Analysis of interatomic Contacts of Structural Units in PDB entry:
2CDB

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 2CDB entry

There are 4 chains in PDB entry 2CDB (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	MET 1	GLU 366
B	MET 1	GLU 366
C	MET 1	GLU 366
D	MET 1	GLU 366

There are 68 helices in PDB entry 2CDB. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	19	23	Right-handed 310
Helix 2	2	A	39	47	Right-handed alpha
Helix 3	3	A	96	101	Right-handed alpha
Helix 4	4	A	103	107	Right-handed 310
Helix 5	5	A	131	133	Right-handed 310
Helix 6	6	A	139	143	Right-handed 310
Helix 7	7	A	145	147	Right-handed 310
Helix 8	8	A	148	166	Right-handed alpha
Helix 9	9	A	167	169	Right-handed 310
Helix 10	10	A	189	204	Right-handed alpha
Helix 11	11	A	216	227	Right-handed alpha
Helix 12	12	A	237	245	Right-handed alpha
Helix 13	13	A	258	265	Right-handed alpha
Helix 14	14	A	289	298	Right-handed alpha
Helix 15	15	A	309	327	Right-handed alpha
Helix 16	16	A	327	334	Right-handed alpha
Helix 17	17	A	343	353	Right-handed alpha
Helix 18	18	B	19	23	Right-handed 310
Helix 19	19	B	39	47	Right-handed alpha
Helix 20	20	B	96	101	Right-handed alpha
Helix 21	21	B	103	107	Right-handed 310
Helix 22	22	B	131	133	Right-handed 310
Helix 23	23	B	139	143	Right-handed 310
Helix 24	24	B	145	147	Right-handed 310
Helix 25	25	B	148	166	Right-handed alpha
Helix 26	26	B	167	169	Right-handed 310
Helix 27	27	B	190	203	Right-handed alpha
Helix 28	28	B	216	227	Right-handed alpha
Helix 29	29	B	237	245	Right-handed alpha
Helix 30	30	B	258	265	Right-handed alpha
Helix 31	31	B	289	298	Right-handed alpha
Helix 32	32	B	309	327	Right-handed alpha
Helix 33	33	B	327	333	Right-handed alpha
Helix 34	34	B	343	353	Right-handed alpha
Helix 35	35	C	19	23	Right-handed 310
Helix 36	36	C	39	47	Right-handed alpha
Helix 37	37	C	96	101	Right-handed alpha
Helix 38	38	C	103	107	Right-handed 310
Helix 39	39	C	131	133	Right-handed 310
Helix 40	40	C	139	143	Right-handed 310
Helix 41	41	C	145	147	Right-handed 310
Helix 42	42	C	148	166	Right-handed alpha
Helix 43	43	C	167	169	Right-handed 310
Helix 44	44	C	190	203	Right-handed alpha
Helix 45	45	C	216	227	Right-handed alpha
Helix 46	46	C	237	245	Right-handed alpha
Helix 47	47	C	258	265	Right-handed alpha
Helix 48	48	C	289	298	Right-handed alpha
Helix 49	49	C	309	327	Right-handed alpha
Helix 50	50	C	327	332	Right-handed alpha
Helix 51	51	C	343	353	Right-handed alpha
Helix 52	52	D	19	23	Right-handed 310
Helix 53	53	D	39	47	Right-handed alpha
Helix 54	54	D	96	101	Right-handed alpha
Helix 55	55	D	103	107	Right-handed 310
Helix 56	56	D	131	133	Right-handed 310
Helix 57	57	D	139	143	Right-handed 310
Helix 58	58	D	145	147	Right-handed 310
Helix 59	59	D	148	166	Right-handed alpha
Helix 60	60	D	167	169	Right-handed 310
Helix 61	61	D	190	203	Right-handed alpha
Helix 62	62	D	216	227	Right-handed alpha
Helix 63	63	D	237	245	Right-handed alpha
Helix 64	64	D	258	265	Right-handed alpha
Helix 65	65	D	289	298	Right-handed alpha
Helix 66	66	D	309	327	Right-handed alpha
Helix 67	67	D	327	333	Right-handed alpha
Helix 68	68	D	343	353	Right-handed alpha

