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

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 8KDA entry

There are 17 chains in PDB entry 8KDA (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
E	MET 1	LEU 189
T	A 0	U 72
M	A 0	U 72
N	A 0	U 72
O	A 0	U 72
P	A 0	U 72
F	MET 1	LEU 189
G	MET 1	LEU 189
H	MET 1	LEU 189
C	ASP 2	LEU 189
D	ASP 2	LEU 189
I	MET 1	LEU 189
J	MET 1	LEU 189
A	ASP 2	LEU 189
B	ASP 2	LEU 189
K	ASP 2	LEU 189
L	MET 1	LEU 189

There are133 helices in PDB entry 8KDA. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	E	8	13	Right-handed alpha
Helix 2	AA2	E	13	18	Right-handed alpha
Helix 3	AA3	E	23	36	Right-handed alpha
Helix 4	AA4	E	45	54	Right-handed alpha
Helix 5	AA5	E	61	68	Right-handed alpha
Helix 6	AA6	E	75	78	Right-handed 310
Helix 7	AA7	E	83	112	Right-handed alpha
Helix 8	AA8	E	118	135	Right-handed alpha
Helix 9	AA9	E	141	155	Right-handed alpha
Helix 10	AB1	E	162	170	Right-handed alpha
Helix 11	AB2	E	178	180	Right-handed 310
Helix 12	AB3	E	181	187	Right-handed alpha
Helix 13	AB4	F	8	12	Right-handed 310
Helix 14	AB5	F	13	18	Right-handed alpha
Helix 15	AB6	F	23	36	Right-handed alpha
Helix 16	AB7	F	46	56	Right-handed alpha
Helix 17	AB8	F	61	69	Right-handed alpha
Helix 18	AB9	F	83	115	Right-handed alpha
Helix 19	AC1	F	118	135	Right-handed alpha
Helix 20	AC2	F	141	155	Right-handed alpha
Helix 21	AC3	F	163	171	Right-handed alpha
Helix 22	AC4	F	178	180	Right-handed 310
Helix 23	AC5	F	181	189	Right-handed alpha
Helix 24	AC6	G	8	11	Right-handed 310
Helix 25	AC7	G	13	18	Right-handed alpha
Helix 26	AC8	G	23	36	Right-handed alpha
Helix 27	AC9	G	45	56	Right-handed alpha
Helix 28	AD1	G	61	69	Right-handed alpha
Helix 29	AD2	G	83	111	Right-handed alpha
Helix 30	AD3	G	112	114	Right-handed 310
Helix 31	AD4	G	118	135	Right-handed alpha
Helix 32	AD5	G	141	155	Right-handed alpha
Helix 33	AD6	G	163	173	Right-handed alpha
Helix 34	AD7	G	178	180	Right-handed 310
Helix 35	AD8	G	181	189	Right-handed alpha
Helix 36	AD9	H	7	13	Right-handed alpha
Helix 37	AE1	H	13	18	Right-handed alpha
Helix 38	AE2	H	23	36	Right-handed alpha
Helix 39	AE3	H	46	56	Right-handed alpha
Helix 40	AE4	H	61	69	Right-handed alpha
Helix 41	AE5	H	75	78	Right-handed 310
Helix 42	AE6	H	83	112	Right-handed alpha
Helix 43	AE7	H	118	136	Right-handed alpha
Helix 44	AE8	H	141	155	Right-handed alpha
Helix 45	AE9	H	163	170	Right-handed alpha
Helix 46	AF1	H	178	180	Right-handed 310
Helix 47	AF2	H	181	187	Right-handed alpha
Helix 48	AF3	C	7	13	Right-handed alpha
Helix 49	AF4	C	13	18	Right-handed alpha
Helix 50	AF5	C	26	36	Right-handed alpha
Helix 51	AF6	C	45	55	Right-handed alpha
Helix 52	AF7	C	61	69	Right-handed alpha
Helix 53	AF8	C	75	78	Right-handed 310
Helix 54	AF9	C	83	112	Right-handed alpha
Helix 55	AG1	C	118	135	Right-handed alpha
Helix 56	AG2	C	141	155	Right-handed alpha
Helix 57	AG3	C	163	170	Right-handed alpha
Helix 58	AG4	C	178	180	Right-handed 310
Helix 59	AG5	C	181	189	Right-handed alpha
Helix 60	AG6	D	7	13	Right-handed alpha
Helix 61	AG7	D	15	19	Right-handed 310
