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

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 8VML entry

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

Chain ID	Initial residue	Terminal residue
A	ALA 81	ARG 682
B	ARG 108	ARG 115
B	PHE 117	SER 166
C	LYS 17	PRO 746
I	GLN 19	ARG 40
L	TYR 80	ARG 441
N	LYS 4	ASN 410
P	ASN 170	ILE 211

There are 46 helices in PDB entry 8VML. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	83	105	Right-handed alpha
Helix 2	AA2	A	111	119	Right-handed 310
Helix 3	AA3	A	131	147	Right-handed alpha
Helix 4	AA4	A	238	243	Right-handed 310
Helix 5	AA5	A	459	470	Right-handed alpha
Helix 6	AA6	A	502	508	Right-handed 310
Helix 7	AA7	A	539	543	Right-handed 310
Helix 8	AA8	A	589	601	Right-handed alpha
Helix 9	AA9	A	607	625	Right-handed alpha
Helix 10	AB1	A	628	630	Right-handed 310
Helix 11	AB2	A	631	651	Right-handed alpha
Helix 12	AB3	A	652	666	Right-handed alpha
Helix 13	AB4	A	670	682	Right-handed alpha
Helix 14	AB5	B	144	151	Right-handed alpha
Helix 15	AB6	B	161	166	Right-handed 310
Helix 16	AB7	C	18	61	Right-handed alpha
Helix 17	AB8	C	138	143	Right-handed alpha
Helix 18	AB9	C	143	154	Right-handed alpha
Helix 19	AC1	C	168	178	Right-handed alpha
Helix 20	AC2	C	221	231	Right-handed alpha
Helix 21	AC3	C	236	250	Right-handed alpha
Helix 22	AC4	C	273	284	Right-handed alpha
Helix 23	AC5	C	328	339	Right-handed alpha
Helix 24	AC6	C	433	448	Right-handed alpha
Helix 25	AC7	C	450	458	Right-handed alpha
Helix 26	AC8	C	462	473	Right-handed alpha
Helix 27	AC9	C	474	477	Right-handed 310
Helix 28	AD1	C	491	495	Right-handed 310
Helix 29	AD2	C	496	510	Right-handed alpha
Helix 30	AD3	C	534	540	Right-handed alpha
Helix 31	AD4	C	571	576	Right-handed alpha
Helix 32	AD5	C	604	609	Right-handed alpha
Helix 33	AD6	C	648	661	Right-handed alpha
Helix 34	AD7	C	682	687	Right-handed 310
Helix 35	AD8	C	729	737	Right-handed alpha
Helix 36	AD9	L	128	130	Right-handed 310
Helix 37	AE1	L	267	278	Right-handed alpha
Helix 38	AE2	L	339	343	Right-handed 310
Helix 39	AE3	N	5	28	Right-handed alpha
Helix 40	AE4	N	155	157	Right-handed 310
Helix 41	AE5	N	355	362	Right-handed alpha
Helix 42	AE6	N	406	409	Right-handed 310
Helix 43	AE7	P	191	210	Right-handed alpha
Helix 44	AE8	P	257	259	Right-handed 310
Helix 45	AE9	P	270	272	Right-handed 310
Helix 46	AF1	P	276	285	Right-handed 310

There are 24 sheets in PDB entry 8VML. 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 7 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	230	233	first strand
Strand 2	A	157	161	anti-parallel
Strand 3	A	354	361	anti-parallel
Strand 4	A	313	318	anti-parallel
Strand 5	P	219	231	anti-parallel
Strand 6	P	237	243	anti-parallel
Strand 7	P	252	255	anti-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	230	233	first strand
Strand 2	A	157	161	anti-parallel
Strand 3	A	354	361	anti-parallel
Strand 4	A	313	318	anti-parallel
Strand 5	P	219	231	anti-parallel
Strand 6	P	264	268	anti-parallel

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There are 4 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	203	211	first strand
Strand 2	A	184	192	anti-parallel
Strand 3	A	245	253	anti-parallel
Strand 4	A	297	300	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	439	443	first strand
Strand 2	A	427	433	anti-parallel
Strand 3	A	484	491	parallel
Strand 4	A	474	478	anti-parallel

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There are 6 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	558	560	first strand
Strand 2	A	525	530	anti-parallel
Strand 3	N	32	39	anti-parallel
Strand 4	N	398	404	anti-parallel
Strand 5	N	389	393	anti-parallel
Strand 6	N	379	381	anti-parallel

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There are 6 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	94	97	first strand
Strand 2	C	82	87	anti-parallel
Strand 3	L	82	89	anti-parallel
Strand 4	L	433	439	anti-parallel
Strand 5	L	424	429	anti-parallel
Strand 6	L	413	418	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	C	114	115	first strand
Strand 2	C	680	681	parallel

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There are 4 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	120	121	first strand
Strand 2	C	644	647	parallel
Strand 3	C	673	676	anti-parallel
Strand 4	C	666	668	anti-parallel

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There are 2 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	285	286	first strand
Strand 2	C	291	292	anti-parallel

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There are 2 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	614	618	first strand
Strand 2	C	624	628	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	637	640	first strand
Strand 2	C	705	712	anti-parallel
Strand 3	C	695	702	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	C	688	689	first strand
Strand 2	C	723	724	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	L	100	101	first strand
Strand 2	L	111	116	anti-parallel
Strand 3	L	120	126	anti-parallel
Strand 4	L	132	139	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	L	147	154	first strand
Strand 2	L	161	167	anti-parallel
Strand 3	L	172	176	anti-parallel
Strand 4	L	181	186	anti-parallel

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There are 5 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	193	198	first strand
Strand 2	L	205	210	anti-parallel
Strand 3	L	215	219	anti-parallel
Strand 4	L	224	229	anti-parallel
Strand 5	L	292	294	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	L	239	244	first strand
Strand 2	L	250	255	anti-parallel
Strand 3	L	260	264	anti-parallel
Strand 4	L	299	301	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	312	315	first strand
Strand 2	L	318	323	anti-parallel
Strand 3	L	327	333	anti-parallel
Strand 4	L	350	357	anti-parallel

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There are 3 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	368	370	first strand
Strand 2	L	376	379	anti-parallel
Strand 3	L	387	390	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	48	49	first strand
Strand 2	N	61	68	anti-parallel
Strand 3	N	77	87	anti-parallel
Strand 4	N	115	123	anti-parallel

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There are 3 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	129	133	first strand
Strand 2	N	136	143	anti-parallel
Strand 3	N	149	153	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	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 4 strands in AC4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	N	230	235	first strand
Strand 2	N	242	247	anti-parallel
Strand 3	N	251	256	anti-parallel
Strand 4	N	267	270	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	N	276	281	first strand
Strand 2	N	288	293	anti-parallel
Strand 3	N	298	302	anti-parallel

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There are 4 strands in AC6 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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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il

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

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