Analysis of interatomic Contacts of Structural Units in PDB entry:
8VDB

Contacts of Structural Units (CSU) are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332).
This page provides analyses of contacts formed by:

chains
helices
sheets
residues

For analysis of ligand-protein contacts, use:

LPC software

3D structure can be seen in additional window with STING software for 8VDB entry

There are 4 chains in PDB entry 8VDB (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	HIS 0	MET 325
B	HIS 0	MET 325
C	HIS 0	MET 325
D	MET 1	MET 325

There are 63 helices in PDB entry 8VDB. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	20	25	Right-handed alpha
Helix 2	AA2	A	30	38	Right-handed alpha
Helix 3	AA3	A	51	65	Right-handed alpha
Helix 4	AA4	A	90	100	Right-handed alpha
Helix 5	AA5	A	111	113	Right-handed 310
Helix 6	AA6	A	114	129	Right-handed alpha
Helix 7	AA7	A	144	147	Right-handed 310
Helix 8	AA8	A	185	189	Right-handed 310
Helix 9	AA9	A	214	224	Right-handed alpha
Helix 10	AB1	A	225	238	Right-handed alpha
Helix 11	AB2	A	240	244	Right-handed 310
Helix 12	AB3	A	253	264	Right-handed alpha
Helix 13	AB4	A	267	271	Right-handed 310
Helix 14	AB5	A	274	279	Right-handed alpha
Helix 15	AB6	A	281	283	Right-handed 310
Helix 16	AB7	A	284	296	Right-handed alpha
Helix 17	AB8	B	20	25	Right-handed alpha
Helix 18	AB9	B	30	39	Right-handed alpha
Helix 19	AC1	B	51	66	Right-handed alpha
Helix 20	AC2	B	90	100	Right-handed alpha
Helix 21	AC3	B	111	113	Right-handed 310
Helix 22	AC4	B	114	129	Right-handed alpha
Helix 23	AC5	B	144	147	Right-handed 310
Helix 24	AC6	B	151	156	Right-handed alpha
Helix 25	AC7	B	185	188	Right-handed 310
Helix 26	AC8	B	214	238	Right-handed alpha
Helix 27	AC9	B	240	244	Right-handed 310
Helix 28	AD1	B	253	264	Right-handed alpha
Helix 29	AD2	B	267	271	Right-handed 310
Helix 30	AD3	B	274	279	Right-handed alpha
Helix 31	AD4	B	281	283	Right-handed 310
Helix 32	AD5	B	284	296	Right-handed alpha
Helix 33	AD6	C	20	25	Right-handed alpha
Helix 34	AD7	C	30	38	Right-handed alpha
Helix 35	AD8	C	51	67	Right-handed alpha
Helix 36	AD9	C	90	100	Right-handed alpha
Helix 37	AE1	C	111	113	Right-handed 310
Helix 38	AE2	C	114	129	Right-handed alpha
Helix 39	AE3	C	144	147	Right-handed 310
Helix 40	AE4	C	151	156	Right-handed alpha
Helix 41	AE5	C	185	189	Right-handed 310
Helix 42	AE6	C	214	238	Right-handed alpha
Helix 43	AE7	C	240	244	Right-handed 310
Helix 44	AE8	C	253	264	Right-handed alpha
Helix 45	AE9	C	267	271	Right-handed 310
Helix 46	AF1	C	274	279	Right-handed alpha
Helix 47	AF2	C	281	283	Right-handed 310
Helix 48	AF3	C	284	296	Right-handed alpha
Helix 49	AF4	D	20	25	Right-handed alpha
Helix 50	AF5	D	30	38	Right-handed alpha
Helix 51	AF6	D	51	67	Right-handed alpha
Helix 52	AF7	D	90	100	Right-handed alpha
Helix 53	AF8	D	111	113	Right-handed 310
Helix 54	AF9	D	114	129	Right-handed alpha
Helix 55	AG1	D	144	147	Right-handed 310
Helix 56	AG2	D	185	189	Right-handed 310
Helix 57	AG3	D	214	237	Right-handed alpha
Helix 58	AG4	D	240	244	Right-handed 310
Helix 59	AG5	D	253	264	Right-handed alpha
Helix 60	AG6	D	267	271	Right-handed 310
Helix 61	AG7	D	274	279	Right-handed alpha
Helix 62	AG8	D	281	283	Right-handed 310
Helix 63	AG9	D	284	296	Right-handed alpha

