Project name: Model3

Status: done

submitted: 2017-03-14 12:05:50, status changed: 2017-03-14 14:47:41
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Chain sequence(s) A: TNIENIGDGAEVIKRTEDVSSKKWGVTQNVQFDFVKDKKYNKDALIVKMQGFINSRTSFSDVKGSGYELTKRMIWPFQYNIGLTTKDPNVSLINYLPKNKIETTDVGQTLGYNIGGNFQSAPSIGGNGSFNYSKTISYTQKSYVSEVDKQNSKSVKWGVKANEFVTPDGKKSAHDRYLFVQSPNGPTGSAREYFAPDNQLPPLVQSGFNPSFITTLSHEKGSSDTSEFEISYGRNLDITYATLFPRTGIYAERKHNAFVNRNFVVRYEVNWKTHEIKVKGHN
Distance of aggregation 5 Å
Dynamic mode Yes
Show buried residues

Minimal score value
-2.083
Maximal score value
2.2402
Average score
-0.3173
Total score value
-89.4704

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
30 T A -0.3039
31 N A -0.8471
32 I A 1.6717
33 E A -0.7225
34 N A -1.3246
35 I A 0.5193
36 G A -0.0029
37 D A -0.4745
38 G A -0.6737
39 A A 0.0000
40 E A -0.5670
41 V A 0.1510
42 I A 0.5117
43 K A -0.4826
44 R A -0.4590
45 T A -0.2319
46 E A -0.5465
47 D A -1.8585
48 V A 0.0000
49 S A -0.2174
50 S A -0.3740
51 K A -2.0067
52 K A -2.0022
53 W A 0.0000
54 G A -0.3906
55 V A 0.0000
56 T A -0.0216
57 Q A 0.0000
58 N A -0.4733
59 V A 0.0000
60 Q A -0.4219
61 F A 0.0000
62 D A 0.0000
63 F A 0.2620
64 V A 0.0000
65 K A -0.5304
66 D A -0.6622
67 K A -1.6719
68 K A -1.7729
69 Y A 0.6106
70 N A -1.3591
71 K A -1.9861
72 D A -0.5572
73 A A -0.0399
74 L A 0.0000
75 I A 0.0000
76 V A 0.0000
77 K A -0.3932
78 M A 0.0000
79 Q A -0.4397
80 G A 0.0000
81 F A 1.9410
82 I A 0.0000
83 N A -0.4799
84 S A -0.5294
85 R A -1.8704
86 T A -0.3679
87 S A 0.3549
88 F A 1.9212
89 S A -0.1718
90 D A -1.7003
91 V A 0.0047
92 K A -1.6198
93 G A -0.5384
94 S A -0.1881
95 G A -0.3074
96 Y A 1.0701
97 E A -0.3286
98 L A 0.3578
99 T A 0.0294
100 K A -0.5636
101 R A -1.0739
102 M A 0.0000
103 I A 0.3305
104 W A 0.0000
105 P A 0.0000
106 F A 0.0000
107 Q A -0.3929
108 Y A 0.0000
109 N A -0.4426
110 I A 0.0000
111 G A -0.2948
112 L A 0.0000
113 T A -0.0603
114 T A 0.0000
115 K A -1.1900
116 D A -0.6911
117 P A -0.3742
118 N A -0.3392
119 V A 0.0000
120 S A 0.0000
121 L A 0.0000
122 I A 1.1346
123 N A 0.0000
124 Y A 0.0000
125 L A 0.2031
126 P A -0.3424
127 K A -1.9342
128 N A -1.8956
129 K A -1.9365
130 I A -0.1603
131 E A -1.6972
132 T A -0.3441
133 T A -0.5436
134 D A -1.7004
135 V A 0.2806
136 G A -0.1460
137 Q A -0.2886
138 T A -0.0582
139 L A 0.0000
140 G A -0.0792
141 Y A 0.0935
142 N A -0.0016
143 I A 1.9190
144 G A 0.1459
145 G A -0.5334
146 N A -1.1157
147 F A 0.6651
148 Q A -0.5679
149 S A -0.3013
150 A A -0.0655
151 P A -0.2756
152 S A 0.2102
153 I A 1.9031
154 G A -0.1879
