Analysis of interatomic Contacts of Structural Units in PDB entry:
8DB4

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 8DB4 entry

There are 10 chains in PDB entry 8DB4 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	GLU 1	CYS 227
B	THR 5	GLU 215
C	GLN 1	PRO 221
D	GLU 1	ARG 211
E	ALA 29	VAL 152
F	ALA 29	GLU 153
G	GLU 1	CYS 227
H	GLN 6	GLU 215
I	GLN 1	LYS 222
J	GLU 1	GLU 213

There are 40 helices in PDB entry 8DB4. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	28	32	Right-handed 310
Helix 2	AA2	A	87	91	Right-handed 310
Helix 3	AA3	A	167	169	Right-handed 310
Helix 4	AA4	A	198	200	Right-handed 310
Helix 5	AA5	A	212	215	Right-handed 310
Helix 6	AA6	B	79	83	Right-handed 310
Helix 7	AA7	B	123	128	Right-handed alpha
Helix 8	AA8	B	185	190	Right-handed alpha
Helix 9	AA9	C	28	32	Right-handed 310
Helix 10	AB1	C	87	91	Right-handed 310
Helix 11	AB2	D	79	83	Right-handed 310
Helix 12	AB3	D	121	126	Right-handed alpha
Helix 13	AB4	D	183	187	Right-handed alpha
Helix 14	AB5	E	30	39	Right-handed alpha
Helix 15	AB6	E	42	55	Right-handed alpha
Helix 16	AB7	E	86	97	Right-handed alpha
Helix 17	AB8	E	101	117	Right-handed alpha
Helix 18	AB9	E	122	135	Right-handed alpha
Helix 19	AC1	E	135	140	Right-handed alpha
Helix 20	AC2	F	32	39	Right-handed alpha
Helix 21	AC3	F	42	54	Right-handed alpha
Helix 22	AC4	F	88	96	Right-handed alpha
Helix 23	AC5	F	97	99	Right-handed 310
Helix 24	AC6	F	101	117	Right-handed alpha
Helix 25	AC7	F	118	120	Right-handed 310
Helix 26	AC8	F	122	140	Right-handed alpha
Helix 27	AC9	G	28	32	Right-handed 310
Helix 28	AD1	G	87	91	Right-handed 310
Helix 29	AD2	G	212	215	Right-handed 310
Helix 30	AD3	H	79	83	Right-handed 310
Helix 31	AD4	H	123	128	Right-handed alpha
Helix 32	AD5	H	185	189	Right-handed alpha
Helix 33	AD6	I	28	32	Right-handed 310
Helix 34	AD7	I	87	91	Right-handed 310
Helix 35	AD8	I	164	166	Right-handed 310
Helix 36	AD9	I	195	197	Right-handed 310
Helix 37	AE1	I	209	212	Right-handed 310
Helix 38	AE2	J	79	83	Right-handed 310
Helix 39	AE3	J	121	127	Right-handed alpha
Helix 40	AE4	J	183	187	Right-handed alpha

There are 44 sheets in PDB entry 8DB4. 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, AD7, AD8, AD9, AE1, AE2, AE3, AE4, AE5, AE6, AE7, AE8,

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	A	3	7	first strand
Strand 2	A	18	25	anti-parallel
Strand 3	A	78	83	anti-parallel
Strand 4	A	68	72	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	A	10	12	first strand
Strand 2	A	118	122	parallel
Strand 3	A	92	99	anti-parallel
Strand 4	A	34	39	anti-parallel
Strand 5	A	45	51	anti-parallel
Strand 6	A	58	60	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	A	10	12	first strand
Strand 2	A	118	122	parallel
Strand 3	A	92	99	anti-parallel
Strand 4	A	111	114	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	A	131	135	first strand
Strand 2	A	146	156	anti-parallel
Strand 3	A	187	196	anti-parallel
Strand 4	A	174	176	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	131	135	first strand
Strand 2	A	146	156	anti-parallel
Strand 3	A	187	196	anti-parallel
Strand 4	A	180	181	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	A	162	165	first strand
Strand 2	A	206	211	anti-parallel
Strand 3	A	216	221	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	B	6	7	first strand
Strand 2	B	19	23	anti-parallel
Strand 3	B	71	75	anti-parallel
Strand 4	B	62	66	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	B	10	13	first strand
Strand 2	B	104	108	parallel
Strand 3	B	84	92	anti-parallel
Strand 4	B	31	38	anti-parallel
Strand 5	B	45	49	anti-parallel
Strand 6	B	53	54	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	B	10	13	first strand
Strand 2	B	104	108	parallel
Strand 3	B	84	92	anti-parallel
Strand 4	B	98	100	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	B	116	120	first strand
Strand 2	B	131	141	anti-parallel
Strand 3	B	175	184	anti-parallel
Strand 4	B	161	165	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	B	155	156	first strand
Strand 2	B	147	152	anti-parallel
Strand 3	B	193	199	anti-parallel
Strand 4	B	207	212	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	3	8	first strand
Strand 2	C	18	25	anti-parallel
Strand 3	C	78	83	anti-parallel
Strand 4	C	68	73	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	10	12	first strand
Strand 2	C	115	119	parallel
Strand 3	C	92	99	anti-parallel
Strand 4	C	34	39	anti-parallel
Strand 5	C	45	51	anti-parallel
Strand 6	C	58	60	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	10	12	first strand
Strand 2	C	115	119	parallel
Strand 3	C	92	99	anti-parallel
Strand 4	C	108	111	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	128	132	first strand
Strand 2	C	143	153	anti-parallel
Strand 3	C	184	193	anti-parallel
Strand 4	C	171	173	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	128	132	first strand
Strand 2	C	143	153	anti-parallel
Strand 3	C	184	193	anti-parallel
Strand 4	C	177	178	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	159	162	first strand
Strand 2	C	203	208	anti-parallel
Strand 3	C	213	218	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	4	7	first strand
Strand 2	D	19	25	anti-parallel
Strand 3	D	70	75	anti-parallel
Strand 4	D	62	66	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	10	13	first strand
Strand 2	D	102	106	parallel
Strand 3	D	85	90	anti-parallel
Strand 4	D	33	38	anti-parallel
Strand 5	D	45	49	anti-parallel
Strand 6	D	53	54	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	10	13	first strand
Strand 2	D	102	106	parallel
Strand 3	D	85	90	anti-parallel
Strand 4	D	97	98	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	114	118	first strand
Strand 2	D	129	139	anti-parallel
Strand 3	D	173	182	anti-parallel
Strand 4	D	159	163	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	153	154	first strand
Strand 2	D	145	150	anti-parallel
Strand 3	D	191	197	anti-parallel
Strand 4	D	205	210	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	G	3	7	first strand
Strand 2	G	17	25	anti-parallel
Strand 3	G	78	84	anti-parallel
Strand 4	G	69	73	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	G	11	12	first strand
Strand 2	G	118	122	parallel
Strand 3	G	92	99	anti-parallel
Strand 4	G	34	39	anti-parallel
Strand 5	G	45	51	anti-parallel
Strand 6	G	58	60	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	G	11	12	first strand
Strand 2	G	118	122	parallel
Strand 3	G	92	99	anti-parallel
Strand 4	G	111	114	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	G	131	135	first strand
Strand 2	G	146	156	anti-parallel
Strand 3	G	187	196	anti-parallel
Strand 4	G	174	176	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	G	131	135	first strand
Strand 2	G	146	156	anti-parallel
Strand 3	G	187	196	anti-parallel
Strand 4	G	180	181	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	G	162	165	first strand
Strand 2	G	205	211	anti-parallel
Strand 3	G	216	222	anti-parallel