There are 17 sheets in PDB entry 8VDB. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2, AB3, AB4, AB5, AB6, AB7, AB8,

There are 10 strands in AA1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	4	12	first strand
Strand 2	A	160	169	anti-parallel
Strand 3	A	134	142	anti-parallel
Strand 4	A	76	80	parallel
Strand 5	A	105	110	parallel
Strand 6	D	105	110	anti-parallel
Strand 7	D	76	80	parallel
Strand 8	D	134	142	parallel
Strand 9	D	160	169	anti-parallel
Strand 10	D	4	12	anti-parallel

Back to list of sheets
Back to top of page

There are 2 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	16	19	first strand
Strand 2	A	42	45	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AA3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	176	183	first strand
Strand 2	A	315	322	anti-parallel
Strand 3	A	304	311	anti-parallel
Strand 4	A	246	249	parallel

Back to list of sheets
Back to top of page

There are 3 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	212	213	first strand
Strand 2	A	191	194	anti-parallel
Strand 3	D	86	88	anti-parallel

Back to list of sheets
Back to top of page

There are 2 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	199	200	first strand
Strand 2	A	203	204	anti-parallel

Back to list of sheets
Back to top of page

There are 10 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	4	12	first strand
Strand 2	B	160	169	anti-parallel
Strand 3	B	134	142	anti-parallel
Strand 4	B	76	80	parallel
Strand 5	B	105	110	parallel
Strand 6	C	105	110	anti-parallel
Strand 7	C	76	80	parallel
Strand 8	C	134	142	parallel
Strand 9	C	160	169	anti-parallel
Strand 10	C	4	12	anti-parallel

Back to list of sheets
Back to top of page

There are 2 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	16	19	first strand
Strand 2	B	42	45	anti-parallel

Back to list of sheets
Back to top of page

There are 3 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	86	88	first strand
Strand 2	C	191	194	anti-parallel
Strand 3	C	211	213	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	176	183	first strand
Strand 2	B	315	322	anti-parallel
Strand 3	B	304	311	anti-parallel
Strand 4	B	246	249	parallel

Back to list of sheets
Back to top of page

There are 3 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	212	213	first strand
Strand 2	B	191	194	anti-parallel
Strand 3	C	86	88	anti-parallel

Back to list of sheets
Back to top of page

There are 2 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	199	200	first strand
Strand 2	B	203	204	anti-parallel

Back to list of sheets
Back to top of page

There are 2 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	16	19	first strand
Strand 2	C	42	45	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	176	183	first strand
Strand 2	C	315	322	anti-parallel
Strand 3	C	304	311	anti-parallel
Strand 4	C	246	249	parallel

Back to list of sheets
Back to top of page

There are 2 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	199	200	first strand
Strand 2	C	203	204	anti-parallel

Back to list of sheets
Back to top of page

There are 2 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	16	19	first strand
Strand 2	D	42	45	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	176	183	first strand
Strand 2	D	315	322	anti-parallel
Strand 3	D	304	311	anti-parallel
Strand 4	D	246	249	parallel

Back to list of sheets
Back to top of page

There are 2 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	191	192	first strand
Strand 2	D	212	213	anti-parallel

Back to list of sheets
Back to top of page

Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il

Analysis of interatomic Contacts of Structural Units in PDB entry: 8VDB

Analysis of interatomic Contacts of Structural Units in PDB entry:
8VDB