Project name: Model1RAT

Status: done

submitted: 2017-03-14 12:08:11, status changed: 2017-03-14 14:45:47
Settings
Chain sequence(s) A: PLFAPGEDCGPAWRAAPAAYDTSDTHLQILGKPVMERWETPYMHSLAAAAASRGGRVLEVGFGMAIAASRVQQAPIKEHWIIECNDGVFQRLQNWALKQPHKVVPLKGLWEEVAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKTHAFRLLKPGGILTYCNLTSWGELMKSKYTDITAMFEETQVPALLEAGFQRENICTEVMALVPPADCRYYAFPQMITPLVTKH
Distance of aggregation 5 Å
Dynamic mode Yes
Show buried residues

Minimal score value
-2.159
Maximal score value
2.0142
Average score
-0.2657
Total score value
-60.8391

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 0.0388
8 L A 1.5360
9 F A 0.4906
10 A A 0.0121
11 P A -0.2607
12 G A -0.6235
13 E A -2.1590
14 D A -2.1301
15 C A 0.0000
16 G A -0.1343
17 P A -0.2692
18 A A -0.0383
19 W A 0.0000
20 R A -0.9304
21 A A -0.1235
22 A A 0.0000
23 P A -0.2484
24 A A -0.0176
25 A A -0.0509
26 Y A -0.1033
27 D A -1.7629
28 T A -0.4461
29 S A -0.5476
30 D A -1.8314
31 T A -0.4240
32 H A -0.3892
33 L A 0.0000
34 Q A -0.8181
35 I A 0.0000
36 L A 1.4637
37 G A -0.2189
38 K A -0.2880
39 P A -0.1658
40 V A 0.1782
41 M A 0.0000
42 E A -0.8477
43 R A -0.5964
44 W A 0.0000
45 E A -0.3096
46 T A -0.1195
47 P A -0.1006
48 Y A 0.0000
49 M A 0.0000
50 H A -0.3228
51 S A -0.0775
52 L A 0.0000
53 A A 0.0000
54 A A 0.0552
55 A A 0.0177
56 A A 0.0000
57 A A -0.0557
58 S A -0.3942
59 R A -1.0364
60 G A -0.3064
61 G A -0.2156
62 R A -0.5212
63 V A 0.0000
64 L A 0.0000
65 E A -0.1917
66 V A 0.0000
67 G A 0.0000
68 F A 0.0000
69 G A -0.0380
70 M A 0.1147
71 A A 0.4593
72 I A 2.0142
73 A A 0.3364
74 A A -0.0132
75 S A -0.3966
76 R A -1.3407
77 V A 0.0000
78 Q A -0.9316
79 Q A -1.4185
80 A A -0.2493
81 P A -0.2517
82 I A 0.0000
83 K A -1.7900
84 E A -0.8786
85 H A -0.1315
86 W A 0.2157
87 I A 0.0000
88 I A 0.0000
89 E A 0.0000
90 C A 0.0000
91 N A 0.0000
92 D A 0.0000
93 G A -0.1371
94 V A 0.0000
95 F A 0.1402
96 Q A -1.3395
97 R A -1.0323
98 L A 0.1488
99 Q A -0.7496
100 N A -1.1468
101 W A 0.9934
102 A A 0.5028
103 L A 1.2230
104 K A -1.6347
105 Q A -1.5691
106 P A -0.5075
107 H A -0.6648
108 K A -1.7174
109 V A 0.0110
110 V A 0.7520
111 P A 0.0279
112 L A 0.2518
113 K A -0.6503
114 G A -0.1927
115 L A 0.1654
116 W A 0.0000
117 E A -1.8828
118 E A -1.8623
119 V A 0.0000
120 A A -0.0066
121 P A -0.2605
122 T A -0.0705
123 L A 0.1962
124 P A -0.5345
125 D A -1.8681
126 G A -0.6476
127 H A -0.8746
128 F A 0.0000
129 D A -0.2786
130 G A 0.0000
131 I A 0.0000
132 L A 0.0000
133 Y A 0.0000
134 D A -0.1780
135 T A 0.0000
136 Y A 0.0000
137 P A -0.0849
138 L A 0.0000
139 S A -0.0887
140 E A -0.6100
141 E A -1.8715
142 T A -0.3309
143 W A 0.0000
144 H A -0.6635
145 T A -0.2427
146 H A -0.3042
147 Q A 0.0000
148 F A 0.3556
149 N A -1.0998
150 F A 0.0785
151 I A 0.0000
152 K A -1.2485
153 T A -0.3148
154 H A -0.1444
155 A A 0.0000
156 F A -0.0431
157 R A -1.4423
158 L A 0.0000
159 L A 0.0000
160 K A -1.5733
161 P A -0.5684
162 G A -0.2513
163 G A 0.0000
164 I A 0.0000
165 L A 0.0000
166 T A 0.0000
167 Y A 0.1315
168 C A 0.0000
169 N A -0.1982
170 L A 0.0000
171 T A -0.0193
172 S A -0.0276
173 W A 0.0000
174 G A -0.1882
175 E A -0.8073
176 L A 0.1352
177 M A -0.1587
178 K A -1.0305
179 S A -0.6798
180 K A -1.6343
181 Y A -0.2571
182 T A -0.2063
183 D A -1.0173
184 I A 0.0000
185 T A -0.0019
186 A A 0.1516
187 M A 0.6652
188 F A 0.0000
189 E A -1.5781
190 E A -2.0477
191 T A -0.3732
192 Q A 0.0408
193 V A 1.0880
194 P A 0.3258
195 A A 0.0227
196 L A 0.4477
197 L A 1.2556
198 E A -1.4149
199 A A -0.4692
200 G A -0.3309
201 F A 0.0000
202 Q A -1.5252
203 R A -2.1245
204 E A -0.8996
205 N A -1.2515
206 I A 0.2728
207 C A 0.4924
208 T A -0.1258
209 E A -0.6480
210 V A 1.6385
211 M A 0.5420
212 A A 0.1028
213 L A 0.5066
214 V A 1.7846
215 P A 0.0000
216 P A -0.2534
217 A A -0.3676
218 D A -1.7350
219 C A -0.3658
220 R A -1.7476
221 Y A -0.0867
222 Y A 0.2194
223 A A 0.0445
224 F A 0.0000
225 P A 0.0109
226 Q A -0.2283
227 M A 0.0000
228 I A 0.0000
229 T A 0.0000
230 P A 0.0000
231 L A 0.3176
232 V A 0.0000
233 T A 0.0000
234 K A -0.7117
235 H A -1.0989

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, -0.2657 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015