Project name: y35m-5 [mutate: YA35M]

Status: done

submitted: 2017-05-19 14:19:44, status changed: 2017-05-19 16:57:01
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Chain sequence(s) A: MRSGSHHHHHHRSDITSLYKKAGSAAAPFTMENLYFQSYQGNSDCYFGNGSAYRGTHSLTESGASCLPWNSMILIGKVYTAQNPSAQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTWEYCDVPSCSTCGLRQYSQPQFRIKGGLFADIASHPWQAAIFAKHRRSPGERFLCGGILISSCWILSAAHCFQERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQLKSDSSRCAQESSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKEAHVRLYPSSRCTSQHLLNRTVTDNMLCAGDTRSGGPQANLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQKDVPGVYTKVTNYLDWIRDNMRP
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues YA35M
Energy difference between WD and mutated (by FoldX) -0.218442 kcal/mol
Show buried residues

Minimal score value
-2.4066
Maximal score value
2.2138
Average score
-0.2502
Total score value
-98.078

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 0.7119
2 R A -1.6880
3 S A -0.6557
4 G A -0.5396
5 S A -0.4993
6 H A -1.2046
7 H A -1.3558
8 H A -1.3680
9 H A -1.2898
10 H A -0.8623
11 H A -0.5692
12 R A -1.2743
13 S A -0.4404
14 D A -0.3440
15 I A 0.0230
16 T A -0.0891
17 S A -0.1753
18 L A 0.3644
19 Y A 0.3666
20 K A -0.3575
21 K A -0.7790
22 A A -0.2175
23 G A -0.4648
24 S A 0.0000
25 A A 0.0089
26 A A 0.2640
27 A A 0.0506
28 P A 0.0000
29 F A 1.7247
30 T A 0.5317
31 M A 0.6963
32 E A -1.6108
33 N A -1.4073
34 L A 0.2613
35 M A 1.3096 mutated: YA35M
36 F A 1.8636
37 Q A -0.8265
38 S A -0.0699
39 Y A 0.1141
40 Q A -0.2905
41 G A -0.6944
42 N A -1.3467
43 S A -0.4803
44 D A -0.9952
45 C A 0.3756
46 Y A 1.7111
47 F A 2.1692
48 G A 0.0000
49 N A -0.5142
50 G A -0.3009
51 S A -0.0696
52 A A 0.2345
53 Y A 1.0754
54 R A -1.0543
55 G A -0.1857
56 T A -0.2310
57 H A -0.6524
58 S A 0.0082
59 L A 1.1971
60 T A 0.0000
61 E A -0.3992
62 S A -0.3311
63 G A -0.3197
64 A A -0.0394
65 S A -0.1862
66 C A 0.0494
67 L A 0.0000
68 P A -0.2549
69 W A 0.0000
70 N A -1.2986
71 S A -0.1789
72 M A 1.3968
73 I A 2.2138
74 L A 0.5264
75 I A 0.3241
76 G A 0.0388
77 K A -1.5895
78 V A 0.0000
79 Y A 1.2452
80 T A 0.2219
81 A A -0.0186
82 Q A -0.1702
83 N A 0.0000
84 P A -0.1000
85 S A -0.1565
86 A A -0.0158
87 Q A 0.0000
88 A A -0.0246
89 L A 0.0000
90 G A 0.0000
91 L A 0.6057
92 G A -0.5743
93 K A -1.8016
94 H A -0.6013
95 N A -0.4319
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 -0.4572
102 G A -0.6680
103 D A -0.6604
104 A A -0.1011
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 0.2412
111 L A 0.0406
112 K A -1.8746
113 N A -1.8919
114 R A -2.4066
115 R A -2.0930
116 L A 0.2456
117 T A 0.1522
118 W A 0.0845
119 E A -0.2603
120 Y A 0.0000
121 C A 0.0000
122 D A -0.5371
123 V A 0.0000
124 P A -0.1878
125 S A -0.0996
126 C A 0.0660
127 S A -0.0245
128 T A -0.0266
129 C A 0.0000
130 G A -0.0818
131 L A 0.0000
132 R A -2.0586
133 Q A -1.2536
134 Y A 1.0596
135 S A -0.0077
136 Q A -1.2281
137 P A -0.5495
138 Q A -0.9408
139 F A 1.1808
140 R A -1.0634
141 I A 1.2940
142 K A -1.3938
143 G A -0.5749
144 G A -0.0793
145 L A 0.6637
146 F A 2.0052
147 A A 0.0527
148 D A -1.7455
149 I A -0.1408
150 A A 0.0808
151 S A -0.1057
152 H A -0.1902
153 P A 0.0000
154 W A 0.0000
155 Q A 0.0000
156 A A 0.0000
157 A A 0.0073
158 I A 0.0000
159 F A 0.0000
160 A A 0.0000
161 K A -1.2109
162 H A -1.2158
163 R A 0.0000
