Project name: bf14e4ab0756b97

Status: done

submitted: 2017-03-13 19:18:05, status changed: 2017-03-13 21:47:49
Settings
Chain sequence(s) A: TPIFAPGENCSPAWGAAPAAYDAADTHLRILGKPVMERWETPYMHALAAAASSKGGRVLEVGFGMAIAASKVQEAPIDEHWIIECNDGVFQRLRDWAPRQTHKVIPLKGLWEDVAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKNHAFRLLKPGGVLTYCNLTSWGELMKSKYSDITIMFEETQVPALLEAGFRRENIRTEVMALVPPADCRYYAFPQMITPLVTK
Distance of aggregation 5 Å
Dynamic mode Yes
Show buried residues

Minimal score value
-2.5166
Maximal score value
2.1521
Average score
-0.29
Total score value
-66.4075

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 A -0.0527
8 P A -0.0515
9 I A 0.6306
10 F A 0.0000
11 A A -0.0364
12 P A -0.3089
13 G A -0.7134
14 E A -2.1407
15 N A -1.6570
16 C A 0.0000
17 S A -0.2607
18 P A -0.2930
19 A A -0.0279
20 W A 0.0000
21 G A -0.4555
22 A A -0.0263
23 A A 0.0000
24 P A -0.1603
25 A A 0.0000
26 A A 0.2130
27 Y A 0.5162
28 D A -1.6237
29 A A -0.2840
30 A A -0.0276
31 D A -0.4909
32 T A -0.1250
33 H A -0.1716
34 L A 0.0000
35 R A -1.8441
36 I A 0.0000
37 L A 1.4592
38 G A -0.1725
39 K A 0.0000
40 P A -0.0648
41 V A 0.0000
42 M A 0.0595
43 E A -0.5993
44 R A -1.8542
45 W A -0.1953
46 E A -0.1649
47 T A -0.0858
48 P A -0.1531
49 Y A 0.0000
50 M A 0.0000
51 H A -0.5989
52 A A -0.0896
53 L A 0.0000
54 A A 0.0000
55 A A 0.0603
56 A A -0.0116
57 A A 0.0000
58 S A -0.2840
59 S A -0.5298
60 K A -1.7679
61 G A -0.4650
62 G A -0.1991
63 R A -0.5558
64 V A 0.0000
65 L A 0.0000
66 E A -0.2276
67 V A 0.0000
68 G A -0.0565
69 F A 0.0000
70 G A -0.1314
71 M A 0.1265
72 A A 0.1258
73 I A 0.3883
74 A A 0.0000
75 A A -0.0044
76 S A -0.3675
77 K A -0.9201
78 V A 0.0000
79 Q A -0.7796
80 E A -1.8888
81 A A -0.3651
82 P A -0.2453
83 I A 0.0000
84 D A -1.8768
85 E A -0.8168
86 H A 0.0000
87 W A 0.0000
88 I A 0.2708
89 I A 0.0000
90 E A 0.0000
91 C A 0.1299
92 N A 0.0000
93 D A -0.9182
94 G A -0.3618
95 V A 0.0000
96 F A 0.0000
97 Q A -0.6489
98 R A -0.2506
99 L A -0.1794
100 R A -1.9420
101 D A -1.6276
102 W A 0.8779
103 A A 0.1880
104 P A -0.4617
105 R A -2.1211
106 Q A -1.5654
107 T A -0.3676
108 H A -0.7892
109 K A -1.7324
110 V A 0.0625
111 I A 0.7506
112 P A -0.0044
113 L A 0.0000
114 K A -1.7174
115 G A -0.2948
116 L A 0.4887
117 W A 0.0000
118 E A -1.5109
119 D A -2.0042
120 V A 0.0000
121 A A 0.0000
122 P A -0.2675
123 T A -0.0889
124 L A 0.0963
125 P A -0.5478
126 D A -1.8346
127 G A 0.0000
128 H A -0.7395
129 F A 0.0000
130 D A -0.2125
131 G A 0.0000
132 I A 0.0000
133 L A 0.0000
134 Y A 0.0000
135 D A 0.0000
136 T A 0.0000
137 Y A 0.0000
138 P A -0.0022
139 L A 0.1270
140 S A -0.3795
141 E A -1.1447
142 E A -1.9702
143 T A -0.3769
144 W A 0.0000
145 H A -0.3961
146 T A -0.2041
147 H A -0.4455
148 Q A 0.0000
149 F A 0.2554
150 N A -0.8103
151 F A 0.0000
152 I A 0.0000
153 K A -1.5116
154 N A -0.6325
155 H A -0.3016
156 A A 0.0000
157 F A 0.0000
158 R A -0.6677
159 L A 0.0000
160 L A 0.0000
161 K A -0.8875
162 P A -0.4579
163 G A -0.5340
164 G A 0.0000
165 V A 0.0000
166 L A 0.0000
167 T A 0.0000
168 Y A 0.1498
169 C A 0.0695
170 N A -0.1319
171 L A 0.0000
172 T A -0.0074
173 S A 0.0000
174 W A 0.0000
175 G A 0.0000
176 E A -0.3074
177 L A 0.4865
178 M A -0.3004
179 K A -1.7100
180 S A -0.7645
181 K A -1.2973
182 Y A 0.9432
183 S A -0.1663
184 D A -0.9976
185 I A 0.0000
186 T A 0.3598
187 I A 2.1521
188 M A 1.2377
189 F A 0.0392
190 E A -2.1327
191 E A -2.1812
192 T A -0.3934
193 Q A -0.0108
194 V A 0.7970
195 P A 0.0055
196 A A 0.0000
197 L A 0.3862
198 L A 0.3470
199 E A -1.6971
200 A A -0.4021
201 G A -0.4078
202 F A -0.1395
203 R A -2.1366
204 R A -2.5166
205 E A -2.3581
206 N A -1.4578
207 I A 0.2347
208 R A -0.9936
209 T A -0.4039
210 E A -0.3062
211 V A 1.8190
212 M A 1.2428
213 A A 0.1697
214 L A 0.0000
215 V A 1.7642
216 P A 0.2439
217 P A -0.2572
218 A A 0.0000
219 D A -1.7219
220 C A 0.0684
221 R A 0.0000
222 Y A 1.3153
223 Y A 0.0000
224 A A 0.0271
225 F A 0.0000
226 P A -0.2913
227 Q A -0.3299
228 M A 0.0000
229 I A 0.0000
230 T A -0.0817
231 P A 0.0000
232 L A 0.0000
233 V A 0.0000
234 T A -0.3211
235 K A -1.7359

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, -0.29 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015