Analysis of interatomic Contacts of Structural Units in PDB entry:
5VM9

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 5VM9 entry

There are 3 chains in PDB entry 5VM9 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	MET 16	ALA 860
B	A 1	U 21
C	LEU 15	LYS 480

There are 47 helices in PDB entry 5VM9. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	59	74	Right-handed alpha
Helix 2	AA2	A	136	140	Right-handed alpha
Helix 3	AA3	A	159	175	Right-handed alpha
Helix 4	AA4	A	230	239	Right-handed alpha
Helix 5	AA5	A	252	264	Right-handed alpha
Helix 6	AA6	A	309	316	Right-handed alpha
Helix 7	AA7	A	358	370	Right-handed alpha
Helix 8	AA8	A	372	387	Right-handed alpha
Helix 9	AA9	A	388	391	Right-handed 310
Helix 10	AB1	A	392	398	Right-handed alpha
Helix 11	AB2	A	464	482	Right-handed alpha
Helix 12	AB3	A	501	513	Right-handed alpha
Helix 13	AB4	A	528	540	Right-handed alpha
Helix 14	AB5	A	550	555	Right-handed alpha
Helix 15	AB6	A	557	572	Right-handed alpha
Helix 16	AB7	A	581	584	Right-handed 310
Helix 17	AB8	A	585	590	Right-handed 310
Helix 18	AB9	A	642	658	Right-handed alpha
Helix 19	AC1	A	676	693	Right-handed alpha
Helix 20	AC2	A	776	789	Right-handed alpha
Helix 21	AC3	A	801	813	Right-handed alpha
Helix 22	AC4	A	814	819	Right-handed alpha
Helix 23	AC5	A	839	846	Right-handed alpha
Helix 24	AC6	A	850	854	Right-handed 310
Helix 25	AC7	C	59	74	Right-handed alpha
Helix 26	AC8	C	133	141	Right-handed alpha
Helix 27	AC9	C	160	169	Right-handed alpha
Helix 28	AD1	C	170	175	Right-handed alpha
Helix 29	AD2	C	230	239	Right-handed alpha
Helix 30	AD3	C	252	264	Right-handed alpha
Helix 31	AD4	C	309	317	Right-handed alpha
Helix 32	AD5	C	358	370	Right-handed alpha
Helix 33	AD6	C	372	388	Right-handed alpha
Helix 34	AD7	C	392	397	Right-handed alpha
Helix 35	AD8	C	464	482	Right-handed alpha
Helix 36	AD9	C	501	513	Right-handed alpha
Helix 37	AE1	C	527	539	Right-handed alpha
Helix 38	AE2	C	549	555	Right-handed alpha
Helix 39	AE3	C	557	572	Right-handed alpha
Helix 40	AE4	C	581	584	Right-handed 310
Helix 41	AE5	C	585	590	Right-handed 310
Helix 42	AE6	C	642	659	Right-handed alpha
Helix 43	AE7	C	676	696	Right-handed alpha
Helix 44	AE8	C	776	789	Right-handed alpha
Helix 45	AE9	C	801	813	Right-handed alpha
Helix 46	AF1	C	841	848	Right-handed alpha
Helix 47	AF2	C	850	854	Right-handed 310

There are 18 sheets in PDB entry 5VM9. 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,

There are 11 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	626	633	first strand
Strand 2	A	611	618	anti-parallel
Strand 3	A	592	600	anti-parallel
Strand 4	A	664	669	parallel
Strand 5	A	702	707	parallel
Strand 6	A	764	771	anti-parallel
Strand 7	A	747	752	anti-parallel
Strand 8	A	735	737	anti-parallel
Strand 9	A	407	413	anti-parallel
Strand 10	A	28	34	anti-parallel
Strand 11	A	716	718	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	36	39	first strand
Strand 2	A	213	226	anti-parallel
Strand 3	A	197	210	anti-parallel
Strand 4	A	192	194	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	181	184	first strand
Strand 2	A	197	210	anti-parallel
Strand 3	A	213	226	anti-parallel
Strand 4	A	351	352	anti-parallel

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There are 5 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	85	86	first strand
Strand 2	A	91	94	anti-parallel
Strand 3	A	47	52	anti-parallel
Strand 4	A	122	126	anti-parallel
Strand 5	A	107	108	anti-parallel

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There are 5 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	338	341	first strand
Strand 2	A	328	331	anti-parallel
Strand 3	A	279	285	anti-parallel
Strand 4	A	267	270	anti-parallel
Strand 5	A	345	347	anti-parallel

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There are 2 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	294	295	first strand
Strand 2	A	307	308	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	428	429	first strand
Strand 2	A	419	420	anti-parallel
Strand 3	A	578	579	anti-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	A	492	495	first strand
Strand 2	A	452	456	parallel
Strand 3	A	518	523	parallel
Strand 4	A	544	545	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	A	492	495	first strand
Strand 2	A	452	456	parallel
Strand 3	A	518	523	parallel
Strand 4	A	548	549	parallel

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There are 9 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	592	595	first strand
Strand 2	C	664	669	parallel
Strand 3	C	702	709	parallel
Strand 4	C	764	771	anti-parallel
Strand 5	C	748	752	anti-parallel
Strand 6	C	735	737	anti-parallel
Strand 7	C	407	413	anti-parallel
Strand 8	C	28	34	anti-parallel
Strand 9	C	716	718	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	C	36	39	first strand
Strand 2	C	213	226	anti-parallel
Strand 3	C	197	210	anti-parallel
Strand 4	C	181	184	anti-parallel

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There are 4 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	36	39	first strand
Strand 2	C	213	226	anti-parallel
Strand 3	C	197	210	anti-parallel
Strand 4	C	192	194	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	C	85	86	first strand
Strand 2	C	91	94	anti-parallel
Strand 3	C	45	54	anti-parallel
Strand 4	C	122	132	anti-parallel
Strand 5	C	107	108	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	C	338	341	first strand
Strand 2	C	328	331	anti-parallel
Strand 3	C	279	285	anti-parallel
Strand 4	C	267	270	anti-parallel
Strand 5	C	345	347	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	C	294	296	first strand
Strand 2	C	306	308	anti-parallel

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There are 3 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	428	429	first strand
Strand 2	C	419	420	anti-parallel
Strand 3	C	578	579	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	C	492	495	first strand
Strand 2	C	452	456	parallel
Strand 3	C	518	522	parallel
Strand 4	C	544	546	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	C	598	600	first strand
Strand 2	C	611	618	anti-parallel
Strand 3	C	626	633	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: 5VM9

Analysis of interatomic Contacts of Structural Units in PDB entry:
5VM9