Analysis of interatomic Contacts of Structural Units in PDB entry:
5DMK

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 5DMK entry

There are 8 chains in PDB entry 5DMK (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ILE 2	LEU 172
B	SER -27	ARG 192
C	ASP 1	GLU 173
D	SER -27	ARG 192
E	ASP 1	GLU 173
F	SER -27	ARG 192
G	ASP 1	GLU 173
H	SER -27	TRP 191

There are 23 helices in PDB entry 5DMK. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	58	79	Right-handed alpha
Helix 2	AA2	B	52	54	Right-handed 310
Helix 3	AA3	B	55	79	Right-handed alpha
Helix 4	AA4	B	79	87	Right-handed alpha
Helix 5	AA5	B	91	95	Right-handed 310
Helix 6	AA6	C	58	79	Right-handed alpha
Helix 7	AA7	D	52	54	Right-handed 310
Helix 8	AA8	D	55	67	Right-handed alpha
Helix 9	AA9	D	67	79	Right-handed alpha
Helix 10	AB1	D	79	87	Right-handed alpha
Helix 11	AB2	D	91	95	Right-handed 310
Helix 12	AB3	E	58	79	Right-handed alpha
Helix 13	AB4	F	52	54	Right-handed 310
Helix 14	AB5	F	55	79	Right-handed alpha
Helix 15	AB6	F	79	87	Right-handed alpha
Helix 16	AB7	F	91	95	Right-handed 310
Helix 17	AB8	G	49	54	Right-handed alpha
Helix 18	AB9	G	58	79	Right-handed alpha
Helix 19	AC1	H	52	54	Right-handed 310
Helix 20	AC2	H	55	67	Right-handed alpha
Helix 21	AC3	H	67	79	Right-handed alpha
Helix 22	AC4	H	79	88	Right-handed alpha
Helix 23	AC5	H	91	95	Right-handed 310

There are 26 sheets in PDB entry 5DMK. 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, AB8, AB9, AC1, AC2, AC3, AC4, AC5, AC6, AC7, AC8,

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	A	42	45	first strand
Strand 2	A	31	37	anti-parallel
Strand 3	A	21	28	anti-parallel
Strand 4	A	6	17	anti-parallel
Strand 5	B	8	19	anti-parallel
Strand 6	B	24	33	anti-parallel
Strand 7	B	36	42	anti-parallel
Strand 8	B	48	50	anti-parallel

Back to list of sheets
Back to top of page

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	90	95	first strand
Strand 2	A	105	114	anti-parallel
Strand 3	A	147	155	anti-parallel
Strand 4	A	134	136	anti-parallel

Back to list of sheets
Back to top of page

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	90	95	first strand
Strand 2	A	105	114	anti-parallel
Strand 3	A	147	155	anti-parallel
Strand 4	A	140	141	anti-parallel

Back to list of sheets
Back to top of page

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	A	128	130	first strand
Strand 2	A	120	125	anti-parallel
Strand 3	A	163	168	anti-parallel

Back to list of sheets
Back to top of page

There are 8 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	101	107	first strand
Strand 2	B	116	125	anti-parallel
Strand 3	B	158	166	anti-parallel
Strand 4	B	145	148	anti-parallel
Strand 5	H	145	148	anti-parallel
Strand 6	H	158	166	anti-parallel
Strand 7	H	116	125	anti-parallel
Strand 8	H	101	106	anti-parallel

Back to list of sheets
Back to top of page

There are 6 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	151	152	first strand
Strand 2	B	158	166	anti-parallel
Strand 3	B	145	148	anti-parallel
Strand 4	H	145	148	anti-parallel
Strand 5	H	158	166	anti-parallel
Strand 6	H	151	152	anti-parallel

Back to list of sheets
Back to top of page

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	B	139	140	first strand
Strand 2	B	131	136	anti-parallel
Strand 3	B	174	179	anti-parallel
Strand 4	B	187	191	anti-parallel

