Analysis of interatomic Contacts of Structural Units in PDB entry:
9VDW

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 9VDW entry

There are 4 chains in PDB entry 9VDW (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	MET 1	ARG 544
B	MET 1	ARG 544
C	LEU 2	ARG 544
D	MET 1	ARG 544

There are 82 helices in PDB entry 9VDW. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	103	107	Right-handed 310
Helix 2	AA2	A	119	123	Right-handed 310
Helix 3	AA3	A	129	133	Right-handed 310
Helix 4	AA4	A	163	170	Right-handed alpha
Helix 5	AA5	A	170	178	Right-handed alpha
Helix 6	AA6	A	205	208	Right-handed 310
Helix 7	AA7	A	209	224	Right-handed alpha
Helix 8	AA8	A	258	264	Right-handed alpha
Helix 9	AA9	A	294	304	Right-handed alpha
Helix 10	AB1	A	317	322	Right-handed alpha
Helix 11	AB2	A	335	345	Right-handed alpha
Helix 12	AB3	A	356	370	Right-handed alpha
Helix 13	AB4	A	372	379	Right-handed alpha
Helix 14	AB5	A	390	396	Right-handed alpha
Helix 15	AB6	A	397	400	Right-handed 310
Helix 16	AB7	A	401	412	Right-handed alpha
Helix 17	AB8	A	421	425	Right-handed 310
Helix 18	AB9	A	441	445	Right-handed 310
Helix 19	AC1	A	446	463	Right-handed alpha
Helix 20	AC2	A	464	469	Right-handed alpha
Helix 21	AC3	A	509	513	Right-handed 310
Helix 22	AC4	B	103	107	Right-handed 310
Helix 23	AC5	B	119	123	Right-handed 310
Helix 24	AC6	B	129	133	Right-handed 310
Helix 25	AC7	B	163	170	Right-handed alpha
Helix 26	AC8	B	170	178	Right-handed alpha
Helix 27	AC9	B	205	208	Right-handed 310
Helix 28	AD1	B	209	224	Right-handed alpha
Helix 29	AD2	B	258	264	Right-handed alpha
Helix 30	AD3	B	292	304	Right-handed alpha
Helix 31	AD4	B	317	323	Right-handed alpha
Helix 32	AD5	B	335	345	Right-handed alpha
Helix 33	AD6	B	356	369	Right-handed alpha
Helix 34	AD7	B	372	379	Right-handed alpha
Helix 35	AD8	B	390	396	Right-handed alpha
Helix 36	AD9	B	397	400	Right-handed 310
Helix 37	AE1	B	401	412	Right-handed alpha
Helix 38	AE2	B	421	425	Right-handed 310
Helix 39	AE3	B	446	463	Right-handed alpha
Helix 40	AE4	B	464	469	Right-handed alpha
Helix 41	AE5	B	509	513	Right-handed 310
Helix 42	AE6	C	103	107	Right-handed 310
Helix 43	AE7	C	117	123	Right-handed 310
Helix 44	AE8	C	129	133	Right-handed 310
Helix 45	AE9	C	163	170	Right-handed alpha
Helix 46	AF1	C	170	178	Right-handed alpha
Helix 47	AF2	C	205	208	Right-handed 310
Helix 48	AF3	C	209	224	Right-handed alpha
Helix 49	AF4	C	258	264	Right-handed alpha
Helix 50	AF5	C	292	304	Right-handed alpha
Helix 51	AF6	C	317	323	Right-handed alpha
Helix 52	AF7	C	335	345	Right-handed alpha
Helix 53	AF8	C	356	369	Right-handed alpha
Helix 54	AF9	C	372	379	Right-handed alpha
Helix 55	AG1	C	390	395	Right-handed alpha
Helix 56	AG2	C	396	400	Right-handed 310
Helix 57	AG3	C	401	412	Right-handed alpha
Helix 58	AG4	C	421	425	Right-handed 310
Helix 59	AG5	C	446	463	Right-handed alpha
Helix 60	AG6	C	464	469	Right-handed alpha
Helix 61	AG7	C	509	513	Right-handed 310
Helix 62	AG8	D	103	107	Right-handed 310
Helix 63	AG9	D	119	123	Right-handed 310
Helix 64	AH1	D	129	133	Right-handed 310
Helix 65	AH2	D	163	170	Right-handed alpha
Helix 66	AH3	D	170	178	Right-handed alpha
Helix 67	AH4	D	205	208	Right-handed 310
Helix 68	AH5	D	209	224	Right-handed alpha
Helix 69	AH6	D	258	264	Right-handed alpha
Helix 70	AH7	D	292	304	Right-handed alpha
Helix 71	AH8	D	317	323	Right-handed alpha
Helix 72	AH9	D	335	345	Right-handed alpha
Helix 73	AI1	D	356	369	Right-handed alpha
Helix 74	AI2	D	372	377	Right-handed alpha
Helix 75	AI3	D	390	396	Right-handed alpha
Helix 76	AI4	D	397	400	Right-handed 310
Helix 77	AI5	D	401	412	Right-handed alpha
Helix 78	AI6	D	421	425	Right-handed 310
Helix 79	AI7	D	441	445	Right-handed 310
Helix 80	AI8	D	446	463	Right-handed alpha
Helix 81	AI9	D	464	469	Right-handed alpha
Helix 82	AJ1	D	509	513	Right-handed 310

There are 28 sheets in PDB entry 9VDW. 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, AB9, AC1, AC2, AC3, AC4, AC5, AC6, AC7, AC8, AC9, AD1,

There are 3 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	3	5	first strand
Strand 2	A	19	27	anti-parallel
Strand 3	A	13	16	anti-parallel

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There are 4 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	3	5	first strand
Strand 2	A	19	27	anti-parallel
Strand 3	A	62	69	anti-parallel
Strand 4	A	51	52	anti-parallel

