Project name: y35l-5 [mutate: YA35L]

Status: done

submitted: 2017-05-19 14:20:57, status changed: 2017-05-19 17:27:12
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Chain sequence(s) A: MRSGSHHHHHHRSDITSLYKKAGSAAAPFTMENLYFQSYQGNSDCYFGNGSAYRGTHSLTESGASCLPWNSMILIGKVYTAQNPSAQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTWEYCDVPSCSTCGLRQYSQPQFRIKGGLFADIASHPWQAAIFAKHRRSPGERFLCGGILISSCWILSAAHCFQERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQLKSDSSRCAQESSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKEAHVRLYPSSRCTSQHLLNRTVTDNMLCAGDTRSGGPQANLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQKDVPGVYTKVTNYLDWIRDNMRP
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues YA35L
Energy difference between WD and mutated (by FoldX) -0.237551 kcal/mol
Show buried residues

Minimal score value
-2.6438
Maximal score value
2.2303
Average score
-0.2559
Total score value
-100.3039

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 0.8147
2 R A -1.2075
3 S A -0.4661
4 G A -0.1380
5 S A -0.2630
6 H A -0.4428
7 H A -1.1724
8 H A -1.2100
9 H A -1.4523
10 H A -1.4094
11 H A -1.0365
12 R A -1.4136
13 S A -0.7181
14 D A -1.7432
15 I A -0.0772
16 T A -0.0765
17 S A -0.1327
18 L A 1.7561
19 Y A 1.4390
20 K A -0.7992
21 K A -0.6219
22 A A -0.1593
23 G A -0.4683
24 S A -0.1180
25 A A 0.0059
26 A A 0.3100
27 A A 0.0478
28 P A 0.0000
29 F A 1.9298
30 T A 0.4908
31 M A 0.7258
32 E A -1.8606
33 N A -1.5297
34 L A 0.3757
35 L A 1.6084 mutated: YA35L
36 F A 0.0000
37 Q A -1.2191
38 S A -0.3362
39 Y A 0.7047
40 Q A -0.1546
41 G A -0.5393
42 N A -1.3455
43 S A -0.5220
44 D A -0.8277
45 C A 0.1367
46 Y A 1.4936
47 F A 2.0653
48 G A -0.0889
49 N A -1.2210
50 G A -0.2801
51 S A -0.0951
52 A A 0.0687
53 Y A 0.3376
54 R A -0.5380
55 G A -0.1995
56 T A -0.2029
57 H A -0.9838
58 S A -0.1764
59 L A 0.4106
60 T A 0.0000
61 E A -0.2619
62 S A -0.2766
63 G A -0.3236
64 A A -0.0345
65 S A -0.1873
66 C A 0.1171
67 L A 0.3333
68 P A -0.1881
69 W A 0.0000
70 N A -1.2785
71 S A -0.0923
72 M A 1.4648
73 I A 2.2303
74 L A 0.6516
75 I A 0.0000
76 G A -0.5610
77 K A -1.7881
78 V A 0.0000
79 Y A 0.9702
80 T A 0.1921
81 A A -0.2079
82 Q A -1.4388
83 N A -1.5033
84 P A 0.0000
85 S A -0.2096
86 A A -0.2643
87 Q A 0.0000
88 A A 0.0224
89 L A 0.1883
90 G A 0.0908
91 L A 0.5844
92 G A -0.2999
93 K A -1.9163
94 H A -1.3622
95 N A -0.2731
96 Y A 0.0662
97 C A 0.0000
98 R A 0.0000
99 N A 0.0000
100 P A 0.0000
101 D A -0.4203
102 G A -0.5657
103 D A -0.3257
104 A A -0.0372
105 K A 0.0000
106 P A -0.0259
107 W A 0.0000
108 C A 0.0000
109 H A 0.0000
110 V A 0.3375
111 L A 0.2857
112 K A -2.0563
113 N A -1.9286
114 R A -2.6438
115 R A -1.9444
116 L A 1.1209
117 T A 0.3595
118 W A 0.5733
119 E A 0.0000
120 Y A 0.0000
121 C A 0.0000
122 D A -0.5282
123 V A 0.1887
124 P A -0.0884
125 S A -0.0368
126 C A 0.0905
127 S A -0.0038
128 T A -0.0113
129 C A 0.0000
130 G A -0.3927
131 L A 0.0000
132 R A -2.0260
133 Q A -1.4589
134 Y A 0.0000
135 S A -0.3545
136 Q A 0.0000
137 P A -0.3695
138 Q A -0.5921
139 F A 0.2955
140 R A -0.8013
141 I A 1.6219
142 K A -0.4432
143 G A -0.3527
144 G A 0.0157
145 L A 1.4348
146 F A 1.7938
147 A A 0.0000
148 D A -0.7265
149 I A 0.0000
150 A A 0.0269
151 S A -0.1401
152 H A 0.0000
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 0.2973
160 A A 0.0000
161 K A -1.8139
162 H A -1.6160
163 R A -2.1682
164 R A -1.1217
165 S A -0.2960
166 P A -0.3481
