Analysis of interatomic Contacts of Structural Units in PDB entry:
6YBS

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 6YBS entry

There are 22 chains in PDB entry 6YBS (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
x	TRP 169	PHE 528
c	THR 2	ILE 314
n	ARG 5	ARG 67
X	GLY 2	GLU 79
h	ILE 17	ALA 119
o	ASN 238	TRP 314
a	MET 1	PRO 99
m	VAL 11	LYS 132
i	TYR 7	ASP 56
b	PHE 15	LYS 124
Z	MET 1	LYS 227
d	GLY 3	LYS 144
e	ASN 45	THR 110
f	VAL 4	THR 145
V	ASP 16	ARG 204
k	HIS 93	ASN 151
Y	PRO 6	ARG 146
A	A 1200	C 1218
A	A 1220	U 1242
A	U 1244	C 1373
A	G 1375	U 1677
A	A 1679	C 1700

There are 78 helices in PDB entry 6YBS. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	x	177	182	Right-handed alpha
Helix 2	AA2	x	204	209	Right-handed alpha
Helix 3	AA3	x	233	238	Right-handed alpha
Helix 4	AA4	x	309	324	Right-handed alpha
Helix 5	AA5	x	325	327	Right-handed 310
Helix 6	AA6	x	409	414	Right-handed alpha
Helix 7	AA7	x	417	429	Right-handed alpha
Helix 8	AA8	x	430	443	Right-handed alpha
Helix 9	AA9	x	475	480	Right-handed alpha
Helix 10	AB1	x	484	499	Right-handed alpha
Helix 11	AB2	X	6	21	Right-handed alpha
Helix 12	AB3	X	22	24	Right-handed 310
Helix 13	AB4	X	27	38	Right-handed alpha
Helix 14	AB5	X	44	62	Right-handed alpha
Helix 15	AB6	X	71	75	Right-handed 310
Helix 16	AB7	h	28	46	Right-handed alpha
Helix 17	AB8	h	94	102	Right-handed alpha
Helix 18	AB9	o	251	260	Right-handed alpha
Helix 19	AC1	o	261	263	Right-handed 310
Helix 20	AC2	o	291	297	Right-handed alpha
Helix 21	AC3	a	4	19	Right-handed alpha
Helix 22	AC4	a	35	39	Right-handed 310
Helix 23	AC5	a	41	54	Right-handed alpha
Helix 24	AC6	a	72	83	Right-handed alpha
Helix 25	AC7	m	13	28	Right-handed alpha
Helix 26	AC8	m	35	44	Right-handed alpha
Helix 27	AC9	m	58	73	Right-handed alpha
Helix 28	AD1	m	81	90	Right-handed alpha
Helix 29	AD2	m	120	132	Right-handed alpha
Helix 30	AD3	i	32	36	Right-handed 310
Helix 31	AD4	i	40	51	Right-handed alpha
Helix 32	AD5	b	21	28	Right-handed alpha
Helix 33	AD6	b	29	35	Right-handed alpha
Helix 34	AD7	b	38	47	Right-handed alpha
Helix 35	AD8	b	50	65	Right-handed alpha
Helix 36	AD9	b	108	112	Right-handed 310
Helix 37	AE1	b	116	120	Right-handed 310
Helix 38	AE2	Z	6	29	Right-handed alpha
Helix 39	AE3	Z	30	32	Right-handed 310
Helix 40	AE4	Z	54	60	Right-handed alpha
Helix 41	AE5	Z	63	78	Right-handed alpha
Helix 42	AE6	Z	97	111	Right-handed alpha
Helix 43	AE7	Z	114	129	Right-handed alpha
Helix 44	AE8	Z	162	166	Right-handed 310
Helix 45	AE9	d	5	9	Right-handed 310
Helix 46	AF1	d	10	25	Right-handed alpha
Helix 47	AF2	d	33	37	Right-handed 310
Helix 48	AF3	d	51	66	Right-handed alpha
Helix 49	AF4	d	71	79	Right-handed alpha
Helix 50	AF5	d	96	110	Right-handed alpha
Helix 51	AF6	d	124	143	Right-handed alpha
Helix 52	AF7	e	51	62	Right-handed alpha
Helix 53	AF8	e	63	65	Right-handed 310
Helix 54	AF9	e	72	77	Right-handed alpha
Helix 55	AG1	e	80	95	Right-handed alpha
Helix 56	AG2	f	25	30	Right-handed alpha
Helix 57	AG3	f	31	33	Right-handed 310
Helix 58	AG4	f	37	48	Right-handed alpha
Helix 59	AG5	f	55	59	Right-handed 310
Helix 60	AG6	f	60	73	Right-handed alpha
Helix 61	AG7	f	74	78	Right-handed 310
Helix 62	AG8	f	80	84	Right-handed 310
Helix 63	AG9	f	101	117	Right-handed alpha
Helix 64	AH1	f	119	128	Right-handed alpha
Helix 65	AH2	V	18	22	Right-handed 310
Helix 66	AH3	V	61	66	Right-handed 310
Helix 67	AH4	V	67	75	Right-handed alpha
Helix 68	AH5	V	85	104	Right-handed alpha
Helix 69	AH6	V	107	120	Right-handed alpha
Helix 70	AH7	V	142	162	Right-handed alpha
Helix 71	AH8	V	168	183	Right-handed alpha
Helix 72	AH9	V	187	203	Right-handed alpha
Helix 73	AI1	Y	40	42	Right-handed 310
Helix 74	AI2	Y	44	46	Right-handed 310
Helix 75	AI3	Y	47	59	Right-handed alpha
Helix 76	AI4	Y	76	100	