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

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 2YMD entry

There are 6 chains in PDB entry 2YMD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	GLN 1	PHE 212
B	GLN 1	GLY 210
C	GLN 1	PHE 212
D	GLN 1	PHE 212
E	GLN 1	PHE 212
F	GLN 1	ASP 195

There are 30 helices in PDB entry 2YMD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	1	13	Right-handed alpha
Helix 2	2	A	66	71	Right-handed 310
Helix 3	3	A	81	83	Right-handed 310
Helix 4	4	B	1	13	Right-handed alpha
Helix 5	5	B	66	71	Right-handed 310
Helix 6	6	B	81	83	Right-handed 310
Helix 7	7	C	1	14	Right-handed alpha
Helix 8	8	C	66	71	Right-handed 310
Helix 9	9	C	81	83	Right-handed 310
Helix 10	10	D	1	13	Right-handed alpha
Helix 11	11	D	66	71	Right-handed 310
Helix 12	12	D	81	83	Right-handed 310
Helix 13	13	E	1	13	Right-handed alpha
Helix 14	14	E	66	71	Right-handed 310
Helix 15	15	E	81	83	Right-handed 310
Helix 16	16	F	1	13	Right-handed alpha
Helix 17	17	F	66	71	Right-handed 310
Helix 18	18	F	81	83	Right-handed 310
Helix 19	19	G	1	13	Right-handed alpha
Helix 20	20	G	66	71	Right-handed 310
Helix 21	21	G	81	83	Right-handed 310
Helix 22	22	H	1	13	Right-handed alpha
Helix 23	23	H	66	71	Right-handed 310
Helix 24	24	H	81	83	Right-handed 310
Helix 25	25	I	1	13	Right-handed alpha
Helix 26	26	I	66	70	Right-handed 310
Helix 27	27	I	81	83	Right-handed 310
Helix 28	28	J	1	13	Right-handed alpha
Helix 29	29	J	66	70	Right-handed 310
Helix 30	30	J	81	83	Right-handed 310

There are 30 sheets in PDB entry 2YMD. Click on sheet of interest to get list of strands forming it: AA, AB, AC, BA, BB, BC, CA, CB, CC, A, DB, C, EA, EB, EC, FA, FB, FC, GA, GB, GC, HA, HB, HC, IA, IB, IC, JA, JB, JC,

There are 6 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	75	79	first strand
Strand 2	A	104	108	anti-parallel
Strand 3	A	110	115	anti-parallel
Strand 4	A	47	64	anti-parallel
Strand 5	A	118	124	parallel
Strand 6	A	98	99	parallel

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There are 6 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	75	79	first strand
Strand 2	A	104	108	anti-parallel
Strand 3	A	110	115	anti-parallel
Strand 4	A	47	64	anti-parallel
Strand 5	A	27	42	anti-parallel
Strand 6	A	152	155	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	88	90	first strand
Strand 2	A	136	144	anti-parallel
Strand 3	A	193	204	anti-parallel
Strand 4	A	172	184	anti-parallel

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There are 6 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	75	79	first strand
Strand 2	B	104	108	anti-parallel
Strand 3	B	110	115	anti-parallel
Strand 4	B	47	64	anti-parallel
Strand 5	B	118	124	parallel
Strand 6	B	98	99	parallel

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There are 6 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	75	79	first strand
Strand 2	B	104	108	anti-parallel
Strand 3	B	110	115	anti-parallel
Strand 4	B	47	64	anti-parallel
Strand 5	B	27	42	anti-parallel
Strand 6	B	152	155	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	88	90	first strand
Strand 2	B	136	144	anti-parallel
Strand 3	B	189	204	anti-parallel
Strand 4	B	172	186	anti-parallel

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There are 6 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	75	79	first strand
Strand 2	C	104	108	anti-parallel
Strand 3	C	110	115	anti-parallel
Strand 4	C	47	64	anti-parallel
Strand 5	C	118	124	parallel
Strand 6	C	98	99	parallel

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There are 6 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	75	79	first strand
Strand 2	C	104	108	anti-parallel
Strand 3	C	110	115	anti-parallel
Strand 4	C	47	64	anti-parallel
Strand 5	C	27	42	anti-parallel
Strand 6	C	152	155	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	88	90	first strand
Strand 2	C	136	144	anti-parallel
Strand 3	C	193	204	anti-parallel
Strand 4	C	172	184	anti-parallel