Back to list of sheets
Back to top of page

There are 8 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	42	45	first strand
Strand 2	C	31	37	anti-parallel
Strand 3	C	21	28	anti-parallel
Strand 4	C	6	17	anti-parallel
Strand 5	D	8	19	anti-parallel
Strand 6	D	24	33	anti-parallel
Strand 7	D	36	42	anti-parallel
Strand 8	D	48	50	anti-parallel

Back to list of sheets
Back to top of page

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	90	95	first strand
Strand 2	C	105	114	anti-parallel
Strand 3	C	147	155	anti-parallel
Strand 4	C	134	136	anti-parallel

Back to list of sheets
Back to top of page

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	90	95	first strand
Strand 2	C	105	114	anti-parallel
Strand 3	C	147	155	anti-parallel
Strand 4	C	140	141	anti-parallel

Back to list of sheets
Back to top of page

There are 3 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	128	130	first strand
Strand 2	C	120	125	anti-parallel
Strand 3	C	165	168	anti-parallel

Back to list of sheets
Back to top of page

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	D	101	107	first strand
Strand 2	D	117	125	anti-parallel
Strand 3	D	158	164	anti-parallel
Strand 4	D	145	147	anti-parallel

Back to list of sheets
Back to top of page

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	D	101	107	first strand
Strand 2	D	117	125	anti-parallel
Strand 3	D	158	164	anti-parallel
Strand 4	D	151	152	anti-parallel

Back to list of sheets
Back to top of page

There are 3 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	131	135	first strand
Strand 2	D	175	179	anti-parallel
Strand 3	D	187	189	anti-parallel

Back to list of sheets
Back to top of page

There are 8 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	43	45	first strand
Strand 2	E	31	36	anti-parallel
Strand 3	E	21	28	anti-parallel
Strand 4	E	6	17	anti-parallel
Strand 5	F	8	19	anti-parallel
Strand 6	F	24	33	anti-parallel
Strand 7	F	36	42	anti-parallel
Strand 8	F	48	50	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	90	95	first strand
Strand 2	E	105	114	anti-parallel
Strand 3	E	147	155	anti-parallel
Strand 4	E	134	136	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	90	95	first strand
Strand 2	E	105	114	anti-parallel
Strand 3	E	147	155	anti-parallel
Strand 4	E	140	141	anti-parallel

Back to list of sheets
Back to top of page

There are 2 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	120	125	first strand
Strand 2	E	163	168	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	101	107	first strand
Strand 2	F	116	125	anti-parallel
Strand 3	F	158	166	anti-parallel
Strand 4	F	145	147	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	101	107	first strand
Strand 2	F	116	125	anti-parallel
Strand 3	F	158	166	anti-parallel
Strand 4	F	151	152	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AC3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	139	140	first strand
Strand 2	F	131	136	anti-parallel
Strand 3	F	174	179	anti-parallel
Strand 4	F	187	190	anti-parallel

Back to list of sheets
Back to top of page

There are 8 strands in AC4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	42	45	first strand
Strand 2	G	31	37	anti-parallel
Strand 3	G	21	28	anti-parallel
Strand 4	G	6	17	anti-parallel
Strand 5	H	8	19	anti-parallel
Strand 6	H	24	33	anti-parallel
Strand 7	H	36	42	anti-parallel
Strand 8	H	48	50	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AC5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	90	95	first strand
Strand 2	G	105	114	anti-parallel
Strand 3	G	147	155	anti-parallel
Strand 4	G	134	136	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AC6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	90	95	first strand
Strand 2	G	105	114	anti-parallel
Strand 3	G	147	155	anti-parallel
Strand 4	G	140	141	anti-parallel

Back to list of sheets
Back to top of page

There are 3 strands in AC7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	128	130	first strand
Strand 2	G	120	125	anti-parallel
Strand 3	G	163	168	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AC8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	139	140	first strand
Strand 2	H	131	136	anti-parallel
Strand 3	H	174	179	anti-parallel
Strand 4	H	187	190	anti-parallel

Back to list of sheets
Back to top of page

Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il

Analysis of interatomic Contacts of Structural Units in PDB entry: 5DMK

Analysis of interatomic Contacts of Structural Units in PDB entry:
5DMK