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

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 5DMG entry

Note, this PDB entry contains modified residue(s) PHOSPHOSERINE (SEP) . This residue is treated as heterogroup (ligand) both in the PDB entry and in LPC/CSU analysis.

There are 12 chains in PDB entry 5DMG (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
H	GLN 102	SER 1101
L	VAL 503	GLU 2105
C	GLN 102	SER 1101
D	GLN 502	GLU 2105
E	GLN 102	PRO 1099
F	GLN 502	GLU 2105
Z	VAL 420	ASP 421
Z	PRO 423	LEU 428
P	MET 419	ASP 421
P	PRO 423	ASP 430
X	MET 419	ASP 421
X	PRO 423	LEU 425

There are 19 helices in PDB entry 5DMG. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	H	295	298	Right-handed 310
Helix 2	AA2	H	321	325	Right-handed 310
Helix 3	AA3	H	1042	1044	Right-handed 310
Helix 4	AA4	H	1087	1090	Right-handed 310
Helix 5	AA5	L	725	729	Right-handed 310
Helix 6	AA6	L	2013	2019	Right-handed alpha
Helix 7	AA7	L	2075	2081	Right-handed alpha
Helix 8	AA8	C	321	325	Right-handed 310
Helix 9	AA9	C	1042	1044	Right-handed 310
Helix 10	AB1	C	1073	1078	Right-handed alpha
Helix 11	AB2	C	1087	1090	Right-handed 310
Helix 12	AB3	D	725	729	Right-handed 310
Helix 13	AB4	D	2013	2018	Right-handed alpha
Helix 14	AB5	D	2075	2080	Right-handed alpha
Helix 15	AB6	E	321	325	Right-handed 310
Helix 16	AB7	E	1042	1044	Right-handed 310
Helix 17	AB8	F	725	729	Right-handed 310
Helix 18	AB9	F	2013	2018	Right-handed alpha
Helix 19	AC1	F	2075	2079	Right-handed alpha

There are 33 sheets in PDB entry 5DMG. 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, AC9, AD1, AD2, AD3, AD4, AD5, AD6,

There are 4 strands in AA1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	103	107	first strand
Strand 2	H	119	125	anti-parallel
Strand 3	H	312	317	anti-parallel
Strand 4	H	302	306	anti-parallel

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There are 6 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	111	112	first strand
Strand 2	H	405	409	parallel
Strand 3	H	326	332	anti-parallel
Strand 4	H	198	204	anti-parallel
Strand 5	H	210	252	anti-parallel
Strand 6	H	291	293	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	H	111	112	first strand
Strand 2	H	405	409	parallel
Strand 3	H	326	332	anti-parallel
Strand 4	H	399	401	anti-parallel

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There are 4 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	1006	1010	first strand
Strand 2	H	1022	1031	anti-parallel
Strand 3	H	1062	1070	anti-parallel
Strand 4	H	1049	1051	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	H	1006	1010	first strand
Strand 2	H	1022	1031	anti-parallel
Strand 3	H	1062	1070	anti-parallel
Strand 4	H	1055	1056	anti-parallel

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There are 3 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	1037	1040	first strand
Strand 2	H	1081	1086	anti-parallel
Strand 3	H	1091	1096	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	L	504	506	first strand
Strand 2	L	519	552	anti-parallel
Strand 3	L	716	721	anti-parallel
Strand 4	L	706	711	anti-parallel

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There are 6 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	511	514	first strand
Strand 2	L	805	810	parallel
Strand 3	L	730	753	anti-parallel
Strand 4	L	598	604	anti-parallel
Strand 5	L	611	615	anti-parallel
Strand 6	L	696	697	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	L	511	514	first strand
Strand 2	L	805	810	parallel
Strand 3	L	730	753	anti-parallel
Strand 4	L	798	801	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	L	2006	2010	first strand
Strand 2	L	2021	2031	anti-parallel
Strand 3	L	2065	2074	anti-parallel
Strand 4	L	2051	2055	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	L	2045	2047	first strand
Strand 2	L	2037	2042	anti-parallel
Strand 3	L	2083	2089	anti-parallel
Strand 4	L	2097	2102	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	C	103	107	first strand
Strand 2	C	118	125	anti-parallel
Strand 3	C	312	317	anti-parallel
Strand 4	C	302	306	anti-parallel

