Project name: mutate1bis

Status: done

submitted: 2017-03-15 22:04:22, status changed: 2017-03-16 00:36:29
Settings
Chain sequence(s) A: TPIFAPGENCSPAWGAAPAAYDAADTHLRILGKPVMERWETPYMHALAAAASSKGGRVLEVGFGMAIAASKVQEAPIDEHWIIECNDGVFQRLRDWAPRQTHKVIPLKGLWEDVAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKNHAFRLLKPGGVLTYCNLTSWGELMKSKYSDITDMFEETQVPALLEAGFRRENIRTEVMANSPPADCRYYAFPQMITPLVTKG
Distance of aggregation 5 Å
Dynamic mode Yes
Show buried residues

Minimal score value
-2.3543
Maximal score value
2.1917
Average score
-0.3067
Total score value
-70.54

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 -0.1174
8 P A 0.0980
9 I A 2.1917
10 F A 1.5520
11 A A 0.2165
12 P A -0.1574
13 G A -0.6571
14 E A -2.0953
15 N A -1.6394
16 C A 0.0000
17 S A -0.5011
18 P A -0.3103
19 A A 0.0226
20 W A 0.1131
21 G A -0.4481
22 A A -0.0197
23 A A -0.0123
24 P A -0.2525
25 A A -0.0315
26 A A 0.0742
27 Y A 0.0115
28 D A -0.8015
29 A A -0.0928
30 A A -0.0001
31 D A -0.3521
32 T A 0.0000
33 H A -0.2185
34 L A 0.0000
35 R A -1.8717
36 I A 0.0000
37 L A 1.4661
38 G A -0.2441
39 K A -0.4028
40 P A -0.5036
41 V A 0.0000
42 M A 0.0000
43 E A -1.0048
44 R A 0.0000
45 W A 0.4016
46 E A 0.0000
47 T A -0.0493
48 P A -0.0995
49 Y A 0.0000
50 M A 0.0000
51 H A -0.5063
52 A A -0.0577
53 L A 0.0000
54 A A 0.0000
55 A A 0.0461
56 A A 0.0257
57 A A 0.0000
58 S A -0.0904
59 S A -0.5458
60 K A -1.7594
61 G A -0.4260
62 G A -0.4263
63 R A -0.9477
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 0.0000
71 M A 0.0000
72 A A 0.0793
73 I A 0.3765
74 A A 0.0790
75 A A -0.0156
76 S A -0.1832
77 K A -0.3295
78 V A 0.0000
79 Q A -0.5317
80 E A -1.8439
81 A A -0.4016
82 P A -0.2689
83 I A 0.0000
84 D A -1.8416
85 E A -0.7152
86 H A 0.0000
87 W A 0.1975
88 I A 0.0000
89 I A 0.0000
90 E A 0.0000
91 C A 0.2719
92 N A 0.0000
93 D A -1.8264
94 G A -0.5319
95 V A 0.0000
96 F A 0.0000
97 Q A -1.4959
98 R A -1.0840
99 L A 0.0000
100 R A -1.7268
101 D A -1.0683
102 W A 0.1057
103 A A 0.0000
104 P A -0.6043
105 R A -1.9953
106 Q A -0.9096
107 T A -0.2336
108 H A -0.6389
109 K A -1.6745
110 V A 0.2295
111 I A 0.6626
112 P A 0.0532
113 L A -0.1157
114 K A -1.6971
115 G A -0.4843
116 L A 0.1798
117 W A 0.0000
118 E A -2.1290
119 D A -2.1038
120 V A 0.0000
121 A A -0.0362
122 P A -0.2656
123 T A -0.0764
124 L A 0.1418
125 P A -0.5457
126 D A -1.8738
127 G A -0.6752
128 H A -0.4917
129 F A 0.0000
130 D A -0.2431
131 G A -0.1027
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 -0.0375
139 L A 0.0000
140 S A -0.3578
141 E A -1.0877
142 E A -1.9589
143 T A -0.4536
144 W A 0.0000
145 H A -0.1497
146 T A -0.0812
147 H A 0.0000
148 Q A 0.0000
149 F A 0.7710
150 N A -0.6145
151 F A 0.0000
152 I A 0.0000
153 K A -1.7927
154 N A -0.9078
155 H A -0.5925
156 A A 0.0000
157 F A 0.4535
158 R A -0.9963
159 L A 0.0000
160 L A 0.0000
161 K A -0.6254
162 P A -0.4813
163 G A -0.5276
164 G A 0.0000
165 V A 0.3778
166 L A 0.0000
167 T A 0.0000
168 Y A 0.0000
169 C A 0.0000
170 N A 0.0000
171 L A 0.0000
172 T A -0.0088
173 S A 0.0000
174 W A 0.0000
175 G A 0.0000
176 E A -0.6157
177 L A 0.0877
178 M A 0.0000
179 K A -1.7331
180 S A -0.7775
181 K A -1.4959
182 Y A 0.9835
183 S A -0.2010
184 D A -1.9542
185 I A 0.0000
186 T A -0.2540
187 D A -1.4143
188 M A 0.1508
189 F A 0.0000
190 E A -0.8222
191 E A -1.8529
192 T A -0.4254
193 Q A 0.0000
194 V A 0.1687
195 P A -0.1792
196 A A 0.0000
197 L A 0.0000
198 L A 0.9988
199 E A -1.3874
200 A A -0.5585
201 G A -0.0528
202 F A 0.0000
203 R A -2.1038
204 R A -2.3543
205 E A -1.5987
206 N A -0.4545
207 I A 0.1082
208 R A -0.7742
209 T A -0.4111
210 E A -0.9326
211 V A 1.2757
212 M A 0.4316
213 A A -0.0151
214 N A -0.5832
215 S A -0.3679
216 P A -0.1594
217 P A -0.1343
218 A A -0.3113
219 D A -1.6372
220 C A 0.2522
221 R A -0.4725
222 Y A 0.8077
223 Y A 0.0000
224 A A 0.0212
225 F A 0.0000
226 P A -0.3779
227 Q A -0.5705
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 -0.0217
235 K A -0.3527
236 G A -0.5905

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, -0.3067 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015