Project name: V208N [mutate: VA208N]

Status: done

submitted: 2017-05-19 15:02:12, status changed: 2017-05-19 17:50:22
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Chain sequence(s) A: MRSGSHHHHHHRSDITSLYKKAGSAAAPFTMENLYFQSYQGNSDCYFGNGSAYRGTHSLTESGASCLPWNSMILIGKVYTAQNPSAQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTWEYCDVPSCSTCGLRQYSQPQFRIKGGLFADIASHPWQAAIFAKHRRSPGERFLCGGILISSCWILSAAHCFQERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQLKSDSSRCAQESSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKEAHVRLYPSSRCTSQHLLNRTVTDNMLCAGDTRSGGPQANLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQKDVPGVYTKVTNYLDWIRDNMRP
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues VA208N
Energy difference between WD and mutated (by FoldX) -0.552111 kcal/mol
Show buried residues

Minimal score value
-2.3452
Maximal score value
2.3249
Average score
-0.2718
Total score value
-106.558

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 -0.1298
2 R A -1.8372
3 S A -0.5597
4 G A -0.1235
5 S A -0.5051
6 H A -1.2166
7 H A -1.3055
8 H A -0.7997
9 H A -0.8316
10 H A -1.2764
11 H A -1.4530
12 R A -1.5301
13 S A -0.5576
14 D A -1.3210
15 I A -0.0041
16 T A -0.2024
17 S A -0.1450
18 L A 0.4460
19 Y A 0.1157
20 K A -1.5925
21 K A -0.7152
22 A A -0.0427
23 G A -0.2870
24 S A -0.0577
25 A A 0.0000
26 A A 0.0094
27 A A 0.0303
28 P A 0.0000
29 F A 0.5701
30 T A 0.2199
31 M A 0.7587
32 E A -1.8474
33 N A -1.3386
34 L A 1.2076
35 Y A 1.0513
36 F A 1.8118
37 Q A -0.8926
38 S A -0.4174
39 Y A 0.0000
40 Q A -0.2694
41 G A -0.7124
42 N A -1.3692
43 S A -0.6072
44 D A -1.4785
45 C A 0.0000
46 Y A 1.1832
47 F A 2.0312
48 G A 0.0529
49 N A -0.2624
50 G A -0.2593
51 S A -0.0534
52 A A 0.0000
53 Y A 0.1268
54 R A -0.6151
55 G A -0.2982
56 T A -0.1298
57 H A -0.1906
58 S A 0.1659
59 L A 1.5324
60 T A 0.0000
61 E A -0.3004
62 S A -0.3372
63 G A -0.4137
64 A A -0.0475
65 S A -0.1883
66 C A 0.2548
67 L A 1.0429
68 P A -0.1676
69 W A 0.0000
70 N A -1.2871
71 S A -0.2672
72 M A 0.5104
73 I A 2.3249
74 L A 1.8635
75 I A 0.0000
76 G A -0.4650
77 K A -1.6985
78 V A -0.0418
79 Y A 0.1619
80 T A -0.0272
81 A A -0.1040
82 Q A -0.8474
83 N A -0.3038
84 P A -0.1141
85 S A -0.1860
86 A A -0.0173
87 Q A 0.0000
88 A A 0.0000
89 L A 0.0000
90 G A -0.0144
91 L A 0.2078
92 G A -0.4676
93 K A -1.8978
94 H A -1.3264
95 N A -0.3833
96 Y A 0.0000
97 C A 0.0000
98 R A 0.0000
99 N A 0.0000
100 P A 0.0000
101 D A 0.0000
102 G A -0.5344
103 D A -0.4412
104 A A -0.0546
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 0.6050
111 L A 0.3803
112 K A -1.8336
113 N A -2.0085
114 R A -1.7384
115 R A -2.0861
116 L A 0.0000
117 T A -0.0451
118 W A 0.0000
119 E A -0.4280
120 Y A 0.0927
121 C A 0.0000
122 D A -1.7469
123 V A -0.1398
124 P A -0.0892
125 S A -0.0452
126 C A 0.0000
127 S A 0.0000
128 T A -0.0096
129 C A 0.0000
130 G A -0.2148
131 L A -0.1560
132 R A -2.0287
133 Q A -1.5586
134 Y A 0.0000
135 S A -0.1945
136 Q A -0.4000
137 P A -0.5465
138 Q A -0.8621
139 F A 1.3696
140 R A -1.4306
141 I A -0.3500
142 K A -1.6591
143 G A -0.4708
144 G A -0.0500
145 L A 1.8164
146 F A 2.1107
147 A A 0.0000
148 D A -0.3396
149 I A 0.0000
150 A A 0.0065
151 S A -0.0770
152 H A -0.1089
153 P A 0.0000
154 W A 0.1121
155 Q A -0.0938
156 A A 0.0000
157 A A 0.0000
158 I A 0.0000
159 F A 0.2766
160 A A 0.0000
161 K A -1.0931
162 H A -1.4995
163 R A -2.3452
164 R A -2.2010
165 S A -0.5766
166 P A -0.6438
167 G A -0.8040
168 E A -1.9018
169 R A -1.8502
