Project name: l285d [mutate: LA285D]

Status: done

submitted: 2017-05-19 14:46:40, status changed: 2017-05-19 17:37:40
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Chain sequence(s) A: MRSGSHHHHHHRSDITSLYKKAGSAAAPFTMENLYFQSYQGNSDCYFGNGSAYRGTHSLTESGASCLPWNSMILIGKVYTAQNPSAQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTWEYCDVPSCSTCGLRQYSQPQFRIKGGLFADIASHPWQAAIFAKHRRSPGERFLCGGILISSCWILSAAHCFQERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQLKSDSSRCAQESSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKEAHVRLYPSSRCTSQHLLNRTVTDNMLCAGDTRSGGPQANLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQKDVPGVYTKVTNYLDWIRDNMRP
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues LA285D
Energy difference between WD and mutated (by FoldX) 1.06659 kcal/mol
Show buried residues

Minimal score value
-2.4727
Maximal score value
2.1639
Average score
-0.253
Total score value
-99.172

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 0.6560
2 R A -1.6560
3 S A -0.5629
4 G A -0.1477
5 S A -0.4080
6 H A -1.1219
7 H A -1.2613
8 H A -0.9353
9 H A -1.2693
10 H A -1.3021
11 H A -1.0985
12 R A -1.0501
13 S A -0.6186
14 D A -1.8126
15 I A 0.0000
16 T A -0.0811
17 S A 0.2814
18 L A 1.5919
19 Y A 0.3453
20 K A -1.1735
21 K A -0.5690
22 A A -0.1183
23 G A -0.4677
24 S A -0.1364
25 A A -0.0459
26 A A 0.2513
27 A A 0.0396
28 P A 0.0000
29 F A 1.9333
30 T A 0.4728
31 M A 0.7081
32 E A -1.8457
33 N A -1.2808
34 L A 1.3221
35 Y A 0.7602
36 F A 1.9640
37 Q A 0.0000
38 S A 0.0230
39 Y A 0.3785
40 Q A -0.6802
41 G A -0.3706
42 N A -0.3584
43 S A -0.4252
44 D A -1.7317
45 C A 0.3632
46 Y A 1.7465
47 F A 2.1639
48 G A 0.2960
49 N A -0.2089
50 G A -0.4094
51 S A 0.0000
52 A A -0.1757
53 Y A 0.2435
54 R A -1.7322
55 G A -0.3998
56 T A -0.2306
57 H A -0.8821
58 S A -0.1413
59 L A 1.1728
60 T A 0.0000
61 E A -1.8574
62 S A -0.6213
63 G A -0.5004
64 A A -0.1045
65 S A -0.0611
66 C A 0.0000
67 L A 0.0000
68 P A -0.2549
69 W A 0.0000
70 N A -1.2991
71 S A -0.1877
72 M A 1.0280
73 I A 0.0000
74 L A 0.8352
75 I A 2.0288
76 G A -0.3133
77 K A -1.6626
78 V A 0.2303
79 Y A 0.0000
80 T A -0.0600
81 A A 0.0453
82 Q A 0.0000
83 N A -0.2186
84 P A -0.1201
85 S A 0.0000
86 A A -0.0871
87 Q A -0.4984
88 A A -0.0592
89 L A 0.1375
90 G A 0.2966
91 L A 1.4073
92 G A -0.5229
93 K A -1.8371
94 H A -0.6882
95 N A -0.6751
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 -0.3223
102 G A 0.0000
103 D A -0.8276
104 A A 0.0000
105 K A 0.0000
106 P A -0.0476
107 W A 0.0000
108 C A 0.0000
109 H A 0.0000
110 V A 0.7847
111 L A 0.9927
112 K A -1.7392
113 N A -2.0908
114 R A -2.4497
115 R A -2.1040
116 L A -0.0348
117 T A 0.1366
118 W A 0.5562
119 E A -0.1857
120 Y A 0.0000
121 C A -0.1050
122 D A -1.7047
123 V A -0.1362
124 P A -0.0416
125 S A 0.0000
126 C A 0.5266
127 S A 0.0697
128 T A 0.0000
129 C A 0.0000
130 G A -0.0813
131 L A 0.0000
132 R A -2.1253
133 Q A -1.6043
134 Y A -0.0964
135 S A -0.2254
136 Q A -0.3308
137 P A -0.3373
138 Q A 0.1175
139 F A 1.5551
140 R A -1.3527
141 I A -0.0089
142 K A -1.6152
143 G A -0.6081
144 G A -0.3627
145 L A 1.0226
146 F A 2.0830
147 A A 0.0000
148 D A -1.6147
149 I A 0.6259
150 A A 0.2268
151 S A -0.0577
152 H A -0.1300
153 P A -0.0216
154 W A 0.1219
155 Q A -0.1332
156 A A 0.0000
157 A A 0.0070
158 I A 0.0000
159 F A 0.4049
160 A A -0.0434
161 K A -1.3252
162 H A -1.4787
163 R A -2.4727
164 R A -2.2975
165 S A -0.5997
166 P A -0.3499
167 G A -0.6981
168 E A -1.3988
