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

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 5VMK entry

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

Chain ID	Initial residue	Terminal residue
A	SER 2	GLN 450
B	THR 3	PRO 449
C	SER 2	GLN 450

There are 36 helices in PDB entry 5VMK. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	13	17	Right-handed 310
Helix 2	AA2	A	21	25	Right-handed 310
Helix 3	AA3	A	31	43	Right-handed alpha
Helix 4	AA4	A	55	63	Right-handed alpha
Helix 5	AA5	A	78	85	Right-handed alpha
Helix 6	AA6	A	86	90	Right-handed 310
Helix 7	AA7	A	107	119	Right-handed alpha
Helix 8	AA8	A	151	155	Right-handed 310
Helix 9	AA9	A	156	161	Right-handed alpha
Helix 10	AB1	A	174	181	Right-handed alpha
Helix 11	AB2	A	196	205	Right-handed alpha
Helix 12	AB3	A	216	221	Right-handed 310
Helix 13	AB4	A	225	248	Right-handed alpha
Helix 14	AB5	B	13	17	Right-handed 310
Helix 15	AB6	B	21	24	Right-handed 310
Helix 16	AB7	B	32	43	Right-handed alpha
Helix 17	AB8	B	55	63	Right-handed alpha
Helix 18	AB9	B	79	85	Right-handed alpha
Helix 19	AC1	B	86	90	Right-handed 310
Helix 20	AC2	B	107	120	Right-handed alpha
Helix 21	AC3	B	151	155	Right-handed 310
Helix 22	AC4	B	158	162	Right-handed 310
Helix 23	AC5	B	174	181	Right-handed alpha
Helix 24	AC6	B	196	205	Right-handed alpha
Helix 25	AC7	B	216	221	Right-handed 310
Helix 26	AC8	B	225	248	Right-handed alpha
Helix 27	AC9	C	13	17	Right-handed 310
Helix 28	AD1	C	21	24	Right-handed 310
Helix 29	AD2	C	32	43	Right-handed alpha
Helix 30	AD3	C	55	63	Right-handed alpha
Helix 31	AD4	C	79	85	Right-handed alpha
Helix 32	AD5	C	107	120	Right-handed alpha
Helix 33	AD6	C	158	162	Right-handed 310
Helix 34	AD7	C	173	181	Right-handed alpha
Helix 35	AD8	C	216	221	Right-handed 310
Helix 36	AD9	C	225	248	Right-handed alpha

There are 22 sheets in PDB entry 5VMK. 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 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	69	72	first strand
Strand 2	A	47	52	parallel
Strand 3	A	3	9	parallel
Strand 4	A	95	100	parallel
Strand 5	A	164	173	anti-parallel
Strand 6	A	123	129	anti-parallel
Strand 7	A	210	212	parallel

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There are 2 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	138	142	first strand
Strand 2	A	145	150	anti-parallel

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There are 7 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	250	251	first strand
Strand 2	A	270	271	parallel
Strand 3	A	288	289	parallel
Strand 4	A	305	306	parallel
Strand 5	A	322	323	parallel
Strand 6	A	340	341	parallel
Strand 7	A	357	358	parallel

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There are 7 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	257	265	first strand
Strand 2	A	275	283	parallel
Strand 3	A	294	296	parallel
Strand 4	A	311	313	parallel
Strand 5	A	327	329	parallel
Strand 6	A	345	348	parallel
Strand 7	A	362	365	parallel

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There are 9 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	257	265	first strand
Strand 2	A	275	283	parallel
Strand 3	A	299	300	parallel
Strand 4	A	316	317	parallel
Strand 5	A	334	335	parallel
Strand 6	A	351	352	parallel
Strand 7	A	367	369	parallel
Strand 8	A	392	394	parallel
Strand 9	A	410	412	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	374	375	first strand
Strand 2	A	399	400	parallel
Strand 3	A	417	418	parallel
Strand 4	A	433	436	parallel
Strand 5	C	440	443	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	380	382	first strand
Strand 2	A	405	407	parallel
Strand 3	A	423	424	parallel

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There are 5 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	440	443	first strand
Strand 2	B	433	436	anti-parallel
Strand 3	B	417	418	parallel
Strand 4	B	399	400	parallel
Strand 5	B	374	375	parallel

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There are 7 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	69	72	first strand
Strand 2	B	47	52	parallel
Strand 3	B	4	9	parallel
Strand 4	B	95	100	parallel
Strand 5	B	164	173	anti-parallel
Strand 6	B	123	129	anti-parallel
Strand 7	B	210	212	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	B	26	27	first strand
Strand 2	B	30	31	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	B	138	142	first strand
Strand 2	B	145	150	anti-parallel

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There are 7 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	250	251	first strand
Strand 2	B	270	271	parallel
Strand 3	B	288	289	parallel
Strand 4	B	305	306	parallel
Strand 5	B	322	323	parallel
Strand 6	B	340	341	parallel
Strand 7	B	357	358	parallel

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There are 7 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	257	265	first strand
Strand 2	B	275	283	parallel
Strand 3	B	294	296	parallel
Strand 4	B	311	313	parallel
Strand 5	B	327	329	parallel
Strand 6	B	345	348	parallel
Strand 7	B	362	365	parallel

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There are 9 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	257	265	first strand
Strand 2	B	275	283	parallel
Strand 3	B	299	300	parallel
Strand 4	B	316	317	parallel
Strand 5	B	334	335	parallel
Strand 6	B	351	352	parallel
Strand 7	B	367	369	parallel
Strand 8	B	392	394	parallel
Strand 9	B	410	412	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	B	380	382	first strand
Strand 2	B	405	407	parallel
Strand 3	B	423	424	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	B	441	443	first strand
Strand 2	C	433	435	anti-parallel
Strand 3	C	417	418	parallel
Strand 4	C	399	400	parallel
Strand 5	C	374	375	parallel

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There are 7 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	69	72	first strand
Strand 2	C	47	52	parallel
Strand 3	C	4	9	parallel
Strand 4	C	96	100	parallel
Strand 5	C	164	172	anti-parallel
Strand 6	C	123	129	anti-parallel
Strand 7	C	210	212	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	C	26	27	first strand
Strand 2	C	30	31	anti-parallel

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There are 7 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	250	251	first strand
Strand 2	C	270	271	parallel
Strand 3	C	288	289	parallel
Strand 4	C	305	306	parallel
Strand 5	C	322	323	parallel
Strand 6	C	340	341	parallel
Strand 7	C	357	358	parallel

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There are 7 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	257	265	first strand
Strand 2	C	275	283	parallel
Strand 3	C	294	296	parallel
Strand 4	C	311	313	parallel
Strand 5	C	327	329	parallel
Strand 6	C	345	348	parallel
Strand 7	C	362	365	parallel

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There are 9 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	257	265	first strand
Strand 2	C	275	283	parallel
Strand 3	C	299	300	parallel
Strand 4	C	316	317	parallel
Strand 5	C	334	335	parallel
Strand 6	C	351	352	parallel
Strand 7	C	367	369	parallel
Strand 8	C	392	394	parallel
Strand 9	C	410	412	parallel

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There are 3 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	380	382	first strand
Strand 2	C	405	407	parallel
Strand 3	C	423	424	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: 5VMK

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