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There are 6 strands in AD2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	10	13	first strand
Strand 2	H	104	108	parallel
Strand 3	H	84	91	anti-parallel
Strand 4	H	32	38	anti-parallel
Strand 5	H	45	49	anti-parallel
Strand 6	H	53	54	anti-parallel

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There are 4 strands in AD3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	10	13	first strand
Strand 2	H	104	108	parallel
Strand 3	H	84	91	anti-parallel
Strand 4	H	98	100	anti-parallel

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There are 3 strands in AD4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	19	24	first strand
Strand 2	H	70	75	anti-parallel
Strand 3	H	62	67	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	H	116	120	first strand
Strand 2	H	131	141	anti-parallel
Strand 3	H	175	184	anti-parallel
Strand 4	H	161	165	anti-parallel

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There are 4 strands in AD6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	155	156	first strand
Strand 2	H	147	152	anti-parallel
Strand 3	H	193	199	anti-parallel
Strand 4	H	207	212	anti-parallel

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There are 4 strands in AD7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	3	7	first strand
Strand 2	I	18	25	anti-parallel
Strand 3	I	78	83	anti-parallel
Strand 4	I	68	73	anti-parallel

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There are 6 strands in AD8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	10	12	first strand
Strand 2	I	115	119	parallel
Strand 3	I	92	99	anti-parallel
Strand 4	I	34	39	anti-parallel
Strand 5	I	45	51	anti-parallel
Strand 6	I	58	60	anti-parallel

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There are 4 strands in AD9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	10	12	first strand
Strand 2	I	115	119	parallel
Strand 3	I	92	99	anti-parallel
Strand 4	I	108	111	anti-parallel

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There are 4 strands in AE1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	128	132	first strand
Strand 2	I	143	153	anti-parallel
Strand 3	I	184	193	anti-parallel
Strand 4	I	171	173	anti-parallel

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There are 4 strands in AE2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	128	132	first strand
Strand 2	I	143	153	anti-parallel
Strand 3	I	184	193	anti-parallel
Strand 4	I	177	178	anti-parallel

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There are 3 strands in AE3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	159	162	first strand
Strand 2	I	203	208	anti-parallel
Strand 3	I	213	218	anti-parallel

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There are 4 strands in AE4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	4	7	first strand
Strand 2	J	19	25	anti-parallel
Strand 3	J	70	75	anti-parallel
Strand 4	J	62	65	anti-parallel

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There are 6 strands in AE5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	10	13	first strand
Strand 2	J	102	106	parallel
Strand 3	J	85	90	anti-parallel
Strand 4	J	33	38	anti-parallel
Strand 5	J	45	49	anti-parallel
Strand 6	J	53	54	anti-parallel

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There are 4 strands in AE6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	10	13	first strand
Strand 2	J	102	106	parallel
Strand 3	J	85	90	anti-parallel
Strand 4	J	97	98	anti-parallel

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There are 4 strands in AE7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	114	118	first strand
Strand 2	J	129	139	anti-parallel
Strand 3	J	173	182	anti-parallel
Strand 4	J	159	163	anti-parallel

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There are 4 strands in AE8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	153	154	first strand
Strand 2	J	145	150	anti-parallel
Strand 3	J	191	197	anti-parallel
Strand 4	J	205	210	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: 8DB4

Analysis of interatomic Contacts of Structural Units in PDB entry:
8DB4