169 R A -0.7213
170 F A 0.6647
171 L A 0.3935
172 C A 0.0000
173 G A -0.0711
174 G A 0.0000
175 I A 0.0000
176 L A 0.0000
177 I A 0.0000
178 S A -0.1012
179 S A -0.0825
180 C A 0.0000
181 W A 0.1359
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 -0.4547
188 C A 0.0234
189 F A 0.1106
190 Q A -1.0489
191 E A -1.5273
192 R A -1.9921
193 F A -0.1712
194 P A -0.2364
195 P A -0.1915
196 H A -0.3271
197 H A -0.6832
198 L A 0.0000
199 T A -0.0915
200 V A 0.0000
201 I A 0.0901
202 L A 0.0000
203 G A -0.2639
204 R A -0.3651
205 T A 0.0004
206 Y A 0.0588
207 R A -1.4549
208 V A 1.5268
209 V A 0.7699
210 P A -0.2576
211 G A -0.8733
212 E A -2.0900
213 E A -1.4702
214 E A -0.9940
215 Q A -0.5737
216 K A -1.6876
217 F A 0.0000
218 E A -0.8001
219 V A 0.0000
220 E A -1.9755
221 K A -1.4755
222 Y A -0.0120
223 I A 0.4892
224 V A 0.6903
225 H A 0.0000
226 K A -0.5183
227 E A 0.0000
228 F A 0.0802
229 D A -1.2841
230 D A -2.3346
231 D A -2.1559
232 T A -0.5382
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 -0.3906
242 L A -0.1958
243 K A -1.6768
244 S A -0.4408
245 D A -0.4559
246 S A 0.0000
247 S A -0.5471
248 R A -1.9082
249 C A 0.0000
250 A A -0.1840
251 Q A -1.5207
252 E A -2.0624
253 S A -0.5017
254 S A 0.0264
255 V A 1.4572
256 V A 0.3844
257 R A -0.5843
258 T A -0.1490
259 V A 0.0000
260 C A 0.7639
261 L A 0.3002
262 P A -0.0513
263 P A -0.0502
264 A A 0.0000
265 D A -1.6921
266 L A 0.0569
267 Q A -0.1624
268 L A 1.4160
269 P A -0.1475
270 D A -1.7336
271 W A 0.1228
272 T A 0.0534
273 E A 0.0000
274 C A 0.0000
275 E A 0.0000
276 L A 0.0000
277 S A -0.0446
278 G A 0.0000
279 Y A 0.1933
280 G A -0.1137
281 K A -0.2538
282 H A -0.6505
283 E A -1.8720
284 A A 0.0000
285 D A -1.8174 mutated: LA285D
286 S A -0.5117
287 P A 0.1980
288 F A 1.9847
289 Y A 0.7092
290 S A -0.1918
291 E A -0.6141
292 R A -1.2062
293 L A 0.0000
294 K A -0.3094
295 E A 0.0000
296 A A 0.0000
297 H A 0.0000
298 V A 0.0000
299 R A -0.7962
300 L A 0.1240
301 Y A 0.3242
302 P A -0.0788
303 S A -0.2639
304 S A -0.3662
305 R A -0.6063
306 C A 0.0000
307 T A 0.0172
308 S A -0.2696
309 Q A -0.3737
310 H A 0.0000
311 L A 0.0000
312 L A 0.7530
313 N A -1.2477
314 R A -1.0984
315 T A 0.0104
316 V A 0.2736
317 T A -0.3269
318 D A -1.7962
319 N A 0.0000
320 M A 0.1824
321 L A 0.2453
322 C A 0.0000
323 A A 0.0000
324 G A 0.0000
325 D A -0.2240
326 T A -0.3698
327 R A -1.6195
328 S A -0.5852
329 G A -0.5241
330 G A -0.5889
331 P A -0.5641
332 Q A -1.2432
333 A A -0.0684
334 N A -0.0429
335 L A 1.4091
336 H A 0.0392
337 D A -0.4182
338 A A 0.0000
339 C A 0.0000
340 Q A -0.6191
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 -0.0293
347 L A 0.0000
348 V A 0.2112
349 C A 0.1466
350 L A 0.0000
351 N A -0.5920
352 D A -1.9323
353 G A -0.9751
354 R A -0.8907
355 M A 0.0000
356 T A -0.0189
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 0.1564
364 G A 0.0119
365 L A 0.1484
366 G A -0.0585
367 C A 0.1764
368 G A -0.6120
369 Q A -1.5089
370 K A -1.8831
371 D A -0.8985
372 V A 0.0000
373 P A 0.0000
374 G A -0.0484
375 V A 0.0000
376 Y A 0.0000
377 T A 0.0000
378 K A -0.2660
379 V A 0.0000
380 T A 0.0000
381 N A 0.0000
382 Y A 0.3374
383 L A 1.2533
384 D A 0.0000
385 W A 0.0000
386 I A 0.2514
387 R A -0.6077
388 D A -0.6110
389 N A -0.7791
390 M A 0.5463
391 R A -1.6929
392 P A -0.5871

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, -0.253 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015