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

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 9VKU entry

There are 8 chains in PDB entry 9VKU (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	MET 1	GLU 499
B	MET 1	LEU 494
C	MET 1	GLN 492
D	MET 1	GLN 492
E	C 1	U 178
F	C 1	U 178
G	C 1	U 178
H	C 1	U 178

There are 94 helices in PDB entry 9VKU. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	2	38	Right-handed alpha
Helix 2	AA2	A	40	44	Right-handed 310
Helix 3	AA3	A	52	56	Right-handed 310
Helix 4	AA4	A	58	61	Right-handed 310
Helix 5	AA5	A	62	67	Right-handed alpha
Helix 6	AA6	A	69	82	Right-handed alpha
Helix 7	AA7	A	110	128	Right-handed alpha
Helix 8	AA8	A	129	132	Right-handed 310
Helix 9	AA9	A	145	159	Right-handed alpha
Helix 10	AB1	A	177	184	Right-handed alpha
Helix 11	AB2	A	193	208	Right-handed alpha
Helix 12	AB3	A	215	226	Right-handed alpha
Helix 13	AB4	A	226	237	Right-handed alpha
Helix 14	AB5	A	253	272	Right-handed alpha
Helix 15	AB6	A	316	336	Right-handed alpha
Helix 16	AB7	A	336	341	Right-handed alpha
Helix 17	AB8	A	355	370	Right-handed alpha
Helix 18	AB9	A	374	384	Right-handed alpha
Helix 19	AC1	A	393	398	Right-handed 310
Helix 20	AC2	A	403	433	Right-handed alpha
Helix 21	AC3	A	439	443	Right-handed 310
Helix 22	AC4	A	448	456	Right-handed alpha
Helix 23	AC5	A	468	490	Right-handed alpha
Helix 24	AC6	B	2	41	Right-handed alpha
Helix 25	AC7	B	52	56	Right-handed 310
Helix 26	AC8	B	58	61	Right-handed 310
Helix 27	AC9	B	62	69	Right-handed alpha
Helix 28	AD1	B	69	84	Right-handed alpha
Helix 29	AD2	B	110	120	Right-handed alpha
Helix 30	AD3	B	123	128	Right-handed alpha
Helix 31	AD4	B	142	144	Right-handed 310
Helix 32	AD5	B	145	159	Right-handed alpha
Helix 33	AD6	B	169	175	Right-handed alpha
Helix 34	AD7	B	177	183	Right-handed alpha
Helix 35	AD8	B	193	208	Right-handed alpha
Helix 36	AD9	B	215	226	Right-handed alpha
Helix 37	AE1	B	227	237	Right-handed alpha
Helix 38	AE2	B	253	272	Right-handed alpha
Helix 39	AE3	B	316	336	Right-handed alpha
Helix 40	AE4	B	337	341	Right-handed 310
Helix 41	AE5	B	355	370	Right-handed alpha
Helix 42	AE6	B	374	384	Right-handed alpha
Helix 43	AE7	B	393	398	Right-handed 310
Helix 44	AE8	B	403	432	Right-handed alpha
Helix 45	AE9	B	439	444	Right-handed alpha
Helix 46	AF1	B	448	456	Right-handed alpha
Helix 47	AF2	B	468	490	Right-handed alpha
Helix 48	AF3	C	2	40	Right-handed alpha
Helix 49	AF4	C	52	56	Right-handed 310
Helix 50	AF5	C	58	61	Right-handed 310
Helix 51	AF6	C	62	69	Right-handed alpha
Helix 52	AF7	C	69	83	Right-handed alpha
Helix 53	AF8	C	110	128	Right-handed alpha
Helix 54	AF9	C	129	132	Right-handed 310
Helix 55	AG1	C	145	159	Right-handed alpha
Helix 56	AG2	C	169	176	Right-handed alpha
Helix 57	AG3	C	177	184	Right-handed alpha
Helix 58	AG4	C	193	208	Right-handed alpha
Helix 59	AG5	C	215	226	Right-handed alpha
Helix 60	AG6	C	226	237	Right-handed alpha
Helix 61	AG7	C	253	272	Right-handed alpha
Helix 62	AG8	C	316	336	Right-handed alpha
Helix 63	AG9	C	337	340	Right-handed 310
Helix 64	AH1	C	355	370	Right-handed alpha
Helix 65	AH2	C	374	384	Right-handed alpha
Helix 66	AH3	C	393	398	Right-handed 310
Helix 67	AH4	C	403	433	Right-handed alpha
Helix 68	AH5	C	439	443	Right-handed 310
Helix 69	AH6	C	450	456	Right-handed alpha
Helix 70	AH7	C	468	490	Right-handed alpha
Helix 71	AH8	D	2	41	Right-handed alpha
Helix 72	AH9	D	52	56	Right-handed 310
Helix 73	AI1	D	58	61	Right-handed 310
Helix 74	AI2	D	62	69	Right-handed alpha
Helix 75	AI3	D	69	84	Right-handed alpha
Helix 76	AI4	D	110	128	Right-handed alpha
Helix 77	AI5	D	129	132	Right-handed 310
Helix 78	AI6	D	145	159	Right-handed alpha
Helix 79	AI7	D	169	175	Right-handed alpha
Helix 80	AI8	D	177	184	Right-handed alpha
Helix 81	AI9	D	185	187	Right-handed 310
Helix 82	AJ1	D	193	207	Right-handed alpha
Helix 83	AJ2	D	215	226	Right-handed alpha
Helix 84	AJ3	D	226	237	Right-handed alpha
Helix 85	AJ4	D	253	272	Right-handed alpha
Helix 86	AJ5	D	316	336	Right-handed alpha
Helix 87	AJ6	D	337	341	Right-handed 310
Helix 88	AJ7	D	355	370	Right-handed alpha
Helix 89	AJ8	D	374	384	Right-handed alpha
Helix 90	AJ9	D	393	397	Right-handed 310
Helix 91	AK1	D	403	432	Right-handed alpha
Helix 92	AK2	D	439	444	Right-handed alpha
Helix 93	AK3	D	450	456	Right-handed alpha
Helix 94	AK4	D	468	490	Right-handed alpha