Helix 62	AG8	D	23	36	Right-handed alpha
Helix 63	AG9	D	46	54	Right-handed alpha
Helix 64	AH1	D	61	69	Right-handed alpha
Helix 65	AH2	D	84	111	Right-handed alpha
Helix 66	AH3	D	112	114	Right-handed 310
Helix 67	AH4	D	118	135	Right-handed alpha
Helix 68	AH5	D	141	155	Right-handed alpha
Helix 69	AH6	D	162	171	Right-handed alpha
Helix 70	AH7	D	178	180	Right-handed 310
Helix 71	AH8	D	181	189	Right-handed alpha
Helix 72	AH9	I	8	13	Right-handed alpha
Helix 73	AI1	I	13	18	Right-handed alpha
Helix 74	AI2	I	23	37	Right-handed alpha
Helix 75	AI3	I	45	56	Right-handed alpha
Helix 76	AI4	I	61	68	Right-handed alpha
Helix 77	AI5	I	75	78	Right-handed 310
Helix 78	AI6	I	83	113	Right-handed alpha
Helix 79	AI7	I	118	136	Right-handed alpha
Helix 80	AI8	I	141	155	Right-handed alpha
Helix 81	AI9	I	162	171	Right-handed alpha
Helix 82	AJ1	I	178	180	Right-handed 310
Helix 83	AJ2	I	181	188	Right-handed alpha
Helix 84	AJ3	J	7	13	Right-handed alpha
Helix 85	AJ4	J	13	18	Right-handed alpha
Helix 86	AJ5	J	23	37	Right-handed alpha
Helix 87	AJ6	J	45	53	Right-handed alpha
Helix 88	AJ7	J	60	69	Right-handed alpha
Helix 89	AJ8	J	83	114	Right-handed alpha
Helix 90	AJ9	J	119	135	Right-handed alpha
Helix 91	AK1	J	145	151	Right-handed alpha
Helix 92	AK2	J	163	171	Right-handed alpha
Helix 93	AK3	J	182	188	Right-handed alpha
Helix 94	AK4	A	13	18	Right-handed alpha
Helix 95	AK5	A	25	36	Right-handed alpha
Helix 96	AK6	A	46	56	Right-handed alpha
Helix 97	AK7	A	61	69	Right-handed alpha
Helix 98	AK8	A	83	110	Right-handed alpha
Helix 99	AK9	A	118	131	Right-handed alpha
Helix 100	AL1	A	141	153	Right-handed alpha
Helix 101	AL2	A	163	173	Right-handed alpha
Helix 102	AL3	A	178	180	Right-handed 310
Helix 103	AL4	A	181	189	Right-handed alpha
Helix 104	AL5	B	13	18	Right-handed alpha
Helix 105	AL6	B	25	37	Right-handed alpha
Helix 106	AL7	B	46	51	Right-handed alpha
Helix 107	AL8	B	83	93	Right-handed alpha
Helix 108	AL9	B	93	114	Right-handed alpha
Helix 109	AM1	B	119	135	Right-handed alpha
Helix 110	AM2	B	141	155	Right-handed alpha
Helix 111	AM3	B	163	170	Right-handed alpha
Helix 112	AM4	B	181	188	Right-handed alpha
Helix 113	AM5	K	7	11	Right-handed 310
Helix 114	AM6	K	23	36	Right-handed alpha
Helix 115	AM7	K	45	56	Right-handed alpha
Helix 116	AM8	K	61	68	Right-handed alpha
Helix 117	AM9	K	83	111	Right-handed alpha
Helix 118	AN1	K	112	114	Right-handed 310
Helix 119	AN2	K	118	135	Right-handed alpha
Helix 120	AN3	K	142	155	Right-handed alpha
Helix 121	AN4	K	162	173	Right-handed alpha
Helix 122	AN5	K	178	180	Right-handed 310
Helix 123	AN6	K	181	186	Right-handed alpha
Helix 124	AN7	L	13	18	Right-handed alpha
Helix 125	AN8	L	23	38	Right-handed alpha
Helix 126	AN9	L	45	56	Right-handed alpha
Helix 127	AO1	L	61	69	Right-handed alpha
Helix 128	AO2	L	83	114	Right-handed alpha
Helix 129	AO3	L	121	135	Right-handed alpha
Helix 130	AO4	L	141	155	Right-handed alpha
Helix 131	AO5	L	162	173	Right-handed alpha
Helix 132	AO6	L	178	180	Right-handed 310
Helix 133	AO7	L	181	188	Right-handed alpha

