Aggrescan3D: Check 2

Project name: Check 2

Status: done

submitted: 2019-03-20 00:12:07, status changed: 2019-03-20 02:34:26

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Chain sequence(s)	N: SELTQDPAVSVALGQTVRVTCQGDSLRSYYASWYQQKPGQAPVLVIYGKNNRPSGIPDRFSGSSSGNTASLTITGAQAEDEADYYCSSRDSSGNHWVFGGGTELTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT
Distance of aggregation	10 Å
Dynamic mode	Yes

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Show buried residues

Minimal score value: -3.5695
Maximal score value: 2.7276
Average score: -0.7862
Total score value: -165.0942

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
2	S	N	-2.2015
3	E	N	-2.1571
4	L	N	0.0000
5	T	N	-1.4800
6	Q	N	0.0000
7	D	N	-2.2501
8	P	N	-1.4418
9	A	N	-1.0662
10	V	N	-0.4420
11	S	N	-0.0838
12	V	N	-0.0646
13	A	N	0.2876
14	L	N	0.7204
15	G	N	-0.4028
16	Q	N	-1.2560
17	T	N	-1.1140
18	V	N	0.0000
19	R	N	-1.5388
20	V	N	0.0000
21	T	N	-0.9526
22	C	N	0.0000
23	Q	N	-2.4829
24	G	N	0.0000
25	D	N	-3.1011
26	S	N	-2.2682
27	L	N	-2.0646
28	R	N	-2.3200
29	S	N	-1.1150
30	Y	N	-1.0371
31	Y	N	-0.2240
32	A	N	0.0000
33	S	N	1.1731
34	W	N	0.0000
35	Y	N	1.5999
36	Q	N	0.0000
37	Q	N	-0.7531
38	K	N	-1.2597
39	P	N	-1.2675
40	G	N	-1.2966
41	Q	N	-1.2594
42	A	N	-0.2861
43	P	N	0.5362
44	V	N	1.9644
45	L	N	2.5482
46	V	N	0.0000
47	I	N	0.9864
48	Y	N	0.0000
49	G	N	-1.2221
50	K	N	-2.7677
51	N	N	-2.5909
52	N	N	-2.1053
53	R	N	-2.5186
54	P	N	-0.9245
55	S	N	-0.7796
56	G	N	-0.2665
57	I	N	1.0180
58	P	N	0.1348
59	D	N	-0.6511
60	R	N	-0.9163
61	F	N	-0.4174
62	S	N	0.0000
63	G	N	0.0000
64	S	N	-1.1905
65	S	N	-1.5637
66	S	N	-1.3923
67	G	N	-1.8867
68	N	N	-2.6707
69	T	N	-1.5115
70	A	N	0.0000
71	S	N	0.0000
72	L	N	0.0000
73	T	N	-0.8179
74	I	N	0.0000
75	T	N	-0.7466
76	G	N	-0.8273
77	A	N	-0.8662
78	Q	N	-1.2590
79	A	N	-1.1540
80	E	N	-1.2772
81	D	N	-1.2668
82	E	N	-1.5085
83	A	N	0.0000
84	D	N	-1.7208
85	Y	N	0.0000
86	Y	N	0.7249
87	C	N	0.0000
88	S	N	0.0000
89	S	N	0.0000
90	R	N	-0.4525
91	D	N	-1.2300
92	S	N	-1.2967
93	S	N	-1.3650
94	G	N	-1.4555
95	N	N	-2.0837
96	H	N	-1.1906
97	W	N	1.2450
98	V	N	2.4001
99	F	N	2.7276
100	G	N	0.6288
101	G	N	0.7971
102	G	N	-0.7885
103	T	N	0.0000
104	E	N	-2.4360
105	L	N	0.0000
106	T	N	-0.8582
107	V	N	0.0000
108	L	N	-0.3541
109	G	N	0.0000
110	Q	N	-1.7020
111	P	N	-1.6565
112	K	N	-2.0145
113	A	N	-1.2092
114	A	N	-0.6856
115	P	N	-0.6364
116	S	N	-0.1290
117	V	N	0.2572
118	T	N	0.7171
119	L	N	1.2712
120	F	N	1.7643
121	P	N	0.4643
122	P	N	-0.8812
123	S	N	-1.2466
124	S	N	-1.8894
125	E	N	-2.8389
126	E	N	-2.5155
127	L	N	-1.8430
128	Q	N	-2.2703
129	A	N	-1.9490
130	N	N	-2.7435
131	K	N	-3.0067
132	A	N	0.0000
133	T	N	-0.1402
134	L	N	0.0000
135	V	N	0.9850
136	C	N	0.0000
137	L	N	1.0810
138	I	N	0.0000
139	S	N	-0.6821
140	D	N	-1.6763
141	F	N	0.0000
142	Y	N	-1.0923
143	P	N	-0.8054
144	G	N	-0.5625
145	A	N	-0.3293
146	V	N	-0.0867
147	T	N	-0.0362
148	V	N	0.3032
149	A	N	-0.6469
150	W	N	0.0000
151	K	N	-2.4031
152	A	N	0.0000
153	D	N	-2.7866
154	S	N	-1.4893
155	S	N	-1.1335
156	P	N	-1.1844
157	V	N	-0.6237
158	K	N	-1.4672
159	A	N	-0.9476
160	G	N	-0.7931
161	V	N	-0.7188
162	E	N	-1.4863
163	T	N	-0.6748
164	T	N	-0.5044
165	T	N	-0.5653
166	P	N	-0.3883
167	S	N	-0.8260
168	K	N	0.0000
169	Q	N	-1.6458
170	S	N	-1.4251
171	N	N	-1.9708
172	N	N	-1.8438
173	K	N	-2.1271
174	Y	N	-1.0617
175	A	N	-0.6285
176	A	N	0.0000
177	S	N	0.0014
178	S	N	0.0000
179	Y	N	0.4226
180	L	N	0.0000
181	S	N	-0.5115
182	L	N	0.0000
183	T	N	-2.0554
184	P	N	-2.6477
185	E	N	-3.5695
186	Q	N	-3.0064
187	W	N	-2.7563
188	K	N	-3.5085
189	S	N	-2.6599
190	H	N	-2.8396
191	R	N	-3.2604
192	S	N	-2.0105
193	Y	N	0.0000
194	S	N	-1.3820
195	C	N	0.0000
196	Q	N	0.0000
197	V	N	0.0000
198	T	N	-0.6725
199	H	N	0.0000
200	E	N	-2.0102
201	G	N	-1.3944
202	S	N	-0.9993
203	T	N	-0.8772
204	V	N	-0.6258
205	E	N	-1.8062
206	K	N	0.0000
207	T	N	-0.4679
208	V	N	0.1240
209	A	N	-0.4148
210	P	N	-0.8628
211	T	N	-0.1517

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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, -0.7862 in this case) is selected and presented in A3D results.