Project name: Model2

Status: done

submitted: 2017-03-14 12:04:13, status changed: 2017-03-14 14:41:53
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Chain sequence(s) C: TPIFAPGENCSPAWGAAPAAYDAADTHLRILGKPVMERWETPYMHALAAAASSKGGRVLEVGFGMAIAASKVQEAPIDEHWIIECNDGVFQRLRDWAPRQTHKVIPLKGLWEDVAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKNHAFRLLKPGGVLTYCNLTSWGELMKSKYSDITIMFEETQVPALLEAGFRRENIRTEVMALVPPADCRYYAFPQMITPLVTKG
Distance of aggregation 5 Å
Dynamic mode Yes
Show buried residues

Minimal score value
-2.2897
Maximal score value
2.0455
Average score
-0.3122
Total score value
-71.7955

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
7 T C -0.0508
8 P C -0.0610
9 I C 0.3133
10 F C 0.7155
11 A C 0.0963
12 P C -0.2664
13 G C -0.4909
14 E C -2.0585
15 N C -1.5679
16 C C -0.1235
17 S C -0.1249
18 P C -0.2647
19 A C 0.0308
20 W C 0.0648
21 G C -0.3006
22 A C -0.0023
23 A C 0.0000
24 P C -0.0805
25 A C -0.0162
26 A C 0.0972
27 Y C 0.0393
28 D C -1.2331
29 A C -0.1755
30 A C -0.2411
31 D C -1.6458
32 T C -0.3256
33 H C 0.0000
34 L C 0.0000
35 R C -1.5578
36 I C 0.0000
37 L C 1.4326
38 G C -0.2176
39 K C -0.3170
40 P C -0.2203
41 V C 0.3005
42 M C 0.0000
43 E C -0.5466
44 R C -1.3608
45 W C 0.0000
46 E C -1.9431
47 T C -0.3929
48 P C -0.1562
49 Y C 0.0000
50 M C 0.0000
51 H C -0.7617
52 A C -0.1059
53 L C 0.0000
54 A C 0.0000
55 A C 0.0534
56 A C 0.0000
57 A C 0.0000
58 S C -0.0429
59 S C -0.3597
60 K C -1.7532
61 G C -0.5520
62 G C 0.0000
63 R C -0.7031
64 V C 0.0000
65 L C 0.0000
66 E C 0.0000
67 V C 0.0000
68 G C -0.0708
69 F C 0.0000
70 G C -0.0749
71 M C 0.0000
72 A C 0.1513
73 I C 0.7289
74 A C 0.0000
75 A C -0.0104
76 S C -0.1016
77 K C -0.4233
78 V C 0.0000
79 Q C -0.5354
80 E C -1.8507
81 A C -0.3428
82 P C -0.2482
83 I C 0.0000
84 D C -1.8610
85 E C -0.8069
86 H C 0.0000
87 W C 0.2079
88 I C 0.0000
89 I C 0.0000
90 E C 0.0000
91 C C 0.1157
92 N C 0.0000
93 D C -1.3594
94 G C -0.7689
95 V C 0.0877
96 F C 0.0000
97 Q C -1.2639
98 R C -1.2522
99 L C -0.5057
100 R C -2.1352
101 D C -1.9645
102 W C 0.3781
103 A C 0.0462
104 P C -0.5823
105 R C -1.9459
106 Q C -1.1429
107 T C -0.3953
108 H C -1.3324
109 K C -1.8494
110 V C -0.0117
111 I C 0.3884
112 P C 0.0877
113 L C -0.0218
114 K C -1.6420
115 G C -0.2993
116 L C 0.2982
117 W C 0.0000
118 E C -2.1370
119 D C -2.1119
120 V C 0.0000
121 A C 0.0000
122 P C -0.2676
123 T C -0.1163
124 L C 0.0000
125 P C -0.4855
126 D C -1.3611
127 G C -0.8046
128 H C -0.6466
129 F C 0.0000
130 D C 0.0000
131 G C 0.0000
132 I C 0.0000
133 L C 0.0000
134 Y C 0.0000
135 D C -0.2231
136 T C 0.0000
137 Y C 0.1261
138 P C 0.0000
139 L C 0.0000
140 S C -0.7656
141 E C -2.1642
142 E C -2.1629
143 T C -0.3318
144 W C 0.0872
145 H C -0.1703
146 T C -0.1066
147 H C -0.4232
148 Q C 0.0000
149 F C 0.1415
150 N C -0.7572
151 F C 0.1313
152 I C 0.0000
153 K C -1.8835
154 N C -1.0061
155 H C -0.5167
156 A C 0.0000
157 F C 1.1894
158 R C -0.9276
159 L C 0.0000
160 L C 0.0000
161 K C -0.6108
162 P C -0.3538
163 G C 0.0000
164 G C 0.0000
165 V C 0.0000
166 L C 0.0000
167 T C 0.0000
168 Y C 0.0000
169 C C 0.0000
170 N C 0.0000
171 L C 0.1721
172 T C 0.0066
173 S C -0.0613
174 W C 0.0000
175 G C 0.0000
176 E C -0.5512
177 L C 0.1049
178 M C 0.0000
179 K C -1.7401
180 S C -0.7764
181 K C -1.1077
182 Y C 1.0602
183 S C -0.1494
184 D C -1.6242
185 I C 0.0000
186 T C 0.3399
187 I C 2.0455
188 M C 1.2404
189 F C 0.0000
190 E C -0.6450
191 E C -1.8276
192 T C -0.3488
193 Q C 0.0000
194 V C 0.8287
195 P C 0.1695
196 A C 0.0000
197 L C 0.0000
198 L C 1.2689
199 E C -1.5628
200 A C -0.2202
201 G C -0.1815
202 F C 0.0000
203 R C -2.1765
204 R C -2.2897
205 E C -1.1798
206 N C -1.2960
207 I C -0.0229
208 R C -1.1811
209 T C -0.3146
210 E C 0.0142
211 V C 1.7344
212 M C 0.4313
213 A C -0.0508
214 L C 0.0000
215 V C 1.7438
216 P C 0.2464
217 P C -0.2600
218 A C 0.0000
219 D C -1.5731
220 C C 0.1197
221 R C -1.6125
222 Y C 0.0124
223 Y C 0.0000
224 A C 0.0379
225 F C 0.0000
226 P C -0.0959
227 Q C -0.9711
228 M C 0.0000
229 I C 0.0000
230 T C 0.0000
231 P C 0.0000
232 L C 0.0000
233 V C 0.0000
234 T C -0.1705
235 K C -0.9079
236 G C -0.6301

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, -0.3122 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015