There are 19 sheets in PDB entry 8KDA. 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,

There are 5 strands in AA1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	69	71	first strand
Strand 2	E	40	44	parallel
Strand 3	E	2	6	parallel
Strand 4	E	157	159	parallel
Strand 5	E	175	176	parallel

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There are 2 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	80	82	first strand
Strand 2	F	80	82	anti-parallel

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There are 5 strands in AA3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	70	72	first strand
Strand 2	F	41	45	parallel
Strand 3	F	3	6	parallel
Strand 4	F	157	159	parallel
Strand 5	F	175	176	parallel

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There are 5 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	70	71	first strand
Strand 2	G	40	44	parallel
Strand 3	G	2	6	parallel
Strand 4	G	157	159	parallel
Strand 5	G	175	176	parallel

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There are 2 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	80	82	first strand
Strand 2	H	80	82	anti-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	H	70	72	first strand
Strand 2	H	40	45	parallel
Strand 3	H	2	5	parallel
Strand 4	H	157	158	parallel

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There are 5 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	70	71	first strand
Strand 2	C	41	44	parallel
Strand 3	C	3	5	parallel
Strand 4	C	157	158	parallel
Strand 5	C	175	176	parallel

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There are 2 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	80	82	first strand
Strand 2	D	80	82	anti-parallel

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There are 5 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	70	72	first strand
Strand 2	D	41	45	parallel
Strand 3	D	3	5	parallel
Strand 4	D	157	158	parallel
Strand 5	D	175	176	parallel

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There are 5 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	69	71	first strand
Strand 2	I	40	44	parallel
Strand 3	I	2	6	parallel
Strand 4	I	157	159	parallel
Strand 5	I	175	176	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	I	80	82	first strand
Strand 2	J	80	82	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	J	70	71	first strand
Strand 2	J	41	44	parallel
Strand 3	J	3	5	parallel
Strand 4	J	157	158	parallel

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There are 3 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	3	4	first strand
Strand 2	A	41	45	parallel
Strand 3	A	70	72	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	A	80	82	first strand
Strand 2	B	80	82	anti-parallel

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There are 2 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	157	158	first strand
Strand 2	A	175	176	parallel

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There are 5 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	70	72	first strand
Strand 2	B	41	45	parallel
Strand 3	B	3	6	parallel
Strand 4	B	157	159	parallel
Strand 5	B	175	176	parallel

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There are 5 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	69	71	first strand
Strand 2	K	41	44	parallel
Strand 3	K	3	5	parallel
Strand 4	K	157	158	parallel
Strand 5	K	175	176	parallel

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There are 2 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	80	82	first strand
Strand 2	L	80	82	anti-parallel

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There are 4 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	70	71	first strand
Strand 2	L	41	44	parallel
Strand 3	L	3	5	parallel
Strand 4	L	157	158	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: 8KDA

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