Project name: dpagg

Status: done

submitted: 2021-09-08 20:40:51, status changed: 2021-09-08 23:16:28
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Chain sequence(s) C: SKYEYVKLFEKENYLLPDTYIIIRVDGKGFHKFSQFYEFEKPNDLKALQVMNSAAEKLMSKYSDVMLAYGDSDEYSFLLRKNCQLYERREMKLTTLFSSLMSTYYMYFWSQYFPDKPLHIDHLPNFDARAVLYPDFKHIRNYFSWRQVDCHINNLYNTTFWNLVLKLKMTPQQAEQRLMGTVASDKNEILFKECGVNYNNESEMYKKGTIIVREFENYETEDEAELSKRQVQRLEKKRKKAELKIYHVDIINDDSWWKSRPWLKD
Distance of aggregation 5 Å
Dynamic mode Yes
Show buried residues
Minimal score value
-2.4518
Maximal score value
1.9499
Average score
-0.3297
Total score value
-87.3816

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
4 S C -0.5161
5 K C -1.4885
6 Y C 0.6476
7 E C -1.3151
8 Y C 1.4026
9 V C 1.8265
10 K C -0.4311
11 L C 1.2440
12 F C 1.7551
13 E C -1.6467
14 K C -1.9188
15 E C -0.4693
16 N C -0.4055
17 Y C 1.3404
18 L C 1.2041
19 L C 1.6314
20 P C -0.3152
21 D C -1.8382
22 T C -0.3088
23 Y C 0.1793
24 I C 0.0000
25 I C 0.0000
26 I C 0.0000
27 R C -0.2871
28 V C 0.0000
29 D C -0.2705
30 G C -0.4794
31 K C -1.8546
32 G C -0.3632
33 F C 0.0000
34 H C -0.7367
35 K C -1.3867
36 F C 0.0000
37 S C 0.0000
38 Q C -0.4128
39 F C 1.1694
40 Y C 0.4027
41 E C -1.6455
42 F C -0.3592
43 E C -1.6511
44 K C -1.9197
45 P C -0.6068
46 N C -1.4623
47 D C -0.2544
48 L C 0.2872
49 K C -1.7125
50 A C 0.0000
51 L C 0.0000
52 Q C -1.3851
53 V C 0.0000
54 M C 0.0000
55 N C -0.2253
56 S C -0.1702
57 A C 0.0000
58 A C 0.0000
59 E C -1.0749
60 K C -1.4496
61 L C 0.0000
62 M C 0.0000
63 S C -0.5314
64 K C -1.7399
65 Y C 0.0000
66 S C -0.0778
67 D C -0.2012
68 V C 0.0000
69 M C 0.0000
70 L C 0.0000
71 A C 0.0000
72 Y C 0.0000
73 G C 0.0000
74 D C 0.0000
75 S C 0.0000
76 D C -0.3644
77 E C 0.0000
78 Y C 0.0000
79 S C 0.0000
80 F C 0.0000
81 L C 0.0000
82 L C 0.0000
83 R C -0.4994
84 K C -1.6344
85 N C 0.0000
86 C C 0.4644
87 Q C -1.0462
88 L C 0.0644
89 Y C 0.0000
90 E C -2.1817
91 R C -2.2547
92 R C -0.6823
93 E C 0.0000
94 M C 0.1325
95 K C -1.5911
96 L C -0.1424
97 T C 0.0000
98 T C 0.2080
99 L C 1.5799
100 F C 0.5732
101 S C 0.0258
102 S C -0.1385
103 L C 0.4331
104 M C 0.0000
105 S C -0.0456
106 T C 0.0195
107 Y C 0.3262
108 Y C 0.0000
109 M C 0.5318
110 Y C 1.3809
111 F C 0.2764
112 W C 0.0000
113 S C -0.2261
114 Q C -1.0415
115 Y C 0.6533
116 F C 0.0000
117 P C -0.6254
118 D C -1.9149
119 K C -0.8357
120 P C -0.2698
121 L C 0.1218
122 H C -0.6398
123 I C 0.9477
124 D C -1.5958
125 H C -0.7472