There are 15 sheets in PDB entry 9VKU. 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,

There are 2 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	92	97	first strand
Strand 2	A	103	108	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	239	241	first strand
Strand 2	A	246	251	anti-parallel
Strand 3	A	163	168	anti-parallel
Strand 4	A	284	285	anti-parallel

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There are 3 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	300	303	first strand
Strand 2	A	306	309	anti-parallel
Strand 3	A	313	315	anti-parallel

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There are 2 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	92	97	first strand
Strand 2	B	103	108	anti-parallel

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There are 4 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	239	242	first strand
Strand 2	B	246	251	anti-parallel
Strand 3	B	167	168	anti-parallel
Strand 4	B	276	277	anti-parallel

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There are 4 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	239	242	first strand
Strand 2	B	246	251	anti-parallel
Strand 3	B	162	164	anti-parallel
Strand 4	B	284	286	anti-parallel

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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	307	308	first strand
Strand 2	B	313	314	anti-parallel

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There are 2 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	92	97	first strand
Strand 2	C	103	108	anti-parallel

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There are 5 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	136	137	first strand
Strand 2	C	239	243	parallel
Strand 3	C	246	251	anti-parallel
Strand 4	C	163	168	anti-parallel
Strand 5	C	276	277	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	C	136	137	first strand
Strand 2	C	239	243	parallel
Strand 3	C	246	251	anti-parallel
Strand 4	C	163	168	anti-parallel
Strand 5	C	284	285	anti-parallel

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There are 3 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	300	303	first strand
Strand 2	C	306	309	anti-parallel
Strand 3	C	313	315	anti-parallel

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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	D	92	97	first strand
Strand 2	D	103	108	anti-parallel

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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	D	239	241	first strand
Strand 2	D	248	251	anti-parallel
Strand 3	D	162	168	anti-parallel
Strand 4	D	276	277	anti-parallel

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There are 5 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	239	241	first strand
Strand 2	D	248	251	anti-parallel
Strand 3	D	162	168	anti-parallel
Strand 4	D	284	286	anti-parallel
Strand 5	D	297	298	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	D	301	303	first strand
Strand 2	D	306	308	anti-parallel
Strand 3	D	313	315	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: 9VKU

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