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

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 9VDG entry

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

Chain ID	Initial residue	Terminal residue
A	MET 1	ARG 559
B	LEU 2	ARG 559
C	MET 1	ARG 559
D	MET 1	ARG 559

There are 82 helices in PDB entry 9VDG. 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	178	185	Right-handed alpha
Helix 5	AA5	A	185	193	Right-handed alpha
Helix 6	AA6	A	220	223	Right-handed 310
Helix 7	AA7	A	224	239	Right-handed alpha
Helix 8	AA8	A	273	277	Right-handed alpha
Helix 9	AA9	A	308	319	Right-handed alpha
Helix 10	AB1	A	332	337	Right-handed alpha
Helix 11	AB2	A	350	360	Right-handed alpha
Helix 12	AB3	A	371	384	Right-handed alpha
Helix 13	AB4	A	387	394	Right-handed alpha
Helix 14	AB5	A	405	410	Right-handed alpha
Helix 15	AB6	A	411	415	Right-handed 310
Helix 16	AB7	A	416	427	Right-handed alpha
Helix 17	AB8	A	436	440	Right-handed 310
Helix 18	AB9	A	456	460	Right-handed 310
Helix 19	AC1	A	461	478	Right-handed alpha
Helix 20	AC2	A	479	484	Right-handed alpha
Helix 21	AC3	A	524	528	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	178	185	Right-handed alpha
Helix 26	AC8	B	185	193	Right-handed alpha
Helix 27	AC9	B	220	223	Right-handed 310
Helix 28	AD1	B	224	239	Right-handed alpha
Helix 29	AD2	B	273	277	Right-handed alpha
Helix 30	AD3	B	308	319	Right-handed alpha
Helix 31	AD4	B	332	337	Right-handed alpha
Helix 32	AD5	B	350	360	Right-handed alpha
Helix 33	AD6	B	371	384	Right-handed alpha
Helix 34	AD7	B	387	394	Right-handed alpha
Helix 35	AD8	B	405	410	Right-handed alpha
Helix 36	AD9	B	411	415	Right-handed 310
Helix 37	AE1	B	416	427	Right-handed alpha
Helix 38	AE2	B	436	440	Right-handed 310
Helix 39	AE3	B	456	460	Right-handed 310
Helix 40	AE4	B	461	478	Right-handed alpha
Helix 41	AE5	B	479	484	Right-handed alpha
Helix 42	AE6	B	524	528	Right-handed 310
Helix 43	AE7	C	103	107	Right-handed 310
Helix 44	AE8	C	119	123	Right-handed 310
Helix 45	AE9	C	129	133	Right-handed 310
Helix 46	AF1	C	178	185	Right-handed alpha
Helix 47	AF2	C	185	193	Right-handed alpha
Helix 48	AF3	C	220	223	Right-handed 310
Helix 49	AF4	C	224	239	Right-handed alpha
Helix 50	AF5	C	308	319	Right-handed alpha
Helix 51	AF6	C	332	337	Right-handed alpha
Helix 52	AF7	C	350	360	Right-handed alpha
Helix 53	AF8	C	371	384	Right-handed alpha
Helix 54	AF9	C	387	394	Right-handed alpha
Helix 55	AG1	C	405	410	Right-handed alpha
Helix 56	AG2	C	411	415	Right-handed 310
Helix 57	AG3	C	416	427	Right-handed alpha
Helix 58	AG4	C	436	440	Right-handed 310
Helix 59	AG5	C	456	460	Right-handed 310
Helix 60	AG6	C	461	478	Right-handed alpha
Helix 61	AG7	C	479	484	Right-handed alpha
Helix 62	AG8	C	524	528	Right-handed 310
Helix 63	AG9	D	103	107	Right-handed 310
Helix 64	AH1	D	119	123	Right-handed 310
Helix 65	AH2	D	129	133	Right-handed 310
Helix 66	AH3	D	178	185	Right-handed alpha
Helix 67	AH4	D	185	193	Right-handed alpha
Helix 68	AH5	D	220	223	Right-handed 310
Helix 69	AH6	D	224	239	Right-handed alpha
Helix 70	AH7	D	273	279	Right-handed alpha
Helix 71	AH8	D	308	319	Right-handed alpha
Helix 72	AH9	D	332	337	Right-handed alpha
Helix 73	AI1	D	350	360	Right-handed alpha
Helix 74	AI2	D	371	384	Right-handed alpha
Helix 75	AI3	D	387	394	Right-handed alpha
Helix 76	AI4	D	405	410	Right-handed alpha
Helix 77	AI5	D	411	415	Right-handed 310
Helix 78	AI6	D	416	427	Right-handed alpha
Helix 79	AI7	D	436	440	Right-handed 310
Helix 80	AI8	D	456	460	Right-handed 310
Helix 81	AI9	D	461	478	Right-handed alpha
Helix 82	AJ1	D	479	484	Right-handed alpha