170 F A -0.0287
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 -0.0693
179 S A -0.2035
180 C A 0.0812
181 W A 0.2313
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 -0.2926
188 C A 0.0000
189 F A 0.0000
190 Q A -1.1732
191 E A -2.0523
192 R A -0.5416
193 F A 1.7900
194 P A 0.1473
195 P A -0.2128
196 H A -0.7303
197 H A -0.6004
198 L A 0.0000
199 T A -0.0092
200 V A 0.0000
201 I A 0.2315
202 L A 0.0000
203 G A -0.2117
204 R A -0.7711
205 T A -0.0974
206 Y A 0.1773
207 R A -1.0748
208 N A -1.1868 mutated: VA208N
209 V A 1.1114
210 P A -0.0525
211 G A -0.5845
212 E A -1.9406
213 E A -1.1284
214 E A -1.9613
215 Q A -0.9490
216 K A -1.6515
217 F A -0.2689
218 E A -1.0706
219 V A 0.0000
220 E A 0.0000
221 K A -0.8298
222 Y A 0.1178
223 I A 0.6715
224 V A 1.8081
225 H A 0.0670
226 K A -0.8829
227 E A -0.0546
228 F A 1.5472
229 D A 0.0000
230 D A -2.0728
231 D A -1.8908
232 T A -0.3485
233 Y A 0.0000
234 D A -0.4355
235 N A -0.2464
236 D A -0.3031
237 I A 0.2023
238 A A 0.0000
239 L A 0.0000
240 L A 0.0000
241 Q A -0.3875
242 L A -0.2050
243 K A -1.6807
244 S A -0.4919
245 D A -0.6903
246 S A 0.0000
247 S A -0.5672
248 R A -1.8845
249 C A 0.0000
250 A A -0.2638
251 Q A -1.5183
252 E A -2.0623
253 S A -0.5498
254 S A -0.1555
255 V A 0.4485
256 V A 0.0000
257 R A -0.2185
258 T A -0.0470
259 V A 0.2396
260 C A 0.3279
261 L A 0.0000
262 P A -0.1015
263 P A -0.1929
264 A A -0.1272
265 D A -0.1856
266 L A 0.9520
267 Q A -0.5140
268 L A 0.0000
269 P A -0.6218
270 D A -1.8148
271 W A -0.2419
272 T A -0.0699
273 E A -0.6732
274 C A 0.0000
275 E A -0.1773
276 L A 0.0000
277 S A -0.0206
278 G A 0.0000
279 Y A 0.0000
280 G A -0.2260
281 K A 0.0000
282 H A -0.3325
283 E A -1.8403
284 A A -0.0684
285 L A 1.0351
286 S A 0.1328
287 P A -0.0094
288 F A 0.4813
289 Y A 1.3458
290 S A -0.1178
291 E A -1.6384
292 R A -0.6240
293 L A 0.0000
294 K A -0.5630
295 E A 0.0000
296 A A 0.0000
297 H A 0.0000
298 V A 0.0000
299 R A -1.8444
300 L A 0.0367
301 Y A 0.0000
302 P A -0.2212
303 S A -0.2842
304 S A -0.3756
305 R A -0.7372
306 C A 0.0000
307 T A 0.0097
308 S A -0.2632
309 Q A -0.2809
310 H A -0.1742
311 L A 0.0000
312 L A 0.5095
313 N A -1.1864
314 R A -0.4794
315 T A 0.0328
316 V A 0.5431
317 T A -0.1803
318 D A -1.3640
319 N A -0.5370
320 M A 0.0000
321 L A 0.1946
322 C A 0.0000
323 A A 0.0000
324 G A 0.0000
325 D A -0.2143
326 T A -0.1887
327 R A -0.6937
328 S A -0.3383
329 G A -0.3091
330 G A -0.2687
331 P A -0.4807
332 Q A -1.2316
333 A A -0.3019
334 N A -0.4976
335 L A 0.6432
336 H A -0.1135
337 D A -0.3848
338 A A 0.0307
339 C A 0.1049
340 Q A -1.1623
341 G A 0.0000
342 D A 0.0000
343 S A 0.0000
344 G A -0.0464
345 G A 0.0000
346 P A -0.0277
347 L A 0.0000
348 V A 0.0000
349 C A 0.0000
350 L A 0.0000
351 N A -0.5835
352 D A -1.9273
353 G A -1.1651
354 R A -1.9144
355 M A -0.1919
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 -0.0013
363 W A 0.1209
364 G A 0.0138
365 L A 0.1916
366 G A -0.0214
367 C A 0.1328
368 G A -0.6518
369 Q A -1.6029
370 K A -2.0342
371 D A -0.8724
372 V A 0.0861
373 P A 0.0052
374 G A -0.0500
375 V A 0.0000
376 Y A 0.0000
377 T A 0.0000
378 K A 0.0000
379 V A 0.2008
380 T A 0.0000
381 N A -0.1313
382 Y A 0.0000
383 L A 0.4364
384 D A 0.0000
385 W A 0.0000
386 I A 0.0000
387 R A -0.4928
388 D A -0.5261
389 N A -0.9072
390 M A 0.7129
391 R A -0.8695
392 P A -0.4240

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, -0.2718 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015