There are 19 sheets in PDB entry 2CDB. Click on sheet of interest to get list of strands forming it: AA, AB, AC, AD, AE, AF, BA, BB, BC, BD, BE, BF, CA, CB, CC, CD, A, DB, C,

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	14	17	first strand
Strand 2	A	2	6	anti-parallel
Strand 3	A	62	63	anti-parallel

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There are 5 strands in AB sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	127	130	first strand
Strand 2	A	29	38	anti-parallel
Strand 3	A	67	72	anti-parallel
Strand 4	A	84	87	anti-parallel
Strand 5	A	135	138	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	127	130	first strand
Strand 2	A	29	38	anti-parallel
Strand 3	A	360	364	anti-parallel
Strand 4	A	335	340	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	90	91	first strand
Strand 2	A	113	114	anti-parallel

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There are 12 strands in AE sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	229	232	first strand
Strand 2	A	206	211	parallel
Strand 3	A	183	187	parallel
Strand 4	A	247	252	parallel
Strand 5	A	268	276	parallel
Strand 6	A	301	304	parallel
Strand 7	C	301	304	anti-parallel
Strand 8	C	268	276	parallel
Strand 9	C	247	252	parallel
Strand 10	C	183	187	parallel
Strand 11	C	206	211	parallel
Strand 12	C	229	232	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	284	288	first strand
Strand 2	C	284	288	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	14	17	first strand
Strand 2	B	2	6	anti-parallel
Strand 3	B	62	63	anti-parallel

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There are 5 strands in BB sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	127	130	first strand
Strand 2	B	29	38	anti-parallel
Strand 3	B	67	72	anti-parallel
Strand 4	B	84	87	anti-parallel
Strand 5	B	135	138	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	127	130	first strand
Strand 2	B	29	38	anti-parallel
Strand 3	B	361	364	anti-parallel
Strand 4	B	337	340	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	90	91	first strand
Strand 2	B	113	114	anti-parallel

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There are 12 strands in BE sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	229	232	first strand
Strand 2	B	206	211	parallel
Strand 3	B	183	187	parallel
Strand 4	B	247	252	parallel
Strand 5	B	268	276	parallel
Strand 6	B	301	304	parallel
Strand 7	D	301	304	anti-parallel
Strand 8	D	268	276	parallel
Strand 9	D	247	252	parallel
Strand 10	D	183	187	parallel
Strand 11	D	206	211	parallel
Strand 12	D	229	232	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	284	288	first strand
Strand 2	D	284	288	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	10	17	first strand
Strand 2	C	2	7	anti-parallel
Strand 3	C	62	63	anti-parallel

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There are 5 strands in CB sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	127	130	first strand
Strand 2	C	29	38	anti-parallel
Strand 3	C	67	72	anti-parallel
Strand 4	C	84	87	anti-parallel
Strand 5	C	135	137	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	127	130	first strand
Strand 2	C	29	38	anti-parallel
Strand 3	C	361	364	anti-parallel
Strand 4	C	337	340	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	90	91	first strand
Strand 2	C	113	114	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	14	17	first strand
Strand 2	D	2	6	anti-parallel
Strand 3	D	62	63	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	127	130	first strand
Strand 2	D	29	38	anti-parallel
Strand 3	D	135	138	first strand
Strand 4	D	84	87	anti-parallel
Strand 5	D	67	72	anti-parallel
Strand 6	D	29	38	anti-parallel
Strand 7	D	337	340	first strand
Strand 8	D	361	364	parallel
Strand 9	D	29	38	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	90	91	first strand
Strand 2	D	113	114	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: 2CDB

Analysis of interatomic Contacts of Structural Units in PDB entry:
2CDB