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There are 6 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	111	112	first strand
Strand 2	C	405	409	parallel
Strand 3	C	326	332	anti-parallel
Strand 4	C	198	204	anti-parallel
Strand 5	C	211	252	anti-parallel
Strand 6	C	291	293	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	C	111	112	first strand
Strand 2	C	405	409	parallel
Strand 3	C	326	332	anti-parallel
Strand 4	C	399	401	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	C	1006	1010	first strand
Strand 2	C	1022	1031	anti-parallel
Strand 3	C	1062	1070	anti-parallel
Strand 4	C	1050	1051	anti-parallel

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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	C	1006	1010	first strand
Strand 2	C	1022	1031	anti-parallel
Strand 3	C	1062	1070	anti-parallel
Strand 4	C	1055	1056	anti-parallel

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There are 3 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	1037	1040	first strand
Strand 2	C	1081	1086	anti-parallel
Strand 3	C	1091	1096	anti-parallel

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There are 4 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	504	506	first strand
Strand 2	D	519	552	anti-parallel
Strand 3	D	716	721	anti-parallel
Strand 4	D	706	711	anti-parallel

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There are 6 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	511	513	first strand
Strand 2	D	805	809	parallel
Strand 3	D	730	753	anti-parallel
Strand 4	D	598	604	anti-parallel
Strand 5	D	611	615	anti-parallel
Strand 6	D	696	697	anti-parallel

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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	D	511	513	first strand
Strand 2	D	805	809	parallel
Strand 3	D	730	753	anti-parallel
Strand 4	D	798	801	anti-parallel

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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	D	2006	2010	first strand
Strand 2	D	2021	2031	anti-parallel
Strand 3	D	2065	2074	anti-parallel
Strand 4	D	2051	2055	anti-parallel

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There are 4 strands in AC4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	2045	2046	first strand
Strand 2	D	2037	2042	anti-parallel
Strand 3	D	2083	2089	anti-parallel
Strand 4	D	2097	2102	anti-parallel

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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	E	103	107	first strand
Strand 2	E	118	125	anti-parallel
Strand 3	E	312	317	anti-parallel
Strand 4	E	302	306	anti-parallel

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There are 6 strands in AC6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	111	112	first strand
Strand 2	E	405	409	parallel
Strand 3	E	326	332	anti-parallel
Strand 4	E	198	204	anti-parallel
Strand 5	E	210	252	anti-parallel
Strand 6	E	291	293	anti-parallel

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There are 4 strands in AC7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	111	112	first strand
Strand 2	E	405	409	parallel
Strand 3	E	326	332	anti-parallel
Strand 4	E	399	401	anti-parallel

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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	E	1006	1010	first strand
Strand 2	E	1022	1031	anti-parallel
Strand 3	E	1062	1070	anti-parallel
Strand 4	E	1049	1051	anti-parallel

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There are 4 strands in AC9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	1006	1010	first strand
Strand 2	E	1022	1031	anti-parallel
Strand 3	E	1062	1070	anti-parallel
Strand 4	E	1055	1056	anti-parallel

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There are 3 strands in AD1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	1037	1040	first strand
Strand 2	E	1080	1086	anti-parallel
Strand 3	E	1091	1097	anti-parallel

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There are 4 strands in AD2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	504	506	first strand
Strand 2	F	519	552	anti-parallel
Strand 3	F	716	721	anti-parallel
Strand 4	F	706	711	anti-parallel

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There are 6 strands in AD3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	511	513	first strand
Strand 2	F	805	809	parallel
Strand 3	F	731	753	anti-parallel
Strand 4	F	598	604	anti-parallel
Strand 5	F	611	615	anti-parallel
Strand 6	F	696	697	anti-parallel

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There are 4 strands in AD4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	511	513	first strand
Strand 2	F	805	809	parallel
Strand 3	F	731	753	anti-parallel
Strand 4	F	798	801	anti-parallel

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There are 4 strands in AD5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	2006	2007	first strand
Strand 2	F	2021	2031	anti-parallel
Strand 3	F	2065	2074	anti-parallel
Strand 4	F	2051	2052	anti-parallel

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There are 3 strands in AD6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	2038	2042	first strand
Strand 2	F	2083	2088	anti-parallel
Strand 3	F	2097	2102	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: 5DMG

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