Analysis of interatomic Contacts of Structural Units in PDB entry:
5VOD

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 5VOD entry

There are 7 chains in PDB entry 5VOD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	LEU 40	ALA 713
B	PRO 37	GLN 273
C	GLU 32	CYS 162
D	ASP 51	VAL 214
E	GLN 19	ASN 129
H	GLU 20	LYS 236
L	ASP 1	CYS 221

There are 54 helices in PDB entry 5VOD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	93	98	Right-handed 310
Helix 2	AA2	A	99	107	Right-handed alpha
Helix 3	AA3	A	114	123	Right-handed alpha
Helix 4	AA4	A	263	266	Right-handed 310
Helix 5	AA5	A	284	288	Right-handed 310
Helix 6	AA6	A	289	293	Right-handed 310
Helix 7	AA7	A	298	303	Right-handed alpha
Helix 8	AA8	A	308	316	Right-handed alpha
Helix 9	AA9	A	316	328	Right-handed alpha
Helix 10	AB1	A	334	353	Right-handed alpha
Helix 11	AB2	A	354	359	Right-handed 310
Helix 12	AB3	A	363	385	Right-handed alpha
Helix 13	AB4	A	387	391	Right-handed 310
Helix 14	AB5	A	396	409	Right-handed alpha
Helix 15	AB6	A	415	429	Right-handed alpha
Helix 16	AB7	A	431	435	Right-handed 310
Helix 17	AB8	A	436	454	Right-handed alpha
Helix 18	AB9	A	460	476	Right-handed alpha
Helix 19	AC1	A	480	494	Right-handed alpha
Helix 20	AC2	A	496	506	Right-handed alpha
Helix 21	AC3	A	514	519	Right-handed 310
Helix 22	AC4	A	520	524	Right-handed 310
Helix 23	AC5	A	531	537	Right-handed alpha
Helix 24	AC6	A	547	558	Right-handed alpha
Helix 25	AC7	A	644	648	Right-handed 310
Helix 26	AC8	A	671	680	Right-handed alpha
Helix 27	AC9	A	681	685	Right-handed 310
Helix 28	AD1	A	706	712	Right-handed alpha
Helix 29	AD2	B	46	57	Right-handed alpha
Helix 30	AD3	B	85	87	Right-handed 310
Helix 31	AD4	B	102	113	Right-handed alpha
Helix 32	AD5	B	117	127	Right-handed alpha
Helix 33	AD6	B	132	143	Right-handed alpha
Helix 34	AD7	B	172	176	Right-handed 310
Helix 35	AD8	B	198	201	Right-handed 310
Helix 36	AD9	B	215	217	Right-handed 310
Helix 37	AE1	B	218	236	Right-handed alpha
Helix 38	AE2	B	240	253	Right-handed alpha
Helix 39	AE3	C	69	81	Right-handed alpha
Helix 40	AE4	C	82	84	Right-handed 310
Helix 41	AE5	C	85	93	Right-handed alpha
Helix 42	AE6	C	145	155	Right-handed alpha
Helix 43	AE7	D	52	57	Right-handed 310
Helix 44	AE8	D	67	69	Right-handed 310
Helix 45	AE9	D	80	84	Right-handed 310
Helix 46	AF1	D	104	118	Right-handed alpha
Helix 47	AF2	D	119	131	Right-handed alpha
Helix 48	AF3	D	140	151	Right-handed alpha
Helix 49	AF4	E	35	41	Right-handed alpha
Helix 50	AF5	E	45	69	Right-handed alpha
Helix 51	AF6	E	73	79	Right-handed alpha
Helix 52	AF7	E	81	95	Right-handed alpha
Helix 53	AF8	H	180	184	Right-handed 310
Helix 54	AF9	H	227	231	Right-handed 310

There are 22 sheets in PDB entry 5VOD. 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,

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	49	51	first strand
Strand 2	A	69	71	parallel

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There are 6 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	65	66	first strand
Strand 2	A	86	92	anti-parallel
Strand 3	A	76	83	anti-parallel
Strand 4	B	178	184	parallel
Strand 5	B	188	197	anti-parallel
Strand 6	B	202	211	anti-parallel

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There are 8 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	136	137	first strand
Strand 2	A	268	271	parallel
Strand 3	A	276	280	anti-parallel
Strand 4	A	246	251	anti-parallel
Strand 5	A	233	239	anti-parallel
Strand 6	A	224	230	anti-parallel
Strand 7	A	207	217	anti-parallel
Strand 8	A	193	197	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	A	182	183	first strand
Strand 2	A	361	362	anti-parallel

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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	204	205	first strand
Strand 2	A	257	258	anti-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	527	528	first strand
Strand 2	A	578	581	anti-parallel
Strand 3	A	587	592	anti-parallel
Strand 4	A	614	619	anti-parallel
Strand 5	A	600	603	anti-parallel

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There are 5 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	637	638	first strand
Strand 2	A	703	705	parallel
Strand 3	A	692	697	anti-parallel
Strand 4	A	652	658	anti-parallel
Strand 5	A	663	669	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	B	82	83	first strand
Strand 2	B	169	170	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	B	150	154	first strand
Strand 2	B	158	163	anti-parallel
Strand 3	D	98	102	parallel
Strand 4	D	87	93	anti-parallel
Strand 5	D	71	78	anti-parallel

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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	C	45	48	first strand
Strand 2	C	54	57	anti-parallel
Strand 3	C	62	65	anti-parallel

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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	C	101	102	first strand
Strand 2	C	121	122	anti-parallel

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There are 6 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	154	165	first strand
Strand 2	D	168	182	anti-parallel
Strand 3	D	188	198	anti-parallel
Strand 4	E	117	126	anti-parallel
Strand 5	E	107	109	anti-parallel
Strand 6	E	97	98	anti-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	D	154	165	first strand
Strand 2	D	168	182	anti-parallel
Strand 3	D	188	198	anti-parallel
Strand 4	E	117	126	anti-parallel
Strand 5	E	111	113	anti-parallel

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There are 4 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	22	25	first strand
Strand 2	H	41	44	anti-parallel
Strand 3	H	97	101	anti-parallel
Strand 4	H	88	92	anti-parallel

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There are 4 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	77	78	first strand
Strand 2	H	64	70	anti-parallel
Strand 3	H	53	58	anti-parallel
Strand 4	H	112	117	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	H	149	151	first strand
Strand 2	H	166	172	anti-parallel
Strand 3	H	203	208	anti-parallel
Strand 4	H	191	192	anti-parallel

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There are 4 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	4	7	first strand
Strand 2	L	19	25	anti-parallel
Strand 3	L	75	80	anti-parallel
Strand 4	L	68	69	anti-parallel

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There are 5 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	12	14	first strand
Strand 2	L	110	114	parallel
Strand 3	L	89	93	anti-parallel
Strand 4	L	40	43	anti-parallel
Strand 5	L	50	53	anti-parallel

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There are 2 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	136	141	first strand
Strand 2	L	184	189	anti-parallel

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There are 4 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	160	161	first strand
Strand 2	L	152	157	anti-parallel
Strand 3	L	198	204	anti-parallel
Strand 4	L	212	213	anti-parallel

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There are 4 strands in AC3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	160	161	first strand
Strand 2	L	152	157	anti-parallel
Strand 3	L	198	204	anti-parallel
Strand 4	L	216	217	anti-parallel

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There are 2 strands in AC4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	170	171	first strand
Strand 2	L	181	182	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: 5VOD

Analysis of interatomic Contacts of Structural Units in PDB entry:
5VOD