Project name: f415e0eba8864bf

Status: done

submitted: 2017-03-10 13:07:12, status changed: 2017-03-10 15:29:25
Settings
Chain sequence(s) A: PLFAPGEDCGPAWRAAPAAYDTSDTHLQILGKPVMERWETPYMHSLAAAAASRGGRVLEVGFGMAIAASRVQQAPIKEHWIIECNDGVFQRLQNWALKQPHKVVPLKGLWEEVAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKTHAFRLLKPGGILTYCNLTSWGELMKSKYTDITAMFEETQVPALLEAGFQRENICTEVMALVPPADCRYYAFPQMITPLVTKH
Distance of aggregation 5 Å
Dynamic mode Yes
Show buried residues

Minimal score value
-2.207
Maximal score value
1.773
Average score
-0.2612
Total score value
-59.8039

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 P A -0.2475
8 L A 0.0000
9 F A 0.1401
10 A A 0.0212
11 P A -0.2906
12 G A -0.6429
13 E A -1.0836
14 D A -0.8103
15 C A 0.0000
16 G A -0.0709
17 P A -0.2418
18 A A -0.0075
19 W A 0.0000
20 R A -1.3673
21 A A -0.1500
22 A A 0.0568
23 P A -0.0503
24 A A 0.0028
25 A A 0.1192
26 Y A 0.2700
27 D A -1.1486
28 T A -0.3543
29 S A -0.2960
30 D A -0.4171
31 T A -0.1109
32 H A -0.2112
33 L A 0.0000
34 Q A -0.6057
35 I A 0.0000
36 L A 1.4643
37 G A -0.2580
38 K A -0.4464
39 P A -0.2149
40 V A 0.0000
41 M A 0.0756
42 E A -0.4524
43 R A -1.1080
44 W A 0.0000
45 E A -0.3054
46 T A -0.1148
47 P A -0.3573
48 Y A 0.0000
49 M A 0.0000
50 H A -0.7516
51 S A -0.2001
52 L A 0.0000
53 A A 0.0000
54 A A 0.0386
55 A A 0.0132
56 A A 0.0000
57 A A -0.0195
58 S A -0.4376
59 R A -1.2816
60 G A -0.3866
61 G A -0.4112
62 R A -0.7934
63 V A 0.0000
64 L A 0.0000
65 E A 0.0000
66 V A 0.0000
67 G A 0.0000
68 F A 0.0000
69 G A 0.0000
70 M A 0.0000
71 A A 0.0526
72 I A 0.2200
73 A A 0.0000
74 A A 0.0018
75 S A -0.1102
76 R A -0.4090
77 V A 0.0000
78 Q A -0.4966
79 Q A -1.2776
80 A A -0.2983
81 P A -0.2530
82 I A 0.0000
83 K A -1.3135
84 E A -0.5170
85 H A 0.0000
86 W A 0.1716
87 I A 0.0000
88 I A 0.0000
89 E A 0.0000
90 C A 0.0000
91 N A -0.7100
92 D A -1.8719
93 G A -0.5724
94 V A 0.0000
95 F A 0.0000
96 Q A -0.8092
97 R A -1.4230
98 L A 0.0000
99 Q A -0.5656
100 N A -0.9233
101 W A 0.1413
102 A A 0.2247
103 L A 1.1176
104 K A -1.4977
105 Q A -0.8906
106 P A -0.4467
107 H A -0.8528
108 K A -1.7427
109 V A 0.0696
110 V A 0.4592
111 P A 0.0677
112 L A 0.0478
113 K A -1.4938
114 G A -0.2711
115 L A 0.5509
116 W A 0.0000
117 E A -1.4864
118 E A -2.0295
119 V A 0.0000
120 A A 0.0000
121 P A -0.2689
122 T A -0.1211
123 L A 0.0000
124 P A -0.4005
125 D A -1.8826
126 G A -0.8528
127 H A -0.4283
128 F A 0.0000
129 D A 0.0000
130 G A 0.0000
131 I A 0.0000
132 L A 0.0000
133 Y A 0.0000
134 D A 0.0000
135 T A -0.0079
136 Y A 0.0000
137 P A 0.0000
138 L A 0.0000
139 S A -0.4665
140 E A -2.1654
141 E A -2.1627
142 T A -0.3365
143 W A 0.1117
144 H A -0.1967
145 T A -0.1112
146 H A 0.0000
147 Q A 0.0000
148 F A 0.4709
149 N A -0.7335
150 F A 0.0000
151 I A 0.0000
152 K A -1.7812
153 T A -0.3680
154 H A -0.1641
155 A A 0.0000
156 F A 0.0642
157 R A -1.6763
158 L A 0.0000
159 L A 0.0000
160 K A -0.5437
161 P A -0.3914
162 G A -0.4303
163 G A 0.0000
164 I A 0.0000
165 L A 0.0000
166 T A 0.0000
167 Y A 0.0000
168 C A 0.0000
169 N A 0.0000
170 L A 0.1564
171 T A 0.0000
172 S A 0.0000
173 W A 0.0000
174 G A 0.0000
175 E A -1.9288
176 L A 0.0365
177 M A -0.1157
178 K A -1.8872
179 S A -0.7084
180 K A -1.4724
181 Y A 0.8761
182 T A -0.0164
183 D A -0.8509
184 I A 0.0000
185 T A -0.0062
186 A A -0.0312
187 M A 0.3921
188 F A 0.0000
189 E A -1.0970
190 E A -1.9385
191 T A -0.3435
192 Q A 0.0000
193 V A 0.0663
194 P A -0.0071
195 A A 0.0000
196 L A 0.0000
197 L A 0.4342
198 E A -1.6645
199 A A 0.0000
200 G A 0.2440
201 F A 1.7073
202 Q A -0.9988
203 R A -1.8634
204 E A -2.2070
205 N A -0.9711
206 I A 0.3248
207 C A 0.2848
208 T A -0.3324
209 E A -1.5223
210 V A 1.4623
211 M A 0.6105
212 A A 0.1457
213 L A 0.5141
214 V A 1.7730
215 P A 0.1342
216 P A -0.0787
217 A A -0.1282
218 D A -0.7670
219 C A 0.2007
220 R A -1.7033
221 Y A 0.0000
222 Y A 0.2683
223 A A 0.3054
224 F A 1.3344
225 P A 0.0000
226 Q A -0.2274
227 M A 0.0000
228 I A 0.0000
229 T A 0.0000
230 P A 0.0000
231 L A 0.2520
232 V A 0.0000
233 T A -0.0124
234 K A 0.0000
235 H A -1.0238

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, -0.2612 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015