Analysis of interatomic Contacts of Structural Units in PDB entry:
4YMD

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 4YMD entry

There are 6 chains in PDB entry 4YMD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	SER 116	GLU 269
B	SER 116	GLU 269
D	SER 116	ASN 270
F	SER 116	GLU 269
C	GLN 117	GLU 269
E	ILE 122	ASN 270

There are 24 helices in PDB entry 4YMD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	117	142	Right-handed alpha
Helix 2	AA2	A	162	173	Right-handed alpha
Helix 3	AA3	A	182	197	Right-handed alpha
Helix 4	AA4	A	235	239	Right-handed 310
Helix 5	AA5	B	117	142	Right-handed alpha
Helix 6	AA6	B	162	173	Right-handed alpha
Helix 7	AA7	B	182	197	Right-handed alpha
Helix 8	AA8	B	235	239	Right-handed 310
Helix 9	AA9	D	117	142	Right-handed alpha
Helix 10	AB1	D	162	173	Right-handed alpha
Helix 11	AB2	D	182	197	Right-handed alpha
Helix 12	AB3	D	235	239	Right-handed 310
Helix 13	AB4	F	117	142	Right-handed alpha
Helix 14	AB5	F	162	173	Right-handed alpha
Helix 15	AB6	F	182	197	Right-handed alpha
Helix 16	AB7	F	235	239	Right-handed 310
Helix 17	AB8	C	118	142	Right-handed alpha
Helix 18	AB9	C	162	173	Right-handed alpha
Helix 19	AC1	C	182	197	Right-handed alpha
Helix 20	AC2	C	235	239	Right-handed 310
Helix 21	AC3	E	123	142	Right-handed alpha
Helix 22	AC4	E	162	173	Right-handed alpha
Helix 23	AC5	E	182	197	Right-handed alpha
Helix 24	AC6	E	235	239	Right-handed 310

There are 12 sheets in PDB entry 4YMD. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2, AB3,

There are 4 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	147	148	first strand
Strand 2	A	152	161	anti-parallel
Strand 3	A	260	267	anti-parallel
Strand 4	A	176	177	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	215	216	first strand
Strand 2	A	200	206	anti-parallel
Strand 3	A	242	246	anti-parallel
Strand 4	A	251	254	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	B	147	148	first strand
Strand 2	B	152	161	anti-parallel
Strand 3	B	260	267	anti-parallel
Strand 4	B	176	177	anti-parallel

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There are 4 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	215	216	first strand
Strand 2	B	200	206	anti-parallel
Strand 3	B	242	246	anti-parallel
Strand 4	B	251	254	anti-parallel

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There are 4 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	147	148	first strand
Strand 2	D	152	161	anti-parallel
Strand 3	D	260	267	anti-parallel
Strand 4	D	176	177	anti-parallel

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There are 4 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	215	216	first strand
Strand 2	D	200	206	anti-parallel
Strand 3	D	242	246	anti-parallel
Strand 4	D	251	254	anti-parallel

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There are 4 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	147	148	first strand
Strand 2	F	152	161	anti-parallel
Strand 3	F	260	267	anti-parallel
Strand 4	F	176	177	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	F	215	216	first strand
Strand 2	F	200	206	anti-parallel
Strand 3	F	242	246	anti-parallel
Strand 4	F	251	254	anti-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	C	147	148	first strand
Strand 2	C	152	161	anti-parallel
Strand 3	C	260	267	anti-parallel
Strand 4	C	176	177	anti-parallel

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There are 4 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	215	216	first strand
Strand 2	C	200	206	anti-parallel
Strand 3	C	242	246	anti-parallel
Strand 4	C	251	254	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	E	147	148	first strand
Strand 2	E	152	161	anti-parallel
Strand 3	E	260	267	anti-parallel
Strand 4	E	176	177	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	E	215	216	first strand
Strand 2	E	200	206	anti-parallel
Strand 3	E	242	246	anti-parallel
Strand 4	E	251	254	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: 4YMD

Analysis of interatomic Contacts of Structural Units in PDB entry:
4YMD