Project name: SyxNoRho

Status: done

submitted: 2018-10-15 20:10:35, status changed: 2018-11-24 16:04:06
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Chain sequence(s) A: QSNSWRELIDGHEKLTRRQCHQQEAVWELLHTEASYIRKLRVIINLFLCCLLNLQESGLLCEVEAERLFSNIPEIAQLHRRLWASVMAPVLEKARRTRALLQPGDFLKGFKMFGSLFKPYIRYCMEEEGCMEYMRGLLRDNDLFRAYITWAEKHPQCQRLKLSDMLAKPHQRLTKYPLLLKSVLRKTEEPRAKEAVVAMIGSVERFIHHVNACMRQRQERQRLAAVVSRIDAYEVVESSSDEVDKLLKEFLHLDLTAPIPGASPEETRQLLLEGSLRMKEGKDSKMDVYCFLFTDLLLVTKAVKKAERTRVIRPPLLVDKIVCRELRDPGSFLLIYLNEFHSAVGAYTFQASGQALCRGWVDTIYNAQNQLQ
Distance of aggregation 10 Å
Dynamic mode Yes
Show buried residues

Minimal score value
-4.2232
Maximal score value
1.283
Average score
-1.0872
Total score value
-404.443

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 Q A -1.7959
2 S A -1.7059
3 N A -1.9756
4 S A -1.8798
5 W A -1.9099
6 R A -2.8465
7 E A -3.1965
8 L A -1.8481
9 I A 0.0000
10 D A -3.2972
11 G A -2.8382
12 H A -2.6996
13 E A -3.2666
14 K A -3.0283
15 L A -2.3464
16 T A -2.1601
17 R A -2.8603
18 R A -2.6926
19 Q A -1.3866
20 C A -1.7709
21 H A -2.0216
22 Q A 0.0000
23 Q A 0.0000
24 E A -1.7671
25 A A 0.0000
26 V A 0.0000
27 W A -0.7318
28 E A -0.7828
29 L A 0.0000
30 L A 0.0000
31 H A -0.6776
32 T A -0.4732
33 E A 0.0000
34 A A -0.4710
35 S A -0.6315
36 Y A -0.5789
37 I A 0.0000
38 R A -1.5471
39 K A -1.5381
40 L A 0.0000
41 R A -1.8605
42 V A -1.1688
43 I A 0.0000
44 I A -0.6103
45 N A -1.0707
46 L A 0.0000
47 F A 0.0000
48 L A 0.4127
49 C A 0.7641
50 C A 0.7031
51 L A 0.0000
52 L A 0.4191
53 N A -0.9812
54 L A 0.0000
55 Q A -0.7879
56 E A -1.8334
57 S A -0.8366
58 G A 0.0686
59 L A 0.8663
60 L A 0.0000
61 C A 0.3304
62 E A -1.0891
63 V A 0.0632
64 E A -0.7479
65 A A -0.9962
66 E A -2.1425
67 R A -1.8422
68 L A 0.0000
69 F A 0.0000
70 S A 0.0000
71 N A -1.5963
72 I A 0.0000
73 P A -1.4171
74 E A -2.3603
75 I A 0.0000
76 A A -1.8492
77 Q A -2.2811
78 L A -1.4982
79 H A 0.0000
80 R A -1.8004
81 R A -2.1323
82 L A 0.0000
83 W A -0.4181
84 A A -0.6284
85 S A -0.6037
86 V A 0.0000
87 M A -0.2070
88 A A -0.5189
89 P A -0.8868
90 V A 0.0000
91 L A -1.1319
92 E A -2.4595
93 K A -1.8079
94 A A 0.0000
95 R A -2.1838
96 R A -2.8460
97 T A -1.7855
98 R A -1.6098
99 A A -0.6088
100 L A 0.0000
101 L A 0.5685
102 Q A -0.7555
103 P A -1.0099
104 G A -1.8420
105 D A -2.0579
106 F A 0.0000
107 L A 0.0000
108 K A -2.5024
109 G A -2.0084
110 F A -1.5461
111 K A -2.0759
112 M A -1.2249
113 F A 0.0000
114 G A -0.9876
115 S A -0.9460
116 L A 0.0000
117 F A 0.0000
118 K A -1.7070
119 P A -1.3999
120 Y A 0.0000
121 I A -0.7764
122 R A -1.1039
123 Y A 0.0000
124 C A 0.0000
125 M A -0.7915
126 E A -1.0416
127 E A 0.0000
128 E A -1.6262
129 G A 0.0000
130 C A 0.0000
131 M A -1.2869
132 E A -2.0179
133 Y A -1.2071
134 M A 0.0000
135 R A -2.0747
136 G A -1.8642
137 L A -1.8976
138 L A -2.1515
139 R A -3.4605
140 D A -3.2425
141 N A -2.5700
142 D A -2.1715
143 L A 0.1680
144 F A 0.0000
145 R A -1.4201
146 A A 0.1553
147 Y A 0.2257
148 I A -0.2067
149 T A -0.6995
150 W A -0.3817
151 A A 0.0000
152 E A -3.7619
153 K A -3.3373
154 H A -2.8345
155 P A -2.8516
156 Q A -2.6256
157 C A 0.0000
158 Q A -4.2232
159 R A -3.7426
160 L A 0.0000
161 K A -3.4046
162 L A 0.0000
163 S A -1.1764
164 D A -1.4017
165 M A 0.0000
166 L A 0.0000
167 A A -0.8860
168 K A -0.9575
169 P A 0.0000