There are 26 sheets in PDB entry 9VDG. 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,

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	196	199	parallel
Strand 3	A	242	246	parallel
Strand 4	A	286	289	parallel
Strand 5	A	323	328	parallel
Strand 6	A	343	346	parallel
Strand 7	A	395	396	parallel
Strand 8	A	430	434	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	485	492	first strand
Strand 2	A	495	502	anti-parallel
Strand 3	A	505	512	anti-parallel
Strand 4	A	552	558	anti-parallel
Strand 5	A	532	536	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	517	520	first strand
Strand 2	A	545	548	anti-parallel
Strand 3	A	540	542	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	3	5	first strand
Strand 2	B	19	27	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	3	5	first strand
Strand 2	B	19	27	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	39	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	39	anti-parallel
Strand 3	B	76	84	anti-parallel
Strand 4	B	108	111	anti-parallel

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There are 9 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	125	128	first strand
Strand 2	B	196	199	parallel
Strand 3	B	242	246	parallel
Strand 4	B	286	288	parallel
Strand 5	B	323	328	parallel
Strand 6	B	343	346	parallel
Strand 7	B	395	396	parallel
Strand 8	B	430	434	parallel
Strand 9	B	125	128	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	485	492	first strand
Strand 2	B	495	502	anti-parallel
Strand 3	B	505	512	anti-parallel
Strand 4	B	552	558	anti-parallel
Strand 5	B	532	536	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	517	520	first strand
Strand 2	B	545	548	anti-parallel
Strand 3	B	540	542	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	45	49	first strand
Strand 2	C	34	40	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	45	49	first strand
Strand 2	C	34	40	anti-parallel
Strand 3	C	76	84	anti-parallel
Strand 4	C	108	111	anti-parallel

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There are 8 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	343	344	first strand
Strand 2	C	323	326	parallel
Strand 3	C	286	288	parallel
Strand 4	C	242	246	parallel
Strand 5	C	196	199	parallel
Strand 6	C	125	128	parallel
Strand 7	C	430	434	parallel
Strand 8	C	395	396	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	485	492	first strand
Strand 2	C	495	502	anti-parallel
Strand 3	C	505	512	anti-parallel
Strand 4	C	552	558	anti-parallel
Strand 5	C	532	536	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	517	520	first strand
Strand 2	C	545	548	anti-parallel
Strand 3	C	540	542	anti-parallel

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There are 8 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	62	69	anti-parallel
Strand 4	D	46	52	anti-parallel
Strand 5	D	34	39	anti-parallel
Strand 6	D	76	84	anti-parallel
Strand 7	D	89	93	anti-parallel
Strand 8	D	96	98	anti-parallel

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There are 7 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	13	16	first strand
Strand 2	D	19	27	anti-parallel
Strand 3	D	62	69	anti-parallel
Strand 4	D	46	52	anti-parallel
Strand 5	D	34	39	anti-parallel
Strand 6	D	76	84	anti-parallel
Strand 7	D	108	111	anti-parallel

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There are 9 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	125	128	first strand
Strand 2	D	196	199	parallel
Strand 3	D	242	246	parallel
Strand 4	D	286	289	parallel
Strand 5	D	323	328	parallel
Strand 6	D	343	346	parallel
Strand 7	D	395	396	parallel
Strand 8	D	430	434	parallel
Strand 9	D	125	128	parallel

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There are 5 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	485	492	first strand
Strand 2	D	495	502	anti-parallel
Strand 3	D	505	512	anti-parallel
Strand 4	D	552	558	anti-parallel
Strand 5	D	532	536	anti-parallel

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There are 3 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	517	520	first strand
Strand 2	D	545	548	anti-parallel
Strand 3	D	540	542	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: 9VDG

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