Aggrescan3D: aggreleb-B

Project name: aggreleb-B

Status: done

submitted: 2019-02-03 20:42:50, status changed: 2019-02-03 21:37:29

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Chain sequence(s)	G: LNCASGWSGYDQHCYKVFDKPKSWADAEKFCKKQTSGGHLVSFHSSEETDFVVKLVSQTLESQILWMGLSKVWNQCDWGWSNGAKLKYKAWAEESYCVYFSSTKKGWRSRACRLLGHFVCKSPA
Distance of aggregation	10 Å
Dynamic mode	Yes

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Show buried residues

Minimal score value: -3.8551
Maximal score value: 1.3321
Average score: -0.8236
Total score value: -102.1302

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
1	L	G	0.9708
2	N	G	-0.2668
3	C	G	0.0547
4	A	G	0.1212
5	S	G	-0.3706
6	G	G	0.0000
7	W	G	-0.1151
8	S	G	-0.5254
9	G	G	-0.8404
10	Y	G	-0.8785
11	D	G	-2.2043
12	Q	G	-2.0658
13	H	G	-1.2491
14	C	G	-0.7609
15	Y	G	0.0000
16	K	G	-0.7094
17	V	G	0.0000
18	F	G	-0.8063
19	D	G	-1.5850
20	K	G	-2.0903
21	P	G	-1.2392
22	K	G	-1.3687
23	S	G	-0.5459
24	W	G	-0.8200
25	A	G	-1.1196
26	D	G	-1.7441
27	A	G	0.0000
28	E	G	-2.8047
29	K	G	-3.3341
30	F	G	-2.6472
31	C	G	0.0000
32	K	G	-3.8551
33	K	G	-3.3796
34	Q	G	-2.3827
35	T	G	-2.1373
36	S	G	-1.3699
37	G	G	-1.5860
38	G	G	-2.1338
39	H	G	-1.8152
40	L	G	0.0000
41	V	G	0.0000
42	S	G	-0.4057
43	F	G	-0.3578
44	H	G	-0.9742
45	S	G	-1.2826
46	S	G	-1.6333
47	E	G	-2.2390
48	E	G	-1.5696
49	T	G	0.0000
50	D	G	-2.6748
51	F	G	-1.2153
52	V	G	0.0000
53	V	G	0.0000
54	K	G	-2.8747
55	L	G	0.0000
56	V	G	0.0000
57	S	G	-1.4442
58	Q	G	-1.5191
59	T	G	-0.6105
60	L	G	0.0347
61	E	G	-1.6421
62	S	G	-0.6860
63	Q	G	0.0000
64	I	G	0.5496
65	L	G	0.0000
66	W	G	0.0000
67	M	G	0.0000
68	G	G	-0.4370
69	L	G	-0.2055
70	S	G	-0.3654
71	K	G	0.0010
72	V	G	1.3321
73	W	G	1.0179
74	N	G	-1.0602
75	Q	G	-1.0318
76	C	G	-0.3526
77	D	G	-1.4692
78	W	G	0.1887
79	G	G	-0.3646
80	W	G	0.4407
81	S	G	-0.3697
82	N	G	-1.4273
83	G	G	-1.0792
84	A	G	-0.7279
85	K	G	-1.4022
86	L	G	0.2703
87	K	G	-1.1569
88	Y	G	0.1807
89	K	G	-1.2264
90	A	G	-0.1323
91	W	G	0.4084
92	A	G	-0.4314
93	E	G	-2.1776
94	E	G	-1.2383
95	S	G	-0.7048
96	Y	G	0.0000
97	C	G	0.0000
98	V	G	0.0000
99	Y	G	0.0000
100	F	G	0.0000
101	S	G	-0.4668
102	S	G	-1.3848
103	T	G	-1.9198
104	K	G	-2.6726
105	K	G	-2.7921
106	G	G	-1.1995
107	W	G	-0.1434
108	R	G	-0.9264
109	S	G	-1.0227
110	R	G	-1.4605
111	A	G	-1.1374
112	C	G	0.0000
113	R	G	-1.5535
114	L	G	0.2948
115	L	G	0.0000
116	G	G	-0.3981
117	H	G	-0.8558
118	F	G	0.0000
119	V	G	0.0000
120	C	G	0.0000
121	K	G	0.0000
122	S	G	-0.9272
123	P	G	-1.0695
124	A	G	-0.8255

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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, -0.8236 in this case) is selected and presented in A3D results.