155 G A -0.7778
156 N A -1.4144
157 G A -0.5926
158 S A 0.0668
159 F A 1.8534
160 N A 0.0810
161 Y A 0.0000
162 S A -0.2402
163 K A -0.3791
164 T A -0.1187
165 I A 0.0000
166 S A -0.1986
167 Y A 0.0993
168 T A -0.2979
169 Q A -0.6314
170 K A -1.5600
171 S A 0.0000
172 Y A 0.0000
173 V A -0.0311
174 S A 0.0000
175 E A -0.9718
176 V A 0.0000
177 D A -1.2850
178 K A -1.2501
179 Q A -1.5634
180 N A -1.6130
181 S A -0.6042
182 K A -0.9125
183 S A -0.3071
184 V A 0.0000
185 K A -1.5894
186 W A -0.2097
187 G A -0.1539
188 V A -0.0770
189 K A -1.2896
190 A A 0.0000
191 N A -0.3250
192 E A -0.6216
193 F A 0.0000
194 V A 0.7886
195 T A 0.0571
196 P A -0.5891
197 D A -1.8698
198 G A -0.8112
199 K A -1.7999
200 K A -0.6974
201 S A -0.1967
202 A A -0.1633
203 H A -0.9839
204 D A 0.0000
205 R A -0.0236
206 Y A 1.4322
207 L A 1.2698
208 F A 0.0000
209 V A 0.1862
210 Q A -0.7697
211 S A -0.2441
212 P A -0.3564
213 N A -1.3675
214 G A -0.7093
215 P A -0.3368
216 T A -0.2077
217 G A -0.4922
218 S A -0.1508
219 A A -0.3502
220 R A -2.0084
221 E A -1.2387
222 Y A 0.0000
223 F A 0.2054
224 A A -0.1056
225 P A -0.5286
226 D A -2.0261
227 N A -1.6276
228 Q A -0.5971
229 L A 0.0761
230 P A 0.0000
231 P A -0.2890
232 L A 0.0000
233 V A -0.0035
234 Q A -0.9737
235 S A 0.0000
236 G A -0.3708
237 F A 0.0000
238 N A -0.5497
239 P A -0.1627
240 S A -0.1185
241 F A 0.0000
242 I A 0.0000
243 T A 0.0000
244 T A -0.0071
245 L A 0.0000
246 S A -0.0263
247 H A 0.0000
248 E A -2.0830
249 K A -1.8238
250 G A -0.7766
251 S A -0.3357
252 S A -0.3019
253 D A -0.3196
254 T A -0.1469
255 S A 0.0000
256 E A -0.2739
257 F A 0.0000
258 E A -0.3454
259 I A 0.0000
260 S A 0.0217
261 Y A 0.0000
262 G A -0.1820
263 R A 0.0000
264 N A 0.0000
265 L A 0.0000
266 D A 0.0000
267 I A 0.2997
268 T A 0.0000
269 Y A 0.0069
270 A A 0.0000
271 T A 0.0032
272 L A 0.6451
273 F A 1.6320
274 P A -0.0515
275 R A -1.8865
276 T A -0.4623
277 G A 0.0627
278 I A 2.2402
279 Y A 1.7194
280 A A 0.1197
281 E A -0.8646
282 R A -1.2853
283 K A -1.8968
284 H A -1.4392
285 N A -1.4351
286 A A 0.1333
287 F A 2.0544
288 V A 0.7566
289 N A -1.0441
290 R A -0.5939
291 N A -0.8635
292 F A 0.0000
293 V A 1.3793
294 V A 0.0000
295 R A -0.4673
296 Y A 0.0000
297 E A -0.4234
298 V A 0.0000
299 N A -0.2697
300 W A -0.2801
301 K A -1.6838
302 T A -0.5212
303 H A -1.1020
304 E A -0.7215
305 I A -0.2175
306 K A -1.5493
307 V A 0.1546
308 K A -0.9293
309 G A -0.7108
310 H A -1.1152
311 N A -1.4205

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, -0.3173 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015