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

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 5MDP entry

There are 3 chains in PDB entry 5MDP (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	GLU 10	PHE 350
B	GLU 10	PHE 350
C	GLU 10	PHE 350

There are 18 helices in PDB entry 5MDP. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	13	17	Right-handed 310
Helix 2	AA2	A	38	46	Right-handed alpha
Helix 3	AA3	A	117	123	Right-handed alpha
Helix 4	AA4	A	130	135	Right-handed alpha
Helix 5	AA5	A	159	162	Right-handed 310
Helix 6	AA6	A	175	179	Right-handed 310
Helix 7	AA7	B	13	17	Right-handed 310
Helix 8	AA8	B	38	46	Right-handed alpha
Helix 9	AA9	B	117	123	Right-handed alpha
Helix 10	AB1	B	130	135	Right-handed alpha
Helix 11	AB2	B	159	162	Right-handed 310
Helix 12	AB3	B	175	179	Right-handed 310
Helix 13	AB4	C	13	17	Right-handed 310
Helix 14	AB5	C	38	46	Right-handed alpha
Helix 15	AB6	C	117	123	Right-handed alpha
Helix 16	AB7	C	130	135	Right-handed alpha
Helix 17	AB8	C	159	162	Right-handed 310
Helix 18	AB9	C	175	179	Right-handed 310

There are 6 sheets in PDB entry 5MDP. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6,

There are 15 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	47	49	first strand
Strand 2	A	20	34	anti-parallel
Strand 3	A	55	62	anti-parallel
Strand 4	A	70	77	anti-parallel
Strand 5	A	91	102	anti-parallel
Strand 6	A	106	114	anti-parallel
Strand 7	A	148	156	anti-parallel
Strand 8	A	164	172	anti-parallel
Strand 9	A	184	194	anti-parallel
Strand 10	A	197	211	anti-parallel
Strand 11	A	214	228	anti-parallel
Strand 12	A	233	246	anti-parallel
Strand 13	A	251	265	anti-parallel
Strand 14	A	280	282	anti-parallel
Strand 15	A	285	287	anti-parallel

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There are 9 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	47	49	first strand
Strand 2	A	20	34	anti-parallel
Strand 3	A	339	349	anti-parallel
Strand 4	A	307	317	anti-parallel
Strand 5	A	292	304	anti-parallel
Strand 6	A	268	277	anti-parallel
Strand 7	A	251	265	anti-parallel
Strand 8	A	280	282	anti-parallel
Strand 9	A	285	287	anti-parallel

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There are 15 strands in AA3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	47	49	first strand
Strand 2	B	20	34	anti-parallel
Strand 3	B	55	62	anti-parallel
Strand 4	B	70	77	anti-parallel
Strand 5	B	91	102	anti-parallel
Strand 6	B	106	114	anti-parallel
Strand 7	B	148	156	anti-parallel
Strand 8	B	164	172	anti-parallel
Strand 9	B	184	194	anti-parallel
Strand 10	B	197	211	anti-parallel
Strand 11	B	214	228	anti-parallel
Strand 12	B	233	246	anti-parallel
Strand 13	B	251	265	anti-parallel
Strand 14	B	280	282	anti-parallel
Strand 15	B	285	287	anti-parallel

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There are 9 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	47	49	first strand
Strand 2	B	20	34	anti-parallel
Strand 3	B	339	349	anti-parallel
Strand 4	B	307	317	anti-parallel
Strand 5	B	292	304	anti-parallel
Strand 6	B	268	277	anti-parallel
Strand 7	B	251	265	anti-parallel
Strand 8	B	280	282	anti-parallel
Strand 9	B	285	287	anti-parallel

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There are 15 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	47	49	first strand
Strand 2	C	20	34	anti-parallel
Strand 3	C	55	62	anti-parallel
Strand 4	C	70	77	anti-parallel
Strand 5	C	91	102	anti-parallel
Strand 6	C	106	114	anti-parallel
Strand 7	C	148	156	anti-parallel
Strand 8	C	164	172	anti-parallel
Strand 9	C	184	194	anti-parallel
Strand 10	C	197	211	anti-parallel
Strand 11	C	214	228	anti-parallel
Strand 12	C	233	246	anti-parallel
Strand 13	C	251	265	anti-parallel
Strand 14	C	280	282	anti-parallel
Strand 15	C	285	287	anti-parallel

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There are 9 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	47	49	first strand
Strand 2	C	20	34	anti-parallel
Strand 3	C	339	349	anti-parallel
Strand 4	C	307	317	anti-parallel
Strand 5	C	292	304	anti-parallel
Strand 6	C	268	277	anti-parallel
Strand 7	C	251	265	anti-parallel
Strand 8	C	280	282	anti-parallel
Strand 9	C	285	287	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: 5MDP

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