Analysis of interatomic Contacts of Structural Units in PDB entry:
8KD9

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 8KD9 entry

There are 17 chains in PDB entry 8KD9 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ASP 2	LEU 187
B	ASP 2	VAL 188
C	ASP 2	HIS 190
D	ASP 2	ARG 189
E	MET 1	VAL 188
F	ASP 2	HIS 190
G	ASP 2	ARG 189
H	ASP 2	VAL 188
I	ASP 2	VAL 188
J	ASP 2	ARG 189
K	VAL 3	VAL 188
L	ASP 2	LEU 187
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

There are128 helices in PDB entry 8KD9. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	7	11	Right-handed 310
Helix 2	AA2	A	15	16	Right-handed 310
Helix 3	AA3	A	18	20	Right-handed 310
Helix 4	AA4	A	26	34	Right-handed alpha
Helix 5	AA5	A	45	55	Right-handed alpha
Helix 6	AA6	A	61	67	Right-handed alpha
Helix 7	AA7	A	83	112	Right-handed alpha
Helix 8	AA8	A	119	131	Right-handed alpha
Helix 9	AA9	A	139	153	Right-handed alpha
Helix 10	AB1	A	160	171	Right-handed alpha
Helix 11	AB2	A	176	178	Right-handed 310
Helix 12	AB3	A	179	185	Right-handed alpha
Helix 13	AB4	B	13	20	Right-handed alpha
Helix 14	AB5	B	26	37	Right-handed alpha
Helix 15	AB6	B	45	56	Right-handed alpha
Helix 16	AB7	B	61	69	Right-handed alpha
Helix 17	AB8	B	83	114	Right-handed alpha
Helix 18	AB9	B	116	132	Right-handed alpha
Helix 19	AC1	B	139	153	Right-handed alpha
Helix 20	AC2	B	160	169	Right-handed alpha
Helix 21	AC3	B	179	184	Right-handed alpha
Helix 22	AC4	C	8	13	Right-handed alpha
Helix 23	AC5	C	13	20	Right-handed alpha
Helix 24	AC6	C	26	36	Right-handed alpha
Helix 25	AC7	C	45	54	Right-handed alpha
Helix 26	AC8	C	60	69	Right-handed alpha
Helix 27	AC9	C	83	112	Right-handed alpha
Helix 28	AD1	C	116	134	Right-handed alpha
Helix 29	AD2	C	139	153	Right-handed alpha
Helix 30	AD3	C	160	167	Right-handed alpha
Helix 31	AD4	C	179	189	Right-handed alpha
Helix 32	AD5	D	8	13	Right-handed alpha
Helix 33	AD6	D	15	20	Right-handed alpha
Helix 34	AD7	D	23	36	Right-handed alpha
Helix 35	AD8	D	45	56	Right-handed alpha
Helix 36	AD9	D	61	66	Right-handed alpha
Helix 37	AE1	D	83	114	Right-handed alpha
Helix 38	AE2	D	116	132	Right-handed alpha
Helix 39	AE3	D	139	153	Right-handed alpha
Helix 40	AE4	D	160	171	Right-handed alpha
Helix 41	AE5	D	176	178	Right-handed 310
Helix 42	AE6	D	179	189	Right-handed alpha
Helix 43	AE7	E	8	12	Right-handed 310
Helix 44	AE8	E	13	20	Right-handed alpha
Helix 45	AE9	E	25	39	Right-handed alpha
Helix 46	AF1	E	45	56	Right-handed alpha
Helix 47	AF2	E	61	69	Right-handed alpha
Helix 48	AF3	E	75	78	Right-handed 310
Helix 49	AF4	E	83	114	Right-handed alpha
Helix 50	AF5	E	116	133	Right-handed alpha
Helix 51	AF6	E	139	153	Right-handed alpha
Helix 52	AF7	E	160	169	Right-handed alpha
Helix 53	AF8	E	179	188	Right-handed alpha
Helix 54	AF9	F	8	13	Right-handed alpha
Helix 55	AG1	F	13	19	Right-handed alpha
Helix 56	AG2	F	23	37	Right-handed alpha
Helix 57	AG3	F	45	56	Right-handed alpha
Helix 58	AG4	F	61	68	Right-handed alpha
Helix 59	AG5	F	83	114	Right-handed alpha
Helix 60	AG6	F	117	133	Right-handed alpha
Helix 61	AG7	F	139	153	Right-handed alpha
Helix 62	AG8	F	160	171	Right-handed alpha
Helix 63	AG9	F	179	189	Right-handed alpha
Helix 64	AH1	G	8	13	Right-handed alpha
Helix 65	AH2	G	15	21	Right-handed alpha
Helix 66	AH3	G	23	36	Right-handed alpha
Helix 67	AH4	G	45	56	Right-handed alpha
Helix 68	AH5	G	60	69	Right-handed alpha
Helix 69	AH6	G	83	113	Right-handed alpha
Helix 70	AH7	G	116	134	Right-handed alpha
Helix 71	AH8	G	139	153	Right-handed alpha
Helix 72	AH9	G	160	171	Right-handed alpha
Helix 73	AI1	G	179	189	Right-handed alpha
Helix 74	AI2	H	8	13	Right-handed alpha
Helix 75	AI3	H	13	20	Right-handed alpha
Helix 76	AI4	H	24	37	Right-handed alpha
Helix 77	AI5	H	45	56	Right-handed alpha
Helix 78	AI6	H	60	69	Right-handed alpha
Helix 79	AI7	H	83	114	Right-handed alpha
Helix 80	AI8	H	116	134	Right-handed alpha
Helix 81	AI9	H	139	153	Right-handed alpha
Helix 82	AJ1	H	160	169	Right-handed alpha
Helix 83	AJ2	H	176	178	Right-handed 310
Helix 84	AJ3	H	179	188	Right-handed alpha
Helix 85	AJ4	I	8	13	Right-handed alpha
Helix 86	AJ5	I	15	20	Right-handed alpha
Helix 87	AJ6	I	23	37	Right-handed alpha
Helix 88	AJ7	I	45	56	Right-handed alpha
Helix 89	AJ8	I	60	68	Right-handed alpha
Helix 90	AJ9	I	83	114	Right-handed alpha
Helix 91	AK1	I	117	133	Right-handed alpha
Helix 92	AK2	I	139	153	Right-handed alpha
Helix 93	AK3	I	160	169	Right-handed alpha
Helix 94	AK4	I	176	178	Right-handed 310
Helix 95	AK5	I	179	188	Right-handed alpha
Helix 96	AK6	J	8	13	Right-handed alpha
Helix 97	AK7	J	13	19	Right-handed alpha
Helix 98	AK8	J	24	37	Right-handed alpha
Helix 99	AK9	J	45	56	Right-handed alpha
Helix 100	AL1	J	60	68	Right-handed alpha
Helix 101	AL2	J	75	78	Right-handed 310
Helix 102	AL3	J	83	113	Right-handed alpha
Helix 103	AL4	J	119	134	Right-handed alpha
Helix 104	AL5	J	139	152	Right-handed alpha
Helix 105	AL6	J	160	169	Right-handed alpha
Helix 106	AL7	J	176	178	Right-handed 310
Helix 107	AL8	J	179	189	Right-handed alpha
Helix 108	AL9	K	8	13	Right-handed alpha
Helix 109	AM1	K	13	20	Right-handed alpha
Helix 110	AM2	K	26	36	Right-handed alpha
Helix 111	AM3	K	45	55	Right-handed alpha
Helix 112	AM4	K	61	66	Right-handed alpha
Helix 113	AM5	K	83	111	Right-handed alpha
Helix 114	AM6	K	112	114	Right-handed 310
Helix 115	AM7	K	116	132	Right-handed alpha
Helix 116	AM8	K	139	153	Right-handed alpha
Helix 117	AM9	K	160	171	Right-handed alpha
Helix 118	AN1	K	179	187	Right-handed alpha
Helix 119	AN2	L	7	11	Right-handed 310
Helix 120	AN3	L	13	20	Right-handed alpha
Helix 121	AN4	L	27	36	Right-handed alpha
Helix 122	AN5	L	45	56	Right-handed alpha
Helix 123	AN6	L	62	66	Right-handed alpha
Helix 124	AN7	L	83	114	Right-handed alpha
Helix 125	AN8	L	116	134	Right-handed alpha
Helix 126	AN9	L	139	153	Right-handed alpha
Helix 127	AO1	L	160	171	Right-handed alpha
Helix 128	AO2	L	176	187	Right-handed alpha

