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

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 8VMI entry

There are 7 chains in PDB entry 8VMI (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	TYR 80	LEU 440
B	ALA 1	THR 3
B	GLN 5	THR 6
L	THR 556	ARG 682
T	ALA 81	LEU 544
N	LYS 4	ASN 410
C	CYS 14	LYS 307

There are 45 helices in PDB entry 8VMI. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	128	130	Right-handed 310
Helix 2	AA2	A	267	279	Right-handed alpha
Helix 3	AA3	A	281	285	Right-handed 310
Helix 4	AA4	L	575	580	Right-handed alpha
Helix 5	AA5	L	589	602	Right-handed alpha
Helix 6	AA6	L	607	625	Right-handed alpha
Helix 7	AA7	L	632	651	Right-handed alpha
Helix 8	AA8	L	652	661	Right-handed alpha
Helix 9	AA9	L	670	682	Right-handed alpha
Helix 10	AB1	T	82	107	Right-handed alpha
Helix 11	AB2	T	111	119	Right-handed 310
Helix 12	AB3	T	134	147	Right-handed alpha
Helix 13	AB4	T	238	244	Right-handed alpha
Helix 14	AB5	T	459	471	Right-handed alpha
Helix 15	AB6	T	502	508	Right-handed 310
Helix 16	AB7	T	539	543	Right-handed 310
Helix 17	AB8	N	5	27	Right-handed alpha
Helix 18	AB9	N	28	30	Right-handed 310
Helix 19	AC1	N	155	157	Right-handed 310
Helix 20	AC2	N	304	306	Right-handed 310
Helix 21	AC3	N	348	350	Right-handed 310
Helix 22	AC4	N	355	362	Right-handed alpha
Helix 23	AC5	N	406	409	Right-handed 310
Helix 24	AC6	C	15	61	Right-handed alpha
Helix 25	AC7	C	168	180	Right-handed alpha
Helix 26	AC8	C	220	231	Right-handed alpha
Helix 27	AC9	C	236	246	Right-handed alpha
Helix 28	AD1	C	273	285	Right-handed alpha
Helix 29	AD2	C	328	339	Right-handed alpha
Helix 30	AD3	C	433	448	Right-handed alpha
Helix 31	AD4	C	450	458	Right-handed alpha
Helix 32	AD5	C	462	477	Right-handed alpha
Helix 33	AD6	C	496	510	Right-handed alpha
Helix 34	AD7	C	534	539	Right-handed alpha
Helix 35	AD8	C	571	576	Right-handed alpha
Helix 36	AD9	C	604	609	Right-handed alpha
Helix 37	AE1	C	648	661	Right-handed alpha
Helix 38	AE2	C	682	687	Right-handed 310
Helix 39	AE3	C	729	738	Right-handed alpha
Helix 40	AE4	F	144	151	Right-handed alpha
Helix 41	AE5	F	157	162	Right-handed 310
Helix 42	AE6	P	191	210	Right-handed alpha
Helix 43	AE7	P	245	249	Right-handed 310
Helix 44	AE8	P	257	259	Right-handed 310
Helix 45	AE9	P	276	281	Right-handed 310

There are 24 sheets in PDB entry 8VMI. 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,

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	96	101	first strand
Strand 2	A	111	117	anti-parallel
Strand 3	A	120	126	anti-parallel
Strand 4	A	132	139	anti-parallel
Strand 5	C	94	100	parallel
Strand 6	C	81	87	anti-parallel
Strand 7	A	82	90	anti-parallel
Strand 8	A	433	439	anti-parallel
Strand 9	A	424	429	anti-parallel
Strand 10	A	413	418	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	147	154	first strand
Strand 2	A	161	167	anti-parallel
Strand 3	A	172	176	anti-parallel
Strand 4	A	181	186	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	193	199	first strand
Strand 2	A	202	210	anti-parallel
Strand 3	A	215	219	anti-parallel
Strand 4	A	225	229	anti-parallel
Strand 5	A	292	294	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	239	244	first strand
Strand 2	A	250	255	anti-parallel
Strand 3	A	260	264	anti-parallel
Strand 4	A	299	301	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	A	309	315	first strand
Strand 2	A	318	323	anti-parallel
Strand 3	A	327	333	anti-parallel
Strand 4	A	350	357	anti-parallel

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There are 3 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	369	370	first strand
Strand 2	A	376	380	anti-parallel
Strand 3	A	386	390	anti-parallel

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There are 6 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	559	560	first strand
Strand 2	T	525	530	anti-parallel
Strand 3	N	32	39	anti-parallel
Strand 4	N	398	404	anti-parallel
Strand 5	N	389	394	anti-parallel
Strand 6	N	377	382	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	T	203	207	first strand
Strand 2	T	183	192	anti-parallel
Strand 3	T	211	212	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	T	203	207	first strand
Strand 2	T	183	192	anti-parallel
Strand 3	T	245	253	anti-parallel
Strand 4	T	297	300	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	T	354	359	first strand
Strand 2	T	313	318	anti-parallel
Strand 3	P	219	232	anti-parallel
Strand 4	P	237	243	anti-parallel
Strand 5	P	252	255	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	T	354	359	first strand
Strand 2	T	313	318	anti-parallel
Strand 3	P	219	232	anti-parallel
Strand 4	P	264	268	anti-parallel

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There are 3 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	T	474	475	first strand
Strand 2	T	484	491	anti-parallel
Strand 3	T	478	481	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	T	474	475	first strand
Strand 2	T	484	491	anti-parallel
Strand 3	T	427	434	parallel
Strand 4	T	438	444	anti-parallel
Strand 5	F	140	141	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	N	48	49	first strand
Strand 2	N	62	67	anti-parallel
Strand 3	N	82	86	anti-parallel
Strand 4	N	115	117	anti-parallel

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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	N	77	78	first strand
Strand 2	N	122	123	anti-parallel

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There are 5 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	N	130	133	first strand
Strand 2	N	136	142	anti-parallel
Strand 3	N	149	153	anti-parallel
Strand 4	N	171	173	anti-parallel
Strand 5	N	216	217	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	N	180	185	first strand
Strand 2	N	192	197	anti-parallel
Strand 3	N	202	206	anti-parallel
Strand 4	N	221	223	anti-parallel

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There are 2 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	N	242	243	first strand
Strand 2	N	255	256	anti-parallel

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There are 4 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	N	280	281	first strand
Strand 2	N	288	292	anti-parallel
Strand 3	N	298	302	anti-parallel
Strand 4	N	312	313	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	N	320	325	first strand
Strand 2	N	332	337	anti-parallel
Strand 3	N	342	346	anti-parallel
Strand 4	N	366	370	anti-parallel

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There are 2 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	114	115	first strand
Strand 2	C	680	681	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	C	614	618	first strand
Strand 2	C	624	628	anti-parallel

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There are 3 strands in AC5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	637	638	first strand
Strand 2	C	705	712	anti-parallel
Strand 3	C	695	702	anti-parallel

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There are 3 strands in AC6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	644	647	first strand
Strand 2	C	673	676	anti-parallel
Strand 3	C	666	668	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: 8VMI

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