Analysis of interatomic Contacts of Structural Units in PDB entry:
1YPO

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 1YPO entry

There are 8 chains in PDB entry 1YPO (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ALA 142	ARG 271
B	MET 141	ALA 272
C	MET 141	ALA 272
D	ALA 142	LEU 270
E	ALA 142	LEU 270
F	MET 141	LEU 270
G	MET 141	ALA 272
H	ALA 142	LEU 270

There are 16 helices in PDB entry 1YPO. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	164	174	Right-handed alpha
Helix 2	2	A	184	195	Right-handed alpha
Helix 3	3	B	164	175	Right-handed alpha
Helix 4	4	B	184	196	Right-handed alpha
Helix 5	5	C	164	174	Right-handed alpha
Helix 6	6	C	184	195	Right-handed alpha
Helix 7	7	D	164	174	Right-handed alpha
Helix 8	8	D	184	194	Right-handed alpha
Helix 9	9	E	165	175	Right-handed alpha
Helix 10	10	E	184	194	Right-handed alpha
Helix 11	11	F	164	175	Right-handed alpha
Helix 12	12	F	184	196	Right-handed alpha
Helix 13	13	G	164	175	Right-handed alpha
Helix 14	14	G	184	196	Right-handed alpha
Helix 15	15	H	164	175	Right-handed alpha
Helix 16	16	H	184	195	Right-handed alpha

There are 15 sheets in PDB entry 1YPO. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O,

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	149	151	first strand
Strand 2	A	154	158	anti-parallel
Strand 3	A	261	267	anti-parallel
Strand 4	A	202	208	parallel
Strand 5	A	216	217	anti-parallel

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There are 6 strands in B sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	178	179	first strand
Strand 2	A	261	267	anti-parallel
Strand 3	A	202	208	parallel
Strand 4	A	242	247	anti-parallel
Strand 5	A	250	255	anti-parallel
Strand 6	A	231	232	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	B	149	151	first strand
Strand 2	B	154	158	anti-parallel
Strand 3	B	261	267	anti-parallel
Strand 4	B	201	208	parallel
Strand 5	B	216	217	anti-parallel

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There are 6 strands in D sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	178	179	first strand
Strand 2	B	261	267	anti-parallel
Strand 3	B	201	208	parallel
Strand 4	B	242	247	anti-parallel
Strand 5	B	250	255	anti-parallel
Strand 6	B	231	232	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	149	151	first strand
Strand 2	C	154	158	anti-parallel
Strand 3	C	261	267	anti-parallel
Strand 4	C	178	179	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	149	151	first strand
Strand 2	C	154	158	anti-parallel
Strand 3	C	261	267	anti-parallel
Strand 4	C	202	208	parallel
Strand 5	C	242	247	anti-parallel
Strand 6	C	250	255	anti-parallel
Strand 7	C	231	232	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	149	151	first strand
Strand 2	D	154	158	anti-parallel
Strand 3	D	261	267	anti-parallel
Strand 4	D	178	179	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	149	151	first strand
Strand 2	D	154	158	anti-parallel
Strand 3	D	261	267	anti-parallel
Strand 4	D	202	208	parallel
Strand 5	D	242	247	anti-parallel
Strand 6	D	250	255	anti-parallel
Strand 7	D	230	232	parallel

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There are 13 strands in I sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	149	151	first strand
Strand 2	E	154	158	anti-parallel
Strand 3	E	259	267	anti-parallel
Strand 4	E	163	164	anti-parallel
Strand 5	E	259	267	anti-parallel
Strand 6	E	178	179	anti-parallel
Strand 7	E	259	267	anti-parallel
Strand 8	E	202	208	parallel
Strand 9	E	216	217	anti-parallel
Strand 10	E	202	208	anti-parallel
Strand 11	E	242	247	anti-parallel
Strand 12	E	250	255	anti-parallel
Strand 13	E	230	232	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	149	151	first strand
Strand 2	F	154	158	anti-parallel
Strand 3	F	261	267	anti-parallel
Strand 4	F	178	179	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	149	151	first strand
Strand 2	F	154	158	anti-parallel
Strand 3	F	261	267	anti-parallel
Strand 4	F	202	208	parallel
Strand 5	F	242	247	anti-parallel
Strand 6	F	250	255	anti-parallel
Strand 7	F	231	232	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	149	151	first strand
Strand 2	G	154	158	anti-parallel
Strand 3	G	261	267	anti-parallel
Strand 4	G	178	179	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	149	151	first strand
Strand 2	G	154	158	anti-parallel
Strand 3	G	261	267	anti-parallel
Strand 4	G	202	208	parallel
Strand 5	G	242	247	anti-parallel
Strand 6	G	250	253	anti-parallel
Strand 7	G	231	232	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	149	151	first strand
Strand 2	H	154	158	anti-parallel
Strand 3	H	261	267	anti-parallel
Strand 4	H	178	179	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	149	151	first strand
Strand 2	H	154	158	anti-parallel
Strand 3	H	261	267	anti-parallel
Strand 4	H	202	208	parallel
Strand 5	H	242	247	anti-parallel
Strand 6	H	250	255	anti-parallel
Strand 7	H	230	232	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: 1YPO

Analysis of interatomic Contacts of Structural Units in PDB entry:
1YPO