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There are 5 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	46	49	first strand
Strand 2	A	34	39	anti-parallel
Strand 3	A	76	84	anti-parallel
Strand 4	A	89	93	anti-parallel
Strand 5	A	96	98	anti-parallel

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There are 4 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	46	49	first strand
Strand 2	A	34	39	anti-parallel
Strand 3	A	76	84	anti-parallel
Strand 4	A	108	111	anti-parallel

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There are 9 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	125	128	first strand
Strand 2	A	181	184	parallel
Strand 3	A	227	231	parallel
Strand 4	A	271	274	parallel
Strand 5	A	308	313	parallel
Strand 6	A	328	331	parallel
Strand 7	A	380	381	parallel
Strand 8	A	415	419	parallel
Strand 9	A	125	128	parallel

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There are 5 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	470	477	first strand
Strand 2	A	480	487	anti-parallel
Strand 3	A	490	497	anti-parallel
Strand 4	A	537	543	anti-parallel
Strand 5	A	517	521	anti-parallel

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There are 3 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	502	505	first strand
Strand 2	A	530	533	anti-parallel
Strand 3	A	525	527	anti-parallel

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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	2	5	first strand
Strand 2	B	19	28	anti-parallel
Strand 3	B	13	16	anti-parallel

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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	2	5	first strand
Strand 2	B	19	28	anti-parallel
Strand 3	B	62	69	anti-parallel
Strand 4	B	51	52	anti-parallel

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There are 5 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	46	49	first strand
Strand 2	B	34	40	anti-parallel
Strand 3	B	76	84	anti-parallel
Strand 4	B	89	93	anti-parallel
Strand 5	B	96	98	anti-parallel

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There are 4 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	46	49	first strand
Strand 2	B	34	40	anti-parallel
Strand 3	B	76	84	anti-parallel
Strand 4	B	108	111	anti-parallel

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There are 8 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	328	329	first strand
Strand 2	B	308	311	parallel
Strand 3	B	271	274	parallel
Strand 4	B	227	231	parallel
Strand 5	B	181	184	parallel
Strand 6	B	125	128	parallel
Strand 7	B	415	419	parallel
Strand 8	B	380	381	parallel

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There are 5 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	470	477	first strand
Strand 2	B	480	487	anti-parallel
Strand 3	B	490	497	anti-parallel
Strand 4	B	537	543	anti-parallel
Strand 5	B	517	521	anti-parallel

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There are 3 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	502	505	first strand
Strand 2	B	530	533	anti-parallel
Strand 3	B	525	527	anti-parallel

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There are 3 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	3	5	first strand
Strand 2	C	19	27	anti-parallel
Strand 3	C	13	16	anti-parallel

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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	C	3	5	first strand
Strand 2	C	19	27	anti-parallel
Strand 3	C	62	69	anti-parallel
Strand 4	C	51	52	anti-parallel

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There are 5 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	46	49	first strand
Strand 2	C	34	39	anti-parallel
Strand 3	C	76	84	anti-parallel
Strand 4	C	89	93	anti-parallel
Strand 5	C	96	98	anti-parallel

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There are 4 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	46	49	first strand
Strand 2	C	34	39	anti-parallel
Strand 3	C	76	84	anti-parallel
Strand 4	C	108	111	anti-parallel

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There are 9 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	125	128	first strand
Strand 2	C	181	184	parallel
Strand 3	C	227	231	parallel
Strand 4	C	271	273	parallel
Strand 5	C	308	313	parallel
Strand 6	C	328	331	parallel
Strand 7	C	380	381	parallel
Strand 8	C	415	419	parallel
Strand 9	C	125	128	parallel

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There are 5 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	470	477	first strand
Strand 2	C	480	487	anti-parallel
Strand 3	C	490	497	anti-parallel
Strand 4	C	537	543	anti-parallel
Strand 5	C	517	521	anti-parallel

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There are 3 strands in AC3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	502	505	first strand
Strand 2	C	530	533	anti-parallel
Strand 3	C	525	527	anti-parallel

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There are 3 strands in AC4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	3	5	first strand
Strand 2	D	19	27	anti-parallel
Strand 3	D	13	16	anti-parallel

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There are 4 strands in AC5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	3	5	first strand
Strand 2	D	19	27	anti-parallel
Strand 3	D	62	69	anti-parallel
Strand 4	D	51	52	anti-parallel

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There are 5 strands in AC6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	45	49	first strand
Strand 2	D	34	40	anti-parallel
Strand 3	D	76	84	anti-parallel
Strand 4	D	89	93	anti-parallel
Strand 5	D	96	98	anti-parallel

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There are 4 strands in AC7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	45	49	first strand
Strand 2	D	34	40	anti-parallel
Strand 3	D	76	84	anti-parallel
Strand 4	D	108	111	anti-parallel

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There are 8 strands in AC8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	328	329	first strand
Strand 2	D	308	311	parallel
Strand 3	D	271	274	parallel
Strand 4	D	227	231	parallel
Strand 5	D	181	184	parallel
Strand 6	D	125	128	parallel
Strand 7	D	415	419	parallel
Strand 8	D	380	381	parallel

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There are 5 strands in AC9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	470	477	first strand
Strand 2	D	480	487	anti-parallel
Strand 3	D	490	497	anti-parallel
Strand 4	D	537	543	anti-parallel
Strand 5	D	517	521	anti-parallel

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There are 3 strands in AD1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	502	505	first strand
Strand 2	D	530	533	anti-parallel
Strand 3	D	525	527	anti-parallel

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

Analysis of interatomic Contacts of Structural Units in PDB entry: 9VDW

Analysis of interatomic Contacts of Structural Units in PDB entry:
9VDW