Analysis of interatomic Contacts of Structural Units in PDB entry:
4YD8

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 4YD8 entry

There are 2 chains in PDB entry 4YD8 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	LEU 3	PRO 369
B	LYS 5	PRO 369

There are 5 helices in PDB entry 4YD8. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	142	146	Right-handed 310
Helix 2	AA2	A	207	213	Right-handed alpha
Helix 3	AA3	B	142	146	Right-handed 310
Helix 4	AA4	B	207	213	Right-handed alpha
Helix 5	AA5	B	214	217	Right-handed 310

There are 14 sheets in PDB entry 4YD8. 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,

There are 5 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	4	5	first strand
Strand 2	A	319	325	parallel
Strand 3	A	311	316	anti-parallel
Strand 4	A	302	307	anti-parallel
Strand 5	A	287	294	anti-parallel

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There are 5 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	330	338	first strand
Strand 2	A	341	349	anti-parallel
Strand 3	A	353	358	anti-parallel
Strand 4	A	7	13	anti-parallel
Strand 5	B	57	59	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	A	25	28	first strand
Strand 2	A	39	43	anti-parallel
Strand 3	A	48	52	anti-parallel
Strand 4	A	68	73	anti-parallel

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There are 5 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	57	59	first strand
Strand 2	B	7	13	parallel
Strand 3	B	353	358	anti-parallel
Strand 4	B	341	349	anti-parallel
Strand 5	B	330	338	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	A	80	84	first strand
Strand 2	A	94	98	anti-parallel
Strand 3	A	102	108	anti-parallel
Strand 4	A	123	130	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	A	135	141	first strand
Strand 2	A	151	156	anti-parallel
Strand 3	A	160	165	anti-parallel
Strand 4	A	168	174	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	A	184	187	first strand
Strand 2	A	192	196	anti-parallel
Strand 3	A	201	206	anti-parallel
Strand 4	A	237	240	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	A	245	251	first strand
Strand 2	A	259	264	anti-parallel
Strand 3	A	267	271	anti-parallel
Strand 4	A	277	282	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	B	25	28	first strand
Strand 2	B	39	43	anti-parallel
Strand 3	B	48	52	anti-parallel
Strand 4	B	68	73	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	B	80	84	first strand
Strand 2	B	94	98	anti-parallel
Strand 3	B	102	109	anti-parallel
Strand 4	B	122	130	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	B	135	141	first strand
Strand 2	B	151	156	anti-parallel
Strand 3	B	160	165	anti-parallel
Strand 4	B	168	174	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	B	184	187	first strand
Strand 2	B	192	196	anti-parallel
Strand 3	B	201	206	anti-parallel
Strand 4	B	237	240	anti-parallel

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There are 4 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	245	250	first strand
Strand 2	B	260	264	anti-parallel
Strand 3	B	267	271	anti-parallel
Strand 4	B	277	282	anti-parallel

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There are 4 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	287	294	first strand
Strand 2	B	302	307	anti-parallel
Strand 3	B	311	316	anti-parallel
Strand 4	B	319	325	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: 4YD8

Analysis of interatomic Contacts of Structural Units in PDB entry:
4YD8