170 H A -0.7341
171 Q A -1.0352
172 R A 0.0000
173 L A 0.0000
174 T A -0.8610
175 K A -0.8096
176 Y A 0.0000
177 P A 0.0000
178 L A 0.0208
179 L A -0.3296
180 L A 0.0000
181 K A -1.5472
182 S A 0.0000
183 V A 0.0000
184 L A 0.0000
185 R A -2.9356
186 K A -2.9008
187 T A 0.0000
188 E A -2.7561
189 E A -2.9252
190 P A -2.7118
191 R A -3.3075
192 A A 0.0000
193 K A -2.9628
194 E A -2.8535
195 A A -1.8575
196 V A 0.0000
197 V A -0.4905
198 A A -0.2634
199 M A -0.7735
200 I A -0.4401
201 G A -0.8952
202 S A -0.8879
203 V A 0.0000
204 E A -2.1042
205 R A -2.7457
206 F A -1.5822
207 I A 0.0000
208 H A -2.4422
209 H A -2.0975
210 V A 0.0000
211 N A -1.7197
212 A A -1.3085
213 C A -1.1022
214 M A 0.0000
215 R A -2.1965
216 Q A -2.2097
217 R A -2.2554
218 Q A -2.1460
219 E A -2.3244
220 R A -2.8670
221 Q A -1.7156
222 R A -1.3370
223 L A -0.8825
224 A A -0.3716
225 A A -0.5151
226 V A 0.0000
227 V A 0.1519
228 S A -0.7251
229 R A -1.5910
230 I A 0.0000
231 D A -2.4237
232 A A -1.8412
233 Y A -1.3983
234 E A -1.5840
235 V A 0.0000
236 V A -1.1630
237 E A -1.8633
238 S A -1.5680
239 S A -1.7602
240 S A -2.0517
241 D A -2.8482
242 E A -2.3742
243 V A 0.0000
244 D A -2.8891
245 K A -3.3240
246 L A 0.0000
247 L A -1.8218
248 K A -2.6343
249 E A -1.8299
250 F A 0.0000
251 L A -1.3013
252 H A -1.3479
253 L A -0.8563
254 D A -1.3321
255 L A 0.0000
256 T A 0.0000
257 A A -0.6542
258 P A 0.0000
259 I A 0.0000
260 P A -0.6890
261 G A -0.2761
262 A A -0.2925
263 S A -0.6348
264 P A -1.0813
265 E A -1.7812
266 E A -2.3720
267 T A -1.4961
268 R A 0.0000
269 Q A -1.6157
270 L A 0.0000
271 L A -0.1585
272 L A -0.1471
273 E A -1.1553
274 G A 0.0000
275 S A -0.9476
276 L A 0.0000
277 R A -2.2373
278 M A 0.0000
279 K A -2.7021
280 E A -2.1982
281 G A -2.3171
282 K A -3.1733
283 D A -3.4807
284 S A -2.5357
285 K A -3.0653
286 M A -1.7169
287 D A -2.1181
288 V A 0.0000
289 Y A -1.0062
290 C A 0.0000
291 F A 0.0000
292 L A 0.0000
293 F A 0.0000
294 T A -0.0801
295 D A 0.0000
296 L A 0.0000
297 L A 0.0000
298 L A 0.0000
299 V A 0.0000
300 T A 0.0000
301 K A -1.6260
302 A A -1.8126
303 V A -0.7804
304 K A -2.6706
305 K A -2.9581
306 A A -2.3419
307 E A -3.3979
308 R A -3.2989
309 T A -2.5775
310 R A -2.0364
311 V A 0.0000
312 I A -0.7638
313 R A -1.3264
314 P A 0.0000
315 P A 0.0000
316 L A 0.0000
317 L A -0.1670
318 V A -0.3554
319 D A -1.5888
320 K A -1.1217
321 I A 0.0000
322 V A 0.4828
323 C A 0.0000
324 R A -1.1271
325 E A -2.2353
326 L A -1.5857
327 R A -2.8723
328 D A -2.7819
329 P A -1.8567
330 G A -2.1354
331 S A -1.7759
332 F A 0.0000
333 L A -0.4442
334 L A 0.0000
335 I A 1.0119
336 Y A 0.7609
337 L A 0.0497
338 N A -1.0270
339 E A -1.4031
340 F A 0.2613
341 H A -0.6124
342 S A -0.4696
343 A A 0.1625
344 V A 1.2830
345 G A 0.6056
346 A A 0.4250
347 Y A -0.4333
348 T A -0.9544
349 F A 0.0000
350 Q A -1.5744
351 A A 0.0000
352 S A -0.9084
353 G A -1.0342
354 Q A -1.5159
355 A A -0.9645
356 L A -0.9112
357 C A 0.0000
358 R A -2.7312
359 G A -1.7677
360 W A 0.0000
361 V A 0.0000
362 D A -2.3854
363 T A -1.3945
364 I A -0.6933
365 Y A -0.6081
366 N A -1.8600
367 A A -1.0518
368 Q A -1.3599
369 N A -2.0827
370 Q A -1.8470
371 L A -0.4598
372 Q A -1.4712

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, -1.0872 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015