Project name: l111d [mutate: LA111D]

Status: done

submitted: 2017-05-19 14:21:36, status changed: 2017-05-19 17:23:28
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Chain sequence(s) A: MRSGSHHHHHHRSDITSLYKKAGSAAAPFTMENLYFQSYQGNSDCYFGNGSAYRGTHSLTESGASCLPWNSMILIGKVYTAQNPSAQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTWEYCDVPSCSTCGLRQYSQPQFRIKGGLFADIASHPWQAAIFAKHRRSPGERFLCGGILISSCWILSAAHCFQERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQLKSDSSRCAQESSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKEAHVRLYPSSRCTSQHLLNRTVTDNMLCAGDTRSGGPQANLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQKDVPGVYTKVTNYLDWIRDNMRP
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues LA111D
Energy difference between WD and mutated (by FoldX) -1.07879 kcal/mol
Show buried residues

Minimal score value
-2.2946
Maximal score value
2.2502
Average score
-0.255
Total score value
-99.9774

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 0.7152
2 R A -1.7006
3 S A -0.5989
4 G A -0.5260
5 S A -0.5040
6 H A -0.4811
7 H A -1.2216
8 H A -1.3382
9 H A -1.3377
10 H A -1.3228
11 H A -1.3065
12 R A -0.9709
13 S A -0.4576
14 D A -1.7129
15 I A 0.1093
16 T A -0.0183
17 S A -0.0043
18 L A 0.8930
19 Y A 0.8045
20 K A 0.0000
21 K A -0.3895
22 A A -0.0221
23 G A -0.0658
24 S A -0.0450
25 A A 0.0000
26 A A 0.2274
27 A A 0.0061
28 P A 0.0000
29 F A 1.9314
30 T A 0.3696
31 M A 0.1939
32 E A -1.7667
33 N A -0.2951
34 L A 1.5544
35 Y A 0.8995
36 F A 1.5668
37 Q A -0.2994
38 S A -0.1840
39 Y A 0.7091
40 Q A -0.1184
41 G A -0.3676
42 N A -1.2963
43 S A -0.5707
44 D A -1.6089
45 C A 0.1032
46 Y A 1.6943
47 F A 2.1677
48 G A 0.2244
49 N A -0.5836
50 G A 0.0000
51 S A -0.0239
52 A A 0.0000
53 Y A 0.0621
54 R A -0.5534
55 G A 0.0000
56 T A -0.1949
57 H A -0.7104
58 S A -0.2113
59 L A 0.5510
60 T A 0.0000
61 E A -1.2169
62 S A -0.5314
63 G A -0.4947
64 A A -0.0687
65 S A -0.2023
66 C A 0.0000
67 L A 0.1069
68 P A -0.2252
69 W A 0.0000
70 N A -1.3266
71 S A -0.1390
72 M A 1.4306
73 I A 2.2502
74 L A 0.6364
75 I A 0.3215
76 G A -0.5768
77 K A -1.7590
78 V A 0.0000
79 Y A 0.1101
80 T A -0.0414
81 A A -0.0046
82 Q A 0.0000
83 N A -1.3177
84 P A -0.4782
85 S A 0.0000
86 A A 0.0099
87 Q A 0.0000
88 A A 0.0896
89 L A 0.0000
90 G A 0.0158
91 L A 1.4498
92 G A -0.4625
93 K A -1.7934
94 H A -0.7678
95 N A -1.3113
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 -0.8809
102 G A -0.6946
103 D A -0.4955
104 A A -0.1592
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 -0.1434
111 D A -2.0299 mutated: LA111D
112 K A -2.2198
113 N A -2.0479
114 R A -2.1355
115 R A -2.2267
116 L A -0.1846
117 T A 0.0621
118 W A 0.1485
119 E A -0.3252
120 Y A 0.0000
121 C A 0.0000
122 D A -0.9337
123 V A 0.1793
124 P A 0.0202
125 S A -0.0741
126 C A 0.0000
127 S A 0.0000
128 T A -0.0077
129 C A 0.0000
130 G A -0.3197
131 L A -0.1567
132 R A -2.0287
133 Q A -1.5422
134 Y A 0.0000
135 S A -0.3305
136 Q A -1.2185
137 P A 0.0000
138 Q A -1.1137
139 F A -0.0461
140 R A -1.4448
141 I A 1.0925
142 K A -0.5893
143 G A -0.6446
144 G A -0.1485
145 L A 1.4578
146 F A 2.0938
147 A A 0.0548
148 D A -1.7480
149 I A -0.1975
150 A A 0.0451
151 S A -0.1831
152 H A -0.1617
153 P A -0.0477
154 W A 0.0041
155 Q A -0.1044
156 A A 0.0000
157 A A 0.0000
158 I A 0.0000
159 F A 0.2139
160 A A -0.0708
161 K A -1.0281
162 H A -1.3029
163 R A -1.4966
164 R A -2.0249
165 S A -0.5007
166 P A -0.3614
167 G A -0.8631
168 E A -2.0388
169 R A -0.9214
170 F A 0.5340
171 L A 0.0000
172 C A 0.0000
173 G A -0.0457
174 G A 0.0000
175 I A 0.0000
176 L A 0.0000
177 I A 0.0000
178 S A -0.0546
179 S A -0.0233
180 C A 0.3136
181 W A 0.2895
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 -0.2808
188 C A 0.0000
189 F A 0.0071
190 Q A -1.2724
191 E A -1.2262
192 R A -1.9100
193 F A 0.0000
194 P A -0.2656
195 P A -0.3010
196 H A -1.1375
197 H A -1.0640
198 L A 0.0000
199 T A -0.0085
200 V A 0.0000
201 I A 0.0000
202 L A 0.0000
203 G A -0.0918
204 R A 0.0000
205 T A 0.0799
206 Y A 0.1965
207 R A 0.2943
208 V A 1.9232
209 V A 1.5829
210 P A -0.0361
211 G A -0.4006
212 E A -1.0438
213 E A -2.0932
214 E A -1.3116
215 Q A -1.0903
216 K A -1.8101
217 F A 0.0000
218 E A -1.4099
219 V A 0.0000
220 E A -1.1412
221 K A -1.7862
222 Y A -0.1418
223 I A 0.4958
224 V A 0.8702
225 H A -0.1403
226 K A -0.7710
227 E A -0.2387
228 F A 1.6922
229 D A -0.8618
230 D A -2.2946
231 D A -2.1317
232 T A -0.3463
233 Y A 0.0000
234 D A 0.0299
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 -0.1396
242 L A -0.1024
243 K A -1.6697
244 S A -0.4660
245 D A -0.3894
246 S A 0.0000
247 S A -0.3914
248 R A -1.8400
249 C A -0.2693
250 A A 0.0000
251 Q A -1.5446
252 E A -2.0590
253 S A -0.4348
254 S A 0.0105
255 V A 1.1642
256 V A 0.0000
257 R A -0.7310
258 T A -0.1811
259 V A 0.0000
260 C A 0.7552
261 L A 0.3775
262 P A -0.0929
263 P A -0.2221
264 A A -0.3621
265 D A -1.7539
266 L A -0.3344
267 Q A -1.0438
268 L A 0.4110
269 P A -0.4632
270 D A -1.7973
271 W A -0.1221
272 T A -0.0452
273 E A -0.2467
274 C A 0.0000
275 E A -0.2040
276 L A 0.0000
277 S A -0.0441
278 G A 0.0000
279 Y A 0.0000
280 G A 0.0000
281 K A 0.0000
282 H A -0.2578
283 E A -0.4787
284 A A 0.0756
285 L A 0.5184
286 S A -0.1428
287 P A 0.1363
288 F A 1.9202
289 Y A 1.0333
290 S A 0.0886
291 E A -0.5503
292 R A -1.8307
293 L A 0.0000
294 K A -0.4178
295 E A 0.0000
296 A A -0.0154
297 H A 0.0000
298 V A 0.0000
299 R A -1.4213
300 L A -0.0800
301 Y A 0.1774
302 P A -0.2477
303 S A -0.2991
304 S A -0.4053
305 R A -0.9155
306 C A 0.0000
307 T A -0.0692
308 S A -0.2523
309 Q A -0.2186
310 H A 0.0000
311 L A 1.2596
312 L A 1.6150
313 N A -0.6224
314 R A -1.7651
315 T A -0.2937
316 V A 0.1882
317 T A -0.1892
318 D A -1.0040
319 N A -0.3142
320 M A 0.2486
321 L A 0.3364
322 C A 0.0000
323 A A 0.0000
324 G A 0.0000
325 D A 0.0000
326 T A -0.1427
327 R A -0.6429
328 S A -0.4973
329 G A -0.5226
330 G A -0.2738
331 P A -0.5111
332 Q A -1.2397
333 A A -0.4058
334 N A -1.1330
335 L A 0.6253
336 H A -0.0215
337 D A -0.2737
338 A A -0.0166
339 C A -0.0528
340 Q A -0.6340
341 G A -0.1645
342 D A 0.0000
343 S A -0.0417
344 G A 0.0000
345 G A 0.0000
346 P A -0.0259
347 L A 0.0000
348 V A 0.0000
349 C A 0.0000
350 L A 0.0000
351 N A -0.4845
352 D A -1.8337
353 G A -0.6579
354 R A -1.4882
355 M A 0.0000
356 T A 0.0000
357 L A 0.0000
358 V A 0.0000
359 G A -0.0814
360 I A 0.0000
361 I A 0.0000
362 S A 0.0000
363 W A 0.1755
364 G A 0.0166
365 L A 0.1631
366 G A 0.0559
367 C A 0.6046
368 G A -0.5568
369 Q A -1.3486
370 K A -0.7065
371 D A -0.4010
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 -0.2290
379 V A 0.0000
380 T A 0.0000
381 N A 0.0000
382 Y A 0.0000
383 L A 0.0000
384 D A 0.0000
385 W A 0.0000
386 I A 0.0000
387 R A -0.9554
388 D A -0.8136
389 N A -0.2683
390 M A 0.2377
391 R A -1.8003
392 P A -0.6414

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, -0.255 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015