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

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 8KDE entry

There are 18 chains in PDB entry 8KDE (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
B	GLY 2	ASP 483
D	THR 2	LEU 352
E	PRO 5	ASN 82
F	VAL 11	ARG 44
H	ASN 14	LYS 86
I	MET 1	ASN 35
K	LYS 10	ARG 46
L	MET 1	ASN 38
M	GLU 2	THR 32
T	MET 1	LYS 31
V	ASN 2	LEU 33
X	ALA 64	LYS 98
Z	MET 1	VAL 61
G	ILE 52	LEU 196
3	ASP 35	LEU 131
C	GLY 12	ASP 461
A	ASN 10	ASN 338
1	ARG 24	LYS 68

There are106 helices in PDB entry 8KDE. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	B	8	13	Right-handed 310
Helix 2	AA2	B	15	45	Right-handed alpha
Helix 3	AA3	B	55	59	Right-handed 310
Helix 4	AA4	B	62	68	Right-handed alpha
Helix 5	AA5	B	92	117	Right-handed alpha
Helix 6	AA6	B	120	124	Right-handed 310
Helix 7	AA7	B	134	157	Right-handed alpha
Helix 8	AA8	B	186	190	Right-handed 310
Helix 9	AA9	B	195	219	Right-handed alpha
Helix 10	AB1	B	222	229	Right-handed alpha
Helix 11	AB2	B	233	259	Right-handed alpha
Helix 12	AB3	B	264	269	Right-handed alpha
Helix 13	AB4	B	271	277	Right-handed alpha
Helix 14	AB5	B	278	295	Right-handed alpha
Helix 15	AB6	B	297	303	Right-handed alpha
Helix 16	AB7	B	306	313	Right-handed alpha
Helix 17	AB8	B	314	318	Right-handed 310
Helix 18	AB9	B	330	335	Right-handed alpha
Helix 19	AC1	B	391	396	Right-handed alpha
Helix 20	AC2	B	413	425	Right-handed alpha
Helix 21	AC3	B	446	475	Right-handed alpha
Helix 22	AC4	B	475	481	Right-handed alpha
Helix 23	AC5	D	13	23	Right-handed alpha
Helix 24	AC6	D	30	54	Right-handed alpha
Helix 25	AC7	D	57	62	Right-handed alpha
Helix 26	AC8	D	66	70	Right-handed 310
Helix 27	AC9	D	100	108	Right-handed alpha
Helix 28	AD1	D	108	136	Right-handed alpha
Helix 29	AD2	D	140	164	Right-handed alpha
Helix 30	AD3	D	166	170	Right-handed 310
Helix 31	AD4	D	175	190	Right-handed alpha
Helix 32	AD5	D	191	193	Right-handed 310
Helix 33	AD6	D	194	220	Right-handed alpha
Helix 34	AD7	D	245	257	Right-handed alpha
Helix 35	AD8	D	263	291	Right-handed alpha
Helix 36	AD9	D	298	308	Right-handed alpha
Helix 37	AE1	D	313	334	Right-handed alpha
Helix 38	AE2	D	335	338	Right-handed 310
Helix 39	AE3	D	348	352	Right-handed 310
Helix 40	AE4	E	9	16	Right-handed alpha
Helix 41	AE5	E	16	40	Right-handed alpha
Helix 42	AE6	E	41	48	Right-handed alpha
Helix 43	AE7	E	71	80	Right-handed alpha
Helix 44	AE8	F	16	41	Right-handed alpha
Helix 45	AE9	H	24	31	Right-handed alpha
Helix 46	AF1	H	32	35	Right-handed 310
Helix 47	AF2	H	46	69	Right-handed alpha
Helix 48	AF3	H	80	85	Right-handed 310
Helix 49	AF4	I	2	24	Right-handed alpha
Helix 50	AF5	I	26	30	Right-handed 310
Helix 51	AF6	K	12	17	Right-handed 310
Helix 52	AF7	K	18	23	Right-handed alpha
Helix 53	AF8	K	24	26	Right-handed 310
Helix 54	AF9	K	27	42	Right-handed alpha
Helix 55	AG1	L	14	38	Right-handed alpha
Helix 56	AG2	M	4	31	Right-handed alpha
Helix 57	AG3	T	2	23	Right-handed alpha
Helix 58	AG4	V	3	29	Right-handed alpha
Helix 59	AG5	X	66	98	Right-handed alpha
Helix 60	AG6	Z	2	29	Right-handed alpha
Helix 61	AG7	Z	36	60	Right-handed alpha
Helix 62	AG8	G	60	67	Right-handed alpha
Helix 63	AG9	G	67	87	Right-handed alpha
