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

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 2YDP entry

There are 3 chains in PDB entry 2YDP (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	GLN 20	LYS 380
B	GLY 22	LYS 380
C	GLY 22	LYS 380

There are 3 helices in PDB entry 2YDP. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	375	379	Right-handed alpha
Helix 2	2	B	375	379	Right-handed alpha
Helix 3	3	C	375	379	Right-handed alpha

There are 18 sheets in PDB entry 2YDP. 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,

There are 4 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	25	31	first strand
Strand 2	A	368	374	anti-parallel
Strand 3	A	350	355	anti-parallel
Strand 4	A	340	344	anti-parallel

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There are 4 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	42	49	first strand
Strand 2	A	55	61	anti-parallel
Strand 3	A	71	76	anti-parallel
Strand 4	A	84	89	anti-parallel

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There are 4 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	98	106	first strand
Strand 2	A	119	125	anti-parallel
Strand 3	A	133	140	anti-parallel
Strand 4	A	148	156	anti-parallel

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There are 4 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	168	176	first strand
Strand 2	A	179	186	anti-parallel
Strand 3	A	196	202	anti-parallel
Strand 4	A	212	215	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	223	231	first strand
Strand 2	A	237	244	anti-parallel
Strand 3	A	259	264	anti-parallel
Strand 4	A	276	278	anti-parallel

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There are 4 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	291	295	first strand
Strand 2	A	303	307	anti-parallel
Strand 3	A	314	317	anti-parallel
Strand 4	A	326	329	anti-parallel

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There are 4 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	25	31	first strand
Strand 2	B	368	374	anti-parallel
Strand 3	B	350	355	anti-parallel
Strand 4	B	340	343	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	42	49	first strand
Strand 2	B	55	61	anti-parallel
Strand 3	B	71	76	anti-parallel
Strand 4	B	84	89	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	98	106	first strand
Strand 2	B	119	125	anti-parallel
Strand 3	B	133	140	anti-parallel
Strand 4	B	148	156	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	168	176	first strand
Strand 2	B	179	186	anti-parallel
Strand 3	B	196	202	anti-parallel
Strand 4	B	212	215	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	223	231	first strand
Strand 2	B	237	244	anti-parallel
Strand 3	B	259	264	anti-parallel
Strand 4	B	276	278	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	291	295	first strand
Strand 2	B	303	307	anti-parallel
Strand 3	B	314	317	anti-parallel
Strand 4	B	326	329	anti-parallel

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There are 4 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	25	31	first strand
Strand 2	C	368	374	anti-parallel
Strand 3	C	350	355	anti-parallel
Strand 4	C	340	343	anti-parallel

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There are 4 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	42	49	first strand
Strand 2	C	55	61	anti-parallel
Strand 3	C	71	76	anti-parallel
Strand 4	C	84	89	anti-parallel

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There are 4 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	98	106	first strand
Strand 2	C	119	125	anti-parallel
Strand 3	C	133	140	anti-parallel
Strand 4	C	148	156	anti-parallel

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There are 4 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	168	176	first strand
Strand 2	C	179	186	anti-parallel
Strand 3	C	196	202	anti-parallel
Strand 4	C	212	215	anti-parallel

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There are 4 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	223	231	first strand
Strand 2	C	237	244	anti-parallel
Strand 3	C	259	264	anti-parallel
Strand 4	C	276	278	anti-parallel

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There are 4 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	291	295	first strand
Strand 2	C	303	307	anti-parallel
Strand 3	C	314	317	anti-parallel
Strand 4	C	326	329	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: 2YDP

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