There are 17 sheets in PDB entry 8KD9. 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,

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

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There are 4 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	42	43	first strand
Strand 2	B	4	6	parallel
Strand 3	B	155	157	parallel
Strand 4	B	173	174	parallel

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There are 3 strands in AA3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	4	5	first strand
Strand 2	C	155	157	parallel
Strand 3	C	173	175	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	C	43	44	first strand
Strand 2	C	70	71	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	C	80	82	first strand
Strand 2	D	80	82	anti-parallel

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There are 5 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	69	71	first strand
Strand 2	D	41	44	parallel
Strand 3	D	3	6	parallel
Strand 4	D	155	157	parallel
Strand 5	D	173	174	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	E	70	71	first strand
Strand 2	E	41	44	parallel
Strand 3	E	3	5	parallel
Strand 4	E	155	156	parallel
Strand 5	E	173	174	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	E	80	82	first strand
Strand 2	F	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	F	69	71	first strand
Strand 2	F	41	44	parallel
Strand 3	F	3	5	parallel
Strand 4	F	155	156	parallel
Strand 5	F	173	174	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	G	70	71	first strand
Strand 2	G	41	44	parallel
Strand 3	G	3	6	parallel
Strand 4	G	155	157	parallel
Strand 5	G	173	174	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	G	80	82	first strand
Strand 2	H	80	82	anti-parallel

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There are 5 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	70	71	first strand
Strand 2	H	42	44	parallel
Strand 3	H	4	6	parallel
Strand 4	H	155	157	parallel
Strand 5	H	173	174	parallel

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There are 5 strands in AB4 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	41	44	parallel
Strand 3	I	3	5	parallel
Strand 4	I	155	156	parallel
Strand 5	I	173	174	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	I	80	82	first strand
Strand 2	J	80	82	anti-parallel

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There are 5 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	69	71	first strand
Strand 2	J	41	44	parallel
Strand 3	J	3	6	parallel
Strand 4	J	155	157	parallel
Strand 5	J	173	174	parallel

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There are 2 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	4	5	first strand
Strand 2	K	155	156	parallel

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There are 2 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	80	82	first strand
Strand 2	L	80	82	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: 8KD9

Analysis of interatomic Contacts of Structural Units in PDB entry:
8KD9