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

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 2VDU entry

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

Chain ID	Initial residue	Terminal residue
B	SER 2	LEU 436
D	SER 2	LEU 436
E	GLN 66	LEU 286
F	GLN 66	LEU 286

There are 26 helices in PDB entry 2VDU. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	B	280	285	Right-handed alpha
Helix 2	2	B	286	288	Right-handed 310
Helix 3	3	B	399	415	Right-handed alpha
Helix 4	4	B	423	427	Right-handed 310
Helix 5	5	D	280	285	Right-handed alpha
Helix 6	6	D	286	288	Right-handed 310
Helix 7	7	D	399	415	Right-handed alpha
Helix 8	8	D	423	427	Right-handed 310
Helix 9	9	E	72	76	Right-handed 310
Helix 10	10	E	82	84	Right-handed 310
Helix 11	11	E	107	117	Right-handed alpha
Helix 12	12	E	128	145	Right-handed alpha
Helix 13	13	E	161	170	Right-handed alpha
Helix 14	14	E	200	208	Right-handed alpha
Helix 15	15	E	221	235	Right-handed alpha
Helix 16	16	E	242	248	Right-handed alpha
Helix 17	17	E	249	257	Right-handed alpha
Helix 18	18	F	72	76	Right-handed 310
Helix 19	19	F	82	84	Right-handed 310
Helix 20	20	F	107	117	Right-handed alpha
Helix 21	21	F	128	145	Right-handed alpha
Helix 22	22	F	161	170	Right-handed alpha
Helix 23	23	F	200	208	Right-handed alpha
Helix 24	24	F	221	235	Right-handed alpha
Helix 25	25	F	242	248	Right-handed alpha
Helix 26	26	F	249	257	Right-handed alpha

There are 20 sheets in PDB entry 2VDU. Click on sheet of interest to get list of strands forming it: BA, BB, BC, BD, BE, BF, BG, BH, A, DB, C, DD, DE, DF, G, DH, EA, EB, FA, FB,

There are 2 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	3	4	first strand
Strand 2	B	421	422	anti-parallel

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There are 4 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	9	12	first strand
Strand 2	B	18	23	anti-parallel
Strand 3	B	26	33	anti-parallel
Strand 4	B	37	45	anti-parallel

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There are 4 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	105	110	first strand
Strand 2	B	116	121	anti-parallel
Strand 3	B	126	132	anti-parallel
Strand 4	B	140	147	anti-parallel

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There are 4 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	152	157	first strand
Strand 2	B	163	168	anti-parallel
Strand 3	B	172	177	anti-parallel
Strand 4	B	192	193	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	198	205	first strand
Strand 2	B	211	217	anti-parallel
Strand 3	B	222	227	anti-parallel
Strand 4	B	233	236	anti-parallel

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There are 4 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	244	249	first strand
Strand 2	B	254	259	anti-parallel
Strand 3	B	263	268	anti-parallel
Strand 4	B	274	279	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	310	315	first strand
Strand 2	B	321	326	anti-parallel
Strand 3	B	331	337	anti-parallel
Strand 4	B	345	352	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	357	363	first strand
Strand 2	B	366	371	anti-parallel
Strand 3	B	384	390	anti-parallel
Strand 4	B	395	398	anti-parallel

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There are 2 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	3	4	first strand
Strand 2	D	421	422	anti-parallel

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There are 4 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	9	12	first strand
Strand 2	D	18	23	anti-parallel
Strand 3	D	26	33	anti-parallel
Strand 4	D	37	45	anti-parallel

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There are 4 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	105	110	first strand
Strand 2	D	116	121	anti-parallel
Strand 3	D	126	132	anti-parallel
Strand 4	D	140	147	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	152	157	first strand
Strand 2	D	163	168	anti-parallel
Strand 3	D	172	177	anti-parallel
Strand 4	D	192	193	anti-parallel

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There are 4 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	198	205	first strand
Strand 2	D	211	217	anti-parallel
Strand 3	D	222	227	anti-parallel
Strand 4	D	233	236	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	244	249	first strand
Strand 2	D	254	259	anti-parallel
Strand 3	D	263	268	anti-parallel
Strand 4	D	273	279	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	310	315	first strand
Strand 2	D	321	326	anti-parallel
Strand 3	D	331	337	anti-parallel
Strand 4	D	345	352	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	357	363	first strand
Strand 2	D	366	371	anti-parallel
Strand 3	D	384	390	anti-parallel
Strand 4	D	395	398	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	86	87	first strand
Strand 2	E	92	93	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	155	159	first strand
Strand 2	E	121	126	parallel
Strand 3	E	97	102	parallel
Strand 4	E	175	181	parallel
Strand 5	E	209	219	parallel
Strand 6	E	273	279	anti-parallel
Strand 7	E	238	240	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	86	87	first strand
Strand 2	F	92	93	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	155	159	first strand
Strand 2	F	121	126	parallel
Strand 3	F	97	102	parallel
Strand 4	F	175	181	parallel
Strand 5	F	209	219	parallel
Strand 6	F	273	279	anti-parallel
Strand 7	F	238	240	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: 2VDU

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