Project name: Model1

Status: done

submitted: 2017-03-14 12:02:00, status changed: 2017-03-14 14:37:31
Settings
Chain sequence(s) A: TPIFAPGENCSPAWGAAPAAYDAADTHLRILGKPVMERWETPYMHALAAAASSKGGRVLEVGFGMAIAASKVQEAPIDEHWIIECNDGVFQRLRDWAPRQTHKVIPLKGLWEDVAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKNHAFRLLKPGGVLTYCNLTSWGELMKSKYSDITIMFEETQVPALLEAGFRRENIRTEVMALVPPADCRYYAFPQMITPLVTKG
Distance of aggregation 5 Å
Dynamic mode Yes
Show buried residues

Minimal score value
-2.1752
Maximal score value
2.01
Average score
-0.2595
Total score value
-59.6833

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 -0.1111
8 P A -0.1798
9 I A 0.2905
10 F A 0.2831
11 A A 0.0458
12 P A -0.2817
13 G A -0.3777
14 E A -1.0960
15 N A -1.4319
16 C A 0.0000
17 S A -0.0894
18 P A -0.2551
19 A A -0.0045
20 W A 0.0000
21 G A -0.2060
22 A A 0.0185
23 A A 0.0000
24 P A -0.2549
25 A A 0.0000
26 A A 0.0754
27 Y A -0.0359
28 D A -0.9497
29 A A -0.2079
30 A A -0.0140
31 D A -0.4247
32 T A -0.1026
33 H A -0.3145
34 L A 0.0000
35 R A -1.2673
36 I A 0.0000
37 L A 1.4665
38 G A -0.2310
39 K A -0.2795
40 P A -0.0557
41 V A 0.1957
42 M A 0.0000
43 E A -1.2248
44 R A -1.9766
45 W A -0.4993
46 E A -1.7955
47 T A -0.3041
48 P A -0.0260
49 Y A 0.0000
50 M A 0.0000
51 H A -0.7080
52 A A -0.1283
53 L A 0.0000
54 A A 0.0000
55 A A 0.0332
56 A A 0.0077
57 A A 0.0000
58 S A -0.2699
59 S A -0.5449
60 K A -1.7562
61 G A -0.3975
62 G A -0.2443
63 R A -0.8839
64 V A 0.0000
65 L A 0.0000
66 E A 0.0000
67 V A 0.0000
68 G A 0.0000
69 F A 0.0000
70 G A -0.0849
71 M A 0.0000
72 A A 0.0823
73 I A 0.4145
74 A A 0.0000
75 A A -0.0189
76 S A -0.2996
77 K A -0.6827
78 V A 0.0000
79 Q A -1.3825
80 E A -2.0441
81 A A -0.5062
82 P A -0.2527
83 I A 0.0000
84 D A -1.8985
85 E A -0.9657
86 H A -0.2592
87 W A 0.0000
88 I A 0.0000
89 I A 0.0000
90 E A 0.0000
91 C A 0.1256
92 N A 0.0000
93 D A -0.7019
94 G A -0.3303
95 V A 0.0000
96 F A -0.0113
97 Q A -1.1981
98 R A -0.4298
99 L A -0.1554
100 R A -1.8511
101 D A -1.6426
102 W A 0.2038
103 A A 0.0000
104 P A -0.6168
105 R A -1.9484
106 Q A -0.7092
107 T A -0.3147
108 H A -1.3203
109 K A -1.8173
110 V A 0.0942
111 I A 0.4979
112 P A -0.0325
113 L A 0.0199
114 K A -1.1510
115 G A -0.1187
116 L A 1.4465
117 W A 0.3929
118 E A -0.5512
119 D A -0.8599
120 V A 0.0000
121 A A 0.0000
122 P A -0.0850
123 T A -0.0405
124 L A 0.1935
125 P A -0.4992
126 D A -1.8393
127 G A -0.4579
128 H A -0.2206
129 F A 0.0000
130 D A 0.0000
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 0.0000
139 L A 0.0000
140 S A -0.6137
141 E A -2.1752
142 E A -2.1713
143 T A -0.3709
144 W A 0.0000
145 H A -1.0026
146 T A -0.2484
147 H A 0.0000
148 Q A 0.0000
149 F A 0.8623
150 N A -0.3111
151 F A 0.0000
152 I A 0.0000
153 K A -1.8681
154 N A -1.0296
155 H A 0.0000
156 A A 0.0000
157 F A 1.8319
158 R A -0.2245
159 L A 0.0000
160 L A 0.0000
161 K A -1.4842
162 P A -0.5893
163 G A -0.5564
164 G A 0.0000
165 V A 0.4063
166 L A 0.0000
167 T A 0.0000
168 Y A 0.0000
169 C A 0.0000
170 N A -0.1085
171 L A 0.1414
172 T A 0.0000
173 S A -0.0723
174 W A 0.0000
175 G A 0.0000
176 E A -0.6180
177 L A 0.2393
178 M A 0.0000
179 K A -1.7905
180 S A -0.8415
181 K A -1.4971
182 Y A 0.9063
183 S A -0.0480
184 D A -0.3370
185 I A 0.0000
186 T A 0.3664
187 I A 2.0100
188 M A 0.9121
189 F A 0.0000
190 E A -0.9724
191 E A -1.9678
192 T A -0.4187
193 Q A 0.0000
194 V A 0.0817
195 P A 0.0512
196 A A 0.0000
197 L A 0.0000
198 L A 1.2073
199 E A -1.5397
200 A A -0.3164
201 G A -0.2734
202 F A 0.0000
203 R A -2.0989
204 R A -1.8430
205 E A -0.7156
206 N A -1.1822
207 I A 0.1441
208 R A -1.7195
209 T A -0.4742
210 E A -0.2199
211 V A 1.7103
212 M A 0.6251
213 A A 0.3575
214 L A 1.8309
215 V A 1.7087
216 P A 0.0000
217 P A -0.0867
218 A A -0.1113
219 D A -0.4230
220 C A 0.2828
221 R A -1.6755
222 Y A -0.1076
223 Y A 0.0000
224 A A 0.0202
225 F A 0.0000
226 P A -0.1308
227 Q A -0.3038
228 M A 0.0000
229 I A 0.0000
230 T A 0.0000
231 P A 0.0000
232 L A 0.0000
233 V A 0.0000
234 T A 0.0134
235 K A 0.0000
236 G A -0.5132

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, -0.2595 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015