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

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 5CDP entry

There are 4 chains in PDB entry 5CDP (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ILE 9	GLY 491
B	LYS 417	ALA 640
C	ASN 10	LEU 490
D	LYS 417	PHE 485

There are 58 helices in PDB entry 5CDP. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	14	33	Right-handed alpha
Helix 2	AA2	A	43	56	Right-handed alpha
Helix 3	AA3	A	67	78	Right-handed alpha
Helix 4	AA4	A	82	94	Right-handed alpha
Helix 5	AA5	A	131	137	Right-handed alpha
Helix 6	AA6	A	165	171	Right-handed alpha
Helix 7	AA7	A	187	201	Right-handed alpha
Helix 8	AA8	A	205	210	Right-handed alpha
Helix 9	AA9	A	227	237	Right-handed alpha
Helix 10	AB1	A	269	283	Right-handed alpha
Helix 11	AB2	A	313	325	Right-handed alpha
Helix 12	AB3	A	347	390	Right-handed alpha
Helix 13	AB4	A	390	400	Right-handed alpha
Helix 14	AB5	A	403	416	Right-handed alpha
Helix 15	AB6	A	418	427	Right-handed alpha
Helix 16	AB7	A	429	434	Right-handed 310
Helix 17	AB8	A	436	461	Right-handed alpha
Helix 18	AB9	A	461	481	Right-handed alpha
Helix 19	AC1	B	436	447	Right-handed alpha
Helix 20	AC2	B	468	475	Right-handed alpha
Helix 21	AC3	B	475	486	Right-handed alpha
Helix 22	AC4	B	489	493	Right-handed 310
Helix 23	AC5	B	494	498	Right-handed 310
Helix 24	AC6	B	510	528	Right-handed alpha
Helix 25	AC7	B	528	534	Right-handed alpha
Helix 26	AC8	B	582	586	Right-handed 310
Helix 27	AC9	B	587	596	Right-handed alpha
Helix 28	AD1	B	610	623	Right-handed alpha
Helix 29	AD2	B	625	637	Right-handed alpha
Helix 30	AD3	C	14	33	Right-handed alpha
Helix 31	AD4	C	43	56	Right-handed alpha
Helix 32	AD5	C	67	78	Right-handed alpha
Helix 33	AD6	C	82	93	Right-handed alpha
Helix 34	AD7	C	129	137	Right-handed alpha
Helix 35	AD8	C	165	171	Right-handed alpha
Helix 36	AD9	C	187	201	Right-handed alpha
Helix 37	AE1	C	205	210	Right-handed alpha
Helix 38	AE2	C	227	237	Right-handed alpha
Helix 39	AE3	C	269	283	Right-handed alpha
Helix 40	AE4	C	313	325	Right-handed alpha
Helix 41	AE5	C	347	390	Right-handed alpha
Helix 42	AE6	C	390	400	Right-handed alpha
Helix 43	AE7	C	403	416	Right-handed alpha
Helix 44	AE8	C	418	427	Right-handed alpha
Helix 45	AE9	C	429	433	Right-handed 310
Helix 46	AF1	C	434	461	Right-handed alpha
Helix 47	AF2	C	461	481	Right-handed alpha
Helix 48	AF3	D	436	447	Right-handed alpha
Helix 49	AF4	D	468	475	Right-handed alpha
Helix 50	AF5	D	475	486	Right-handed alpha
Helix 51	AF6	D	489	493	Right-handed 310
Helix 52	AF7	D	494	498	Right-handed 310
Helix 53	AF8	D	510	528	Right-handed alpha
Helix 54	AF9	D	528	534	Right-handed alpha
Helix 55	AG1	D	582	586	Right-handed 310
Helix 56	AG2	D	587	596	Right-handed alpha
Helix 57	AG3	D	610	623	Right-handed alpha
Helix 58	AG4	D	625	637	Right-handed alpha

There are 14 sheets in PDB entry 5CDP. 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,

There are 6 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	11	13	first strand
Strand 2	B	604	607	parallel
Strand 3	B	537	539	anti-parallel
Strand 4	B	502	506	parallel
Strand 5	B	430	435	parallel
Strand 6	B	452	457	parallel

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There are 3 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	65	66	first strand
Strand 2	A	125	128	anti-parallel
Strand 3	A	104	107	anti-parallel

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There are 2 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	146	148	first strand
Strand 2	A	155	157	anti-parallel

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There are 2 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	172	175	first strand
Strand 2	A	180	183	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	A	328	334	first strand
Strand 2	A	238	244	anti-parallel
Strand 3	A	223	225	anti-parallel
Strand 4	A	487	489	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	A	246	253	first strand
Strand 2	A	256	263	anti-parallel
Strand 3	A	304	308	anti-parallel
Strand 4	A	289	294	anti-parallel

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There are 2 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	336	339	first strand
Strand 2	A	342	345	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	C	11	13	first strand
Strand 2	D	604	607	parallel
Strand 3	D	537	539	anti-parallel
Strand 4	D	502	506	parallel
Strand 5	D	430	434	parallel
Strand 6	D	452	456	parallel

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There are 3 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	65	66	first strand
Strand 2	C	125	128	anti-parallel
Strand 3	C	104	107	anti-parallel

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There are 2 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	146	148	first strand
Strand 2	C	155	157	anti-parallel

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There are 2 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	172	175	first strand
Strand 2	C	180	183	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	328	334	first strand
Strand 2	C	238	244	anti-parallel
Strand 3	C	223	225	anti-parallel
Strand 4	C	487	489	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	C	246	253	first strand
Strand 2	C	256	263	anti-parallel
Strand 3	C	304	308	anti-parallel
Strand 4	C	289	294	anti-parallel

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There are 2 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	336	339	first strand
Strand 2	C	342	345	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: 5CDP

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