126 L C 0.0000
127 P C -0.2847
128 N C -1.4024
129 F C -0.0943
130 D C -0.4900
131 A C -0.2818
132 R C -1.0665
133 A C -0.0962
134 V C 0.6337
135 L C 1.2970
136 Y C 0.5764
137 P C -0.3831
138 D C -1.0751
139 F C 0.3448
140 K C -1.7212
141 H C -1.3857
142 I C 0.0000
143 R C -1.4980
144 N C -1.4809
145 Y C -0.0912
146 F C 0.0000
147 S C 0.1406
148 W C 1.2800
149 R C 0.0000
150 Q C -0.0049
151 V C 0.8804
152 D C 0.0000
153 C C 0.0000
154 H C -0.2001
155 I C 0.4397
156 N C 0.0000
157 N C -0.0937
158 L C 0.4856
159 Y C 0.2186
160 N C -0.1529
161 T C 0.0023
162 T C 0.0000
163 F C 0.2612
164 W C 0.2976
165 N C -0.0578
166 L C 0.1850
167 V C 0.7433
168 L C 1.4558
169 K C -0.9196
170 L C 0.9492
171 K C -1.3157
172 M C 0.3619
173 T C 0.0692
174 P C -0.3322
175 Q C -1.4278
176 Q C -1.4088
177 A C 0.0000
178 E C -1.3213
179 Q C -1.7206
180 R C -1.9286
181 L C 0.0000
182 M C 0.9710
183 G C -0.2827
184 T C 0.2384
185 V C 1.7702
186 A C 0.0000
187 S C -0.4025
188 D C -1.1412
189 K C -0.3405
190 N C -0.8973
191 E C -1.4170
192 I C 1.6486
193 L C 0.0000
194 F C 0.5171
195 K C -1.7479
196 E C -1.4290
197 C C -0.0676
198 G C -0.1150
199 V C 1.4750
200 N C -0.6957
201 Y C 0.9444
202 N C -0.7413
203 N C -1.7567
204 E C -2.0654
205 S C -0.7320
206 E C -1.8724
207 M C -0.0312
208 Y C 0.2550
209 K C -0.9699
210 K C -0.5001
211 G C 0.0000
212 T C -0.0104
213 I C 0.0000
214 I C 0.0000
215 V C 0.0000
216 R C 0.0000
217 E C 0.0000
218 F C 0.0000
219 E C -1.8991
220 N C -0.7987
221 Y C 0.0000
222 E C -0.3202
223 T C -0.4558
224 E C -1.9857
225 D C -1.4930
226 E C -1.9602
227 A C -0.5864
228 E C -1.5097
229 L C 1.1607
230 S C -0.1757
231 K C -2.0624
232 R C -2.4518
233 Q C -1.2230
234 V C 0.5673
235 Q C -1.3389
236 R C -1.8818
237 L C 0.1662
238 E C -1.0559
239 K C -2.0596
240 K C -1.8135
241 R C -0.9557
242 K C -2.0857
243 K C -2.1483
244 A C -0.6457
245 E C -1.5200
246 L C 1.0944
247 K C 0.1582
248 I C 1.9499
249 Y C 0.4625
250 H C -0.3697
251 V C 1.4776
252 D C -0.0936
253 I C 0.2269
254 I C 0.2110
255 N C -1.2870
256 D C -1.0605
257 D C -1.9174
258 S C -0.4895
259 W C 0.2292
260 W C -0.0565
261 K C -1.7438
262 S C -0.5565
263 R C -0.5198
264 P C -0.1021
265 W C 0.0000
266 L C 0.0000
267 K C -1.8368
268 D C -1.0577

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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, -0.3297 in this case) is selected and presented in A3D results.


 
Laboratory of Theory of Biopolymers 2015