Helix 64	AH1	G	97	116	Right-handed alpha
Helix 65	AH2	G	121	127	Right-handed alpha
Helix 66	AH3	G	130	142	Right-handed alpha
Helix 67	AH4	G	145	164	Right-handed alpha
Helix 68	AH5	G	166	188	Right-handed alpha
Helix 69	AH6	G	189	194	Right-handed alpha
Helix 70	AH7	3	66	105	Right-handed alpha
Helix 71	AH8	3	120	128	Right-handed alpha
Helix 72	AH9	C	15	20	Right-handed alpha
Helix 73	AI1	C	22	31	Right-handed 310
Helix 74	AI2	C	33	62	Right-handed alpha
Helix 75	AI3	C	68	72	Right-handed 310
Helix 76	AI4	C	76	83	Right-handed alpha
Helix 77	AI5	C	88	92	Right-handed 310
Helix 78	AI6	C	96	123	Right-handed alpha
Helix 79	AI7	C	143	170	Right-handed alpha
Helix 80	AI8	C	193	200	Right-handed alpha
Helix 81	AI9	C	217	241	Right-handed alpha
Helix 82	AJ1	C	245	252	Right-handed alpha
Helix 83	AJ2	C	255	281	Right-handed alpha
Helix 84	AJ3	C	286	291	Right-handed alpha
Helix 85	AJ4	C	293	313	Right-handed alpha
Helix 86	AJ5	C	341	347	Right-handed 310
Helix 87	AJ6	C	354	358	Right-handed 310
Helix 88	AJ7	C	364	371	Right-handed alpha
Helix 89	AJ8	C	373	385	Right-handed alpha
Helix 90	AJ9	C	409	442	Right-handed alpha
Helix 91	AK1	C	452	457	Right-handed 310
Helix 92	AK2	A	12	23	Right-handed alpha
Helix 93	AK3	A	30	55	Right-handed alpha
Helix 94	AK4	A	95	99	Right-handed 310
Helix 95	AK5	A	101	109	Right-handed alpha
Helix 96	AK6	A	109	137	Right-handed alpha
Helix 97	AK7	A	142	166	Right-handed alpha
Helix 98	AK8	A	167	171	Right-handed 310
Helix 99	AK9	A	175	191	Right-handed alpha
Helix 100	AL1	A	192	194	Right-handed 310
Helix 101	AL2	A	195	223	Right-handed alpha
Helix 102	AL3	A	250	259	Right-handed alpha
Helix 103	AL4	A	267	295	Right-handed alpha
Helix 104	AL5	A	308	312	Right-handed 310
Helix 105	AL6	A	316	333	Right-handed alpha
Helix 106	AL7	1	31	63	Right-handed alpha

There are 8 sheets in PDB entry 8KDE. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8,

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	B	166	169	first strand
Strand 2	B	176	179	anti-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	B	322	323	first strand
Strand 2	D	293	294	parallel

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There are 6 strands in AA3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	377	380	first strand
Strand 2	B	369	371	anti-parallel
Strand 3	B	353	356	anti-parallel
Strand 4	B	336	347	anti-parallel
Strand 5	B	398	402	anti-parallel
Strand 6	B	410	411	anti-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	B	377	380	first strand
Strand 2	B	369	371	anti-parallel
Strand 3	B	353	356	anti-parallel
Strand 4	B	336	347	anti-parallel
Strand 5	B	429	433	anti-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	D	77	78	first strand
Strand 2	D	173	174	anti-parallel

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There are 2 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	3	43	44	first strand
Strand 2	3	53	54	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	C	173	175	first strand
Strand 2	C	183	185	anti-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	329	331	first strand
Strand 2	C	337	339	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: 8KDE

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