Analysis of interatomic Contacts of Structural Units in PDB entry:
2VKM

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 2VKM entry

There are 4 chains in PDB entry 2VKM (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	GLY 45	ASN 385
B	GLY 45	ASN 385
C	GLY 45	ASN 385
D	GLY 45	ASN 385

There are 49 helices in PDB entry 2VKM. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	53	57	Right-handed 310
Helix 2	2	A	123	127	Right-handed 310
Helix 3	3	A	135	144	Right-handed alpha
Helix 4	4	A	162	168	Right-handed alpha
Helix 5	5	A	180	182	Right-handed 310
Helix 6	6	A	216	222	Right-handed 310
Helix 7	7	A	238	252	Right-handed alpha
Helix 8	8	A	258	263	Right-handed alpha
Helix 9	9	A	276	280	Right-handed 310
Helix 10	10	A	301	305	Right-handed alpha
Helix 11	11	A	334	339	Right-handed alpha
Helix 12	12	A	378	383	Right-handed 310
Helix 13	13	B	53	57	Right-handed 310
Helix 14	14	B	123	127	Right-handed 310
Helix 15	15	B	135	144	Right-handed alpha
Helix 16	16	B	162	168	Right-handed alpha
Helix 17	17	B	180	182	Right-handed 310
Helix 18	18	B	216	222	Right-handed 310
Helix 19	19	B	238	252	Right-handed alpha
Helix 20	20	B	258	263	Right-handed alpha
Helix 21	21	B	276	280	Right-handed 310
Helix 22	22	B	301	305	Right-handed alpha
Helix 23	23	B	334	339	Right-handed alpha
Helix 24	24	B	347	349	Right-handed 310
Helix 25	25	B	378	383	Right-handed 310
Helix 26	26	C	53	57	Right-handed 310
Helix 27	27	C	123	127	Right-handed 310
Helix 28	28	C	135	144	Right-handed alpha
Helix 29	29	C	162	168	Right-handed alpha
Helix 30	30	C	180	182	Right-handed 310
Helix 31	31	C	216	222	Right-handed 310
Helix 32	32	C	238	252	Right-handed alpha
Helix 33	33	C	258	263	Right-handed alpha
Helix 34	34	C	276	280	Right-handed 310
Helix 35	35	C	301	305	Right-handed alpha
Helix 36	36	C	334	339	Right-handed alpha
Helix 37	37	C	378	383	Right-handed 310
Helix 38	38	D	53	57	Right-handed 310
Helix 39	39	D	123	127	Right-handed 310
Helix 40	40	D	135	144	Right-handed alpha
Helix 41	41	D	162	168	Right-handed alpha
Helix 42	42	D	180	182	Right-handed 310
Helix 43	43	D	216	222	Right-handed 310
Helix 44	44	D	238	252	Right-handed alpha
Helix 45	45	D	258	263	Right-handed alpha
Helix 46	46	D	276	280	Right-handed 310
Helix 47	47	D	301	305	Right-handed alpha
Helix 48	48	D	334	339	Right-handed alpha
Helix 49	49	D	378	383	Right-handed 310

There are 23 sheets in PDB entry 2VKM. Click on sheet of interest to get list of strands forming it: AA, AB, AC, AD, AE, AF, BA, BB, BC, BD, BE, BF, CA, CB, CC, CD, CE, CF, A, DB, C, DD, DE,

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	6	7	first strand
Strand 2	A	15	20	anti-parallel
Strand 3	A	25	32	anti-parallel
Strand 4	A	117	120	parallel
Strand 5	A	38	41	anti-parallel
Strand 6	A	95	106	parallel
Strand 7	A	75	86	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	6	7	first strand
Strand 2	A	15	20	anti-parallel
Strand 3	A	75	86	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	172	176	first strand
Strand 2	A	150	154	anti-parallel
Strand 3	A	341	346	anti-parallel
Strand 4	A	351	357	anti-parallel
Strand 5	A	184	192	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	211	212	first strand
Strand 2	A	203	208	anti-parallel
Strand 3	A	283	288	anti-parallel
Strand 4	A	294	300	anti-parallel
Strand 5	A	369	375	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	225	227	first strand
Strand 2	A	331	333	parallel
Strand 3	A	234	237	anti-parallel
Strand 4	A	324	327	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	268	270	first strand
Strand 2	A	318	322	anti-parallel
Strand 3	A	306	309	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	6	7	first strand
Strand 2	B	15	20	anti-parallel
Strand 3	B	25	32	anti-parallel
Strand 4	B	117	120	parallel
Strand 5	B	38	41	anti-parallel
Strand 6	B	94	106	parallel
Strand 7	B	75	86	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	6	7	first strand
Strand 2	B	15	20	anti-parallel
Strand 3	B	75	86	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	172	176	first strand
Strand 2	B	150	154	anti-parallel
Strand 3	B	341	346	anti-parallel
Strand 4	B	351	357	anti-parallel
Strand 5	B	184	192	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	211	212	first strand
Strand 2	B	203	208	anti-parallel
Strand 3	B	283	288	anti-parallel
Strand 4	B	294	300	anti-parallel
Strand 5	B	369	375	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	225	227	first strand
Strand 2	B	331	333	parallel
Strand 3	B	234	237	anti-parallel
Strand 4	B	324	327	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	268	270	first strand
Strand 2	B	318	322	anti-parallel
Strand 3	B	306	308	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	6	9	first strand
Strand 2	C	13	20	anti-parallel
Strand 3	C	25	32	anti-parallel
Strand 4	C	117	120	parallel
Strand 5	C	38	41	anti-parallel
Strand 6	C	95	106	parallel
Strand 7	C	75	86	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	6	9	first strand
Strand 2	C	13	20	anti-parallel
Strand 3	C	75	86	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	172	176	first strand
Strand 2	C	150	154	anti-parallel
Strand 3	C	341	346	anti-parallel
Strand 4	C	351	357	anti-parallel
Strand 5	C	184	192	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	200	201	first strand
Strand 2	C	225	227	anti-parallel
Strand 3	C	331	333	parallel
Strand 4	C	234	237	anti-parallel
Strand 5	C	324	327	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	211	212	first strand
Strand 2	C	203	208	anti-parallel
Strand 3	C	283	288	anti-parallel
Strand 4	C	294	300	anti-parallel
Strand 5	C	369	375	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	268	270	first strand
Strand 2	C	318	322	anti-parallel
Strand 3	C	306	308	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	6	9	first strand
Strand 2	D	13	20	anti-parallel
Strand 3	D	61	70	first strand
Strand 4	D	75	86	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	172	176	first strand
Strand 2	D	150	154	anti-parallel
Strand 3	D	341	346	anti-parallel
Strand 4	D	351	357	anti-parallel
Strand 5	D	184	192	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	211	212	first strand
Strand 2	D	203	208	anti-parallel
Strand 3	D	283	288	anti-parallel
Strand 4	D	294	300	anti-parallel
Strand 5	D	369	375	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	225	227	first strand
Strand 2	D	331	333	parallel
Strand 3	D	234	237	anti-parallel
Strand 4	D	324	327	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	268	270	first strand
Strand 2	D	318	322	anti-parallel
Strand 3	D	306	309	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: 2VKM

Analysis of interatomic Contacts of Structural Units in PDB entry:
2VKM