189 F A 0.0508
190 Q A -1.4767
191 E A -2.3434
192 R A -2.1233
193 F A -0.1358
194 P A -0.2381
195 P A -0.3662
196 H A -1.0368
197 H A -0.3100
198 L A 0.0000
199 T A 0.0000
200 V A 0.0000
201 I A 0.5471
202 L A 0.0000
203 G A -0.1050
204 R A -0.2380
205 T A 0.1884
206 Y A 1.0145
207 R A -1.2579
208 H A -1.2016 mutated: VA208H
209 V A -0.0835
210 P A -0.4070
211 G A -0.8142
212 E A -1.8356
213 E A -1.1993
214 E A -1.5858
215 Q A -0.9388
216 K A -1.7650
217 F A 0.0000
218 E A -0.6320
219 V A 0.0000
220 E A -1.1406
221 K A -1.8157
222 Y A 0.0521
223 I A 0.8324
224 V A 1.8590
225 H A 0.0000
226 K A -1.0804
227 E A -0.1058
228 F A 1.0810
229 D A -1.8666
230 D A -2.3070
231 D A -1.3019
232 T A -0.4311
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 -0.3608
242 L A 0.0000
243 K A -1.7178
244 S A -0.4316
245 D A -0.2484
246 S A 0.0000
247 S A -0.3919
248 R A -1.9909
249 C A 0.0000
250 A A -0.3982
251 Q A -1.7247
252 E A -2.0693
253 S A -0.5581
254 S A -0.0299
255 V A 0.2229
256 V A 0.0000
257 R A -0.6093
258 T A -0.1203
259 V A 0.0000
260 C A 0.4601
261 L A 0.0000
262 P A -0.1083
263 P A -0.1028
264 A A -0.2479
265 D A -1.0745
266 L A 1.0687
267 Q A -0.8766
268 L A -0.2750
269 P A -0.4190
270 D A -1.7515
271 W A -0.1702
272 T A -0.0381
273 E A 0.0000
274 C A 0.0000
275 E A 0.0000
276 L A 0.0000
277 S A -0.0383
278 G A 0.0000
279 Y A 0.1158
280 G A 0.0850
281 K A 0.0000
282 H A -0.7077
283 E A -1.8861
284 A A -0.0517
285 L A 1.5095
286 S A 0.0415
287 P A -0.2053
288 F A 0.6791
289 Y A 1.3920
290 S A -0.0661
291 E A -1.6318
292 R A -0.5547
293 L A 0.0726
294 K A 0.0258
295 E A 0.0000
296 A A -0.0650
297 H A 0.0000
298 V A -0.1672
299 R A -1.8130
300 L A 0.0000
301 Y A 0.0000
302 P A -0.1708
303 S A -0.2622
304 S A -0.3657
305 R A -0.6602
306 C A 0.0000
307 T A -0.1342
308 S A -0.2945
309 Q A -1.2314
310 H A -0.3184
311 L A 0.3913
312 L A 1.1373
313 N A -1.1334
314 R A -0.7242
315 T A -0.0461
316 V A 0.5219
317 T A 0.0312
318 D A 0.0000
319 N A -0.1538
320 M A 0.3375
321 L A 0.0000
322 C A 0.0000
323 A A 0.0000
324 G A 0.0000
325 D A -0.2963
326 T A -0.1459
327 R A -0.2850
328 S A -0.1932
329 G A -0.5449
330 G A -0.4985
331 P A -0.5788
332 Q A -1.2651
333 A A -0.4020
334 N A -0.9504
335 L A 1.1740
336 H A -0.3625
337 D A -0.3133
338 A A 0.0000
339 C A 0.0934
340 Q A -0.5600
341 G A -0.2128
342 D A 0.0000
343 S A -0.0305
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 0.0000
351 N A -0.7369
352 D A -1.8797
353 G A -0.8039
354 R A -2.0944
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 0.0764
364 G A -0.3959
365 L A 0.1539
366 G A -0.1811
367 C A 0.0469
368 G A -0.4823
369 Q A -1.4904
370 K A -1.5689
371 D A -0.4735
372 V A 0.0000
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 -0.2029
379 V A 0.0000
380 T A 0.0000
381 N A -0.1348
382 Y A 0.0000
383 L A 0.0000
384 D A -0.4043
385 W A 0.0000
386 I A 0.0000
387 R A -0.9714
388 D A -1.3305
389 N A -1.4726
390 M A 0.0002
391 R A -1.9745
392 P A -0.6232

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, -0.2688 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015