Analysis of interatomic Contacts of Structural Units in PDB entry:
6MKD

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 6MKD entry

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

Chain ID	Initial residue	Terminal residue
C	ILE 0	HIS 177
D	ARG -26	ALA 191
A	GLN 1	PRO 203
B	ALA 1	ALA 239

There are 13 helices in PDB entry 6MKD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	C	45	52	Right-handed alpha
Helix 2	AA2	C	55	77	Right-handed alpha
Helix 3	AA3	D	53	62	Right-handed alpha
Helix 4	AA4	D	64	78	Right-handed alpha
Helix 5	AA5	D	78	85	Right-handed alpha
Helix 6	AA6	D	90	94	Right-handed 310
Helix 7	AA7	A	81	85	Right-handed 310
Helix 8	AA8	A	94	98	Right-handed 310
Helix 9	AA9	A	186	191	Right-handed alpha
Helix 10	AB1	B	80	84	Right-handed 310
Helix 11	AB2	B	112	116	Right-handed 310
Helix 12	AB3	B	127	132	Right-handed alpha
Helix 13	AB4	B	194	198	Right-handed alpha

There are 16 sheets in PDB entry 6MKD. 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, AB6, AB7,

There are 8 strands in AA1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	40	43	first strand
Strand 2	C	30	35	anti-parallel
Strand 3	C	19	26	anti-parallel
Strand 4	C	4	15	anti-parallel
Strand 5	D	7	18	anti-parallel
Strand 6	D	23	32	anti-parallel
Strand 7	D	35	41	anti-parallel
Strand 8	D	47	49	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	C	88	93	first strand
Strand 2	C	105	112	anti-parallel
Strand 3	C	145	150	anti-parallel
Strand 4	C	133	134	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	C	88	93	first strand
Strand 2	C	105	112	anti-parallel
Strand 3	C	145	150	anti-parallel
Strand 4	C	138	139	anti-parallel

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There are 3 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	118	120	first strand
Strand 2	C	164	166	anti-parallel
Strand 3	C	174	175	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	99	104	first strand
Strand 2	D	114	121	anti-parallel
Strand 3	D	157	164	anti-parallel
Strand 4	D	143	145	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	138	139	first strand
Strand 2	D	129	134	anti-parallel
Strand 3	D	171	177	anti-parallel
Strand 4	D	185	190	anti-parallel

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There are 5 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	3	4	first strand
Strand 2	A	18	24	anti-parallel
Strand 3	A	72	77	anti-parallel
Strand 4	A	62	67	anti-parallel
Strand 5	A	56	59	anti-parallel

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There are 5 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	9	13	first strand
Strand 2	A	108	113	parallel
Strand 3	A	87	92	anti-parallel
Strand 4	A	31	37	anti-parallel
Strand 5	A	44	50	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	A	9	13	first strand
Strand 2	A	108	113	parallel
Strand 3	A	87	92	anti-parallel
Strand 4	A	103	104	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	A	122	126	first strand
Strand 2	A	136	140	anti-parallel
Strand 3	A	172	178	anti-parallel
Strand 4	A	162	165	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	2	5	first strand
Strand 2	B	20	23	anti-parallel
Strand 3	B	71	76	anti-parallel
Strand 4	B	62	65	anti-parallel

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There are 6 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	8	12	first strand
Strand 2	B	105	110	parallel
Strand 3	B	85	92	anti-parallel
Strand 4	B	29	36	anti-parallel
Strand 5	B	40	47	anti-parallel
Strand 6	B	54	55	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	8	12	first strand
Strand 2	B	105	110	parallel
Strand 3	B	85	92	anti-parallel
Strand 4	B	100	101	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	120	124	first strand
Strand 2	B	136	146	anti-parallel
Strand 3	B	184	193	anti-parallel
Strand 4	B	166	168	anti-parallel

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There are 4 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	120	124	first strand
Strand 2	B	136	146	anti-parallel
Strand 3	B	184	193	anti-parallel
Strand 4	B	173	174	anti-parallel

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There are 3 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	151	157	first strand
Strand 2	B	203	210	anti-parallel
Strand 3	B	229	236	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: 6MKD

Analysis of interatomic Contacts of Structural Units in PDB entry:
6MKD