167 G A -0.8253
168 E A -1.9862
169 R A -0.7796
170 F A 0.1459
171 L A 0.0000
172 C A 0.0679
173 G A -0.0445
174 G A 0.0000
175 I A 0.0000
176 L A 0.0000
177 I A 0.0000
178 S A -0.0750
179 S A -0.2033
180 C A 0.0549
181 W A 0.0000
182 I A 0.0000
183 L A 0.0000
184 S A 0.0000
185 A A 0.0057
186 A A 0.0000
187 H A -0.0854
188 C A 0.0585
189 F A 0.0000
190 Q A -1.2657
191 E A -2.0836
192 R A -0.9372
193 F A 0.0000
194 P A -0.3030
195 P A -0.3265
196 H A -0.2666
197 H A -0.5361
198 L A 0.0000
199 T A -0.0163
200 V A 0.0000
201 I A 0.0141
202 L A 0.0000
203 G A -0.1159
204 R A -0.4342
205 T A 0.0000
206 Y A 0.1143
207 R A -0.5796
208 V A 1.8809
209 V A 1.4097
210 P A 0.0000
211 G A -0.7965
212 E A -2.0201
213 E A -1.0989
214 E A -0.9845
215 Q A -1.1305
216 K A -1.8044
217 F A 0.0000
218 E A -1.5893
219 V A 0.0000
220 E A -1.1615
221 K A -1.5917
222 Y A 1.0479
223 I A 0.8822
224 V A 1.5200
225 H A 0.0000
226 K A -0.2774
227 E A 0.0000
228 F A 0.0000
229 D A -1.0957
230 D A -2.2313
231 D A -2.1100
232 T A -0.3690
233 Y A 0.1271
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 -0.0888
242 L A 0.1612
243 K A -1.6477
244 S A -0.6626
245 D A -0.8032
246 S A 0.0000
247 S A -0.4215
248 R A -2.0180
249 C A -0.2375
250 A A 0.0000
251 Q A -1.7997
252 E A -2.0448
253 S A -0.4165
254 S A -0.1003
255 V A 0.5876
256 V A 0.0000
257 R A -0.3461
258 T A -0.1186
259 V A 0.0000
260 C A 0.7316
261 L A 0.0000
262 P A -0.1287
263 P A -0.1046
264 A A 0.1273
265 D A -0.0124
266 L A 0.0659
267 Q A 0.0077
268 L A 0.8760
269 P A -0.3599
270 D A -1.6628
271 W A -0.1945
272 T A -0.0677
273 E A -0.2509
274 C A 0.0000
275 E A 0.0000
276 L A 0.0000
277 S A 0.0000
278 G A -0.0581
279 Y A 0.0000
280 G A -0.1044
281 K A 0.0000
282 H A -0.6932
283 E A -1.8824
284 A A -0.1982
285 L A 0.7368
286 S A -0.1131
287 P A 0.0420
288 F A 1.9510
289 Y A 0.6283
290 S A -0.1111
291 E A -0.6129
292 R A -1.8863
293 L A 0.0000
294 K A -1.7000
295 E A 0.0000
296 A A -0.0106
297 H A 0.0000
298 V A -0.0264
299 R A -1.5818
300 L A -0.0874
301 Y A 0.1351
302 P A -0.2617
303 S A -0.2908
304 S A -0.4227
305 R A -0.9293
306 C A 0.0000
307 T A -0.0732
308 S A -0.3417
309 Q A -0.2806
310 H A -0.4846
311 L A 0.0000
312 L A 1.3111
313 N A -0.9853
314 R A 0.0000
315 T A -0.0709
316 V A 0.0000
317 T A -0.2225
318 D A -1.0786
319 N A 0.0000
320 M A 0.0000
321 L A 0.2029
322 C A 0.0000
323 A A 0.0000
324 G A 0.0000
325 D A -0.2687
326 T A -0.4305
327 R A -1.8593
328 S A -0.5588
329 G A -0.5686
330 G A -0.6139
331 P A -0.5943
332 Q A -1.2421
333 A A -0.2126
334 N A -0.2184
335 L A 0.5716
336 H A -0.4840
337 D A -1.8360
338 A A -0.3465
339 C A 0.1181
340 Q A -0.3184
341 G A -0.1298
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 0.0920
350 L A 0.0000
351 N A 0.0000
352 D A -1.8724
353 G A -1.1315
354 R A -1.9318
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 0.2164
362 S A 0.0000
363 W A 0.2849
364 G A -0.3014
365 L A 0.0969
366 G A 0.0214
367 C A 0.0934
368 G A -0.5975
369 Q A -1.5834
370 K A -2.0220
371 D A -0.9243
372 V A 0.0000
373 P A 0.0000
374 G A -0.0977
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 -0.2929
382 Y A 0.0000
383 L A 0.0000
384 D A -0.2147
385 W A 0.0000
386 I A 0.0000
387 R A -0.4129
388 D A -1.3223
389 N A -0.1692
390 M A 0.6261
391 R A -1.7882
392 P A -0.5780

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, -0.2559 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015