164 R A -1.6909
165 S A -0.5085
166 P A -0.3230
167 G A -0.3361
168 E A -0.5039
169 R A -0.5733
170 F A 0.1040
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 -0.0651
179 S A -0.0196
180 C A 0.1960
181 W A 0.1491
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 -0.2968
188 C A 0.0000
189 F A 0.0000
190 Q A -0.6461
191 E A -1.8172
192 R A -1.0521
193 F A 1.7082
194 P A 0.1725
195 P A -0.3320
196 H A -1.1330
197 H A -0.8204
198 L A 0.0000
199 T A -0.0117
200 V A 0.0000
201 I A -0.0045
202 L A 0.0000
203 G A -0.0631
204 R A 0.0000
205 T A 0.0527
206 Y A 0.0307
207 R A -1.6860
208 V A 0.6322
209 V A 1.8819
210 P A 0.2231
211 G A -0.9794
212 E A -2.2740
213 E A -2.3285
214 E A -0.8904
215 Q A -0.6973
216 K A -1.6823
217 F A -0.3351
218 E A -1.0641
219 V A 0.0000
220 E A -1.2410
221 K A -1.8705
222 Y A -0.0932
223 I A 0.5491
224 V A 0.5461
225 H A 0.0000
226 K A -0.3641
227 E A 0.0000
228 F A 0.1352
229 D A -1.9092
230 D A -1.7257
231 D A -1.9834
232 T A -0.4466
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 -0.4214
242 L A -0.2070
243 K A -1.6773
244 S A -0.6942
245 D A -1.7979
246 S A 0.0000
247 S A -0.3732
248 R A -1.8273
249 C A -0.2405
250 A A 0.0000
251 Q A -0.7096
252 E A -1.8962
253 S A -0.4686
254 S A -0.1582
255 V A 0.2630
256 V A 0.0000
257 R A -0.5571
258 T A -0.1288
259 V A 0.0000
260 C A 0.7316
261 L A 0.0000
262 P A -0.1098
263 P A 0.0000
264 A A -0.3343
265 D A -1.6303
266 L A 0.3671
267 Q A -0.1880
268 L A 1.2942
269 P A -0.0751
270 D A -0.4713
271 W A 0.0000
272 T A -0.0674
273 E A -0.2645
274 C A 0.0000
275 E A 0.0000
276 L A 0.0000
277 S A -0.0617
278 G A 0.0000
279 Y A 0.2078
280 G A -0.0615
281 K A 0.0000
282 H A -0.5155
283 E A -1.6375
284 A A 0.0287
285 L A 1.5501
286 S A 0.2045
287 P A -0.2608
288 F A 0.0000
289 Y A 1.1472
290 S A -0.0678
291 E A -1.4822
292 R A -1.9876
293 L A -0.2131
294 K A -1.2669
295 E A -0.4240
296 A A 0.0000
297 H A -0.1821
298 V A 0.0000
299 R A -1.8139
300 L A -0.0905
301 Y A 0.2844
302 P A -0.2402
303 S A -0.3538
304 S A -0.3600
305 R A -0.6181
306 C A 0.0000
307 T A -0.0425
308 S A -0.3388
309 Q A -1.2692
310 H A -0.6438
311 L A 0.0000
312 L A 1.2369
313 N A -1.2231
314 R A -0.8998
315 T A 0.0794
316 V A 0.2110
317 T A -0.0542
318 D A -0.5596
319 N A -0.5099
320 M A 0.1381
321 L A 0.5413
322 C A 0.0000
323 A A 0.0000
324 G A 0.0000
325 D A -0.4993
326 T A 0.0000
327 R A -1.8866
328 S A -0.6607
329 G A -0.5863
330 G A -0.7636
331 P A -0.5620
332 Q A -1.2908
333 A A -0.4515
334 N A -0.6449
335 L A 1.3226
336 H A -0.0312
337 D A -0.4929
338 A A -0.0517
339 C A 0.0895
340 Q A -0.2412
341 G A 0.0000
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 0.2008
349 C A 0.0000
350 L A 0.2679
351 N A -0.8950
352 D A -1.9887
353 G A -0.9215
354 R A -0.7076
355 M A 0.0195
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 -0.0447
365 L A 0.0000
366 G A 0.0000
367 C A 0.2119
368 G A -0.5738
369 Q A -1.5866
370 K A -2.1818
371 D A -1.6894
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 -0.1896
379 V A 0.0000
380 T A 0.0000
381 N A -0.2366
382 Y A 0.0000
383 L A 0.3398
384 D A 0.0000
385 W A 0.0000
386 I A 0.0000
387 R A -0.5812
388 D A -0.4648
389 N A -0.3248
390 M A 0.6087
391 R A -1.7449
392 P A -0.5997

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, -0.2502 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015