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There are 6 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	75	79	first strand
Strand 2	D	104	108	anti-parallel
Strand 3	D	110	115	anti-parallel
Strand 4	D	47	64	anti-parallel
Strand 5	D	118	124	parallel
Strand 6	D	98	99	parallel

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There are 6 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	75	79	first strand
Strand 2	D	104	108	anti-parallel
Strand 3	D	110	115	anti-parallel
Strand 4	D	47	64	anti-parallel
Strand 5	D	27	42	anti-parallel
Strand 6	D	152	155	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	88	90	first strand
Strand 2	D	136	144	anti-parallel
Strand 3	D	193	204	anti-parallel
Strand 4	D	172	184	anti-parallel

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There are 6 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	75	79	first strand
Strand 2	E	104	108	anti-parallel
Strand 3	E	110	115	anti-parallel
Strand 4	E	47	64	anti-parallel
Strand 5	E	118	124	parallel
Strand 6	E	98	99	parallel

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There are 6 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	75	79	first strand
Strand 2	E	104	108	anti-parallel
Strand 3	E	110	115	anti-parallel
Strand 4	E	47	64	anti-parallel
Strand 5	E	27	42	anti-parallel
Strand 6	E	152	155	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	88	90	first strand
Strand 2	E	136	144	anti-parallel
Strand 3	E	193	204	anti-parallel
Strand 4	E	172	184	anti-parallel

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There are 6 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	75	79	first strand
Strand 2	F	104	108	anti-parallel
Strand 3	F	110	115	anti-parallel
Strand 4	F	47	64	anti-parallel
Strand 5	F	118	124	parallel
Strand 6	F	98	99	parallel

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There are 6 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	75	79	first strand
Strand 2	F	104	108	anti-parallel
Strand 3	F	110	115	anti-parallel
Strand 4	F	47	64	anti-parallel
Strand 5	F	27	42	anti-parallel
Strand 6	F	152	155	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	88	90	first strand
Strand 2	F	136	144	anti-parallel
Strand 3	F	189	204	anti-parallel
Strand 4	F	172	186	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	75	79	first strand
Strand 2	G	104	108	anti-parallel
Strand 3	G	110	115	anti-parallel
Strand 4	G	47	64	anti-parallel
Strand 5	G	118	124	parallel
Strand 6	G	98	99	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	75	79	first strand
Strand 2	G	104	108	anti-parallel
Strand 3	G	110	115	anti-parallel
Strand 4	G	47	64	anti-parallel
Strand 5	G	27	42	anti-parallel
Strand 6	G	152	155	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	88	90	first strand
Strand 2	G	136	144	anti-parallel
Strand 3	G	193	204	anti-parallel
Strand 4	G	172	184	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	75	79	first strand
Strand 2	H	104	108	anti-parallel
Strand 3	H	110	115	anti-parallel
Strand 4	H	47	64	anti-parallel
Strand 5	H	118	124	parallel
Strand 6	H	98	99	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	75	79	first strand
Strand 2	H	104	108	anti-parallel
Strand 3	H	110	115	anti-parallel
Strand 4	H	47	64	anti-parallel
Strand 5	H	27	42	anti-parallel
Strand 6	H	152	155	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	88	90	first strand
Strand 2	H	136	144	anti-parallel
Strand 3	H	193	204	anti-parallel
Strand 4	H	172	184	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	75	79	first strand
Strand 2	I	104	108	anti-parallel
Strand 3	I	110	115	anti-parallel
Strand 4	I	47	64	anti-parallel
Strand 5	I	118	124	parallel
Strand 6	I	98	99	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	75	79	first strand
Strand 2	I	104	108	anti-parallel
Strand 3	I	110	115	anti-parallel
Strand 4	I	47	64	anti-parallel
Strand 5	I	27	42	anti-parallel
Strand 6	I	152	155	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	88	90	first strand
Strand 2	I	136	144	anti-parallel
Strand 3	I	193	204	anti-parallel
Strand 4	I	172	184	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	75	79	first strand
Strand 2	J	104	108	anti-parallel
Strand 3	J	110	115	anti-parallel
Strand 4	J	47	64	anti-parallel
Strand 5	J	118	124	parallel
Strand 6	J	98	99	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	75	79	first strand
Strand 2	J	104	108	anti-parallel
Strand 3	J	110	115	anti-parallel
Strand 4	J	47	64	anti-parallel
Strand 5	J	27	42	anti-parallel
Strand 6	J	152	155	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	88	90	first strand
Strand 2	J	136	144	anti-parallel
Strand 3	J	189	204	anti-parallel
Strand 4	J	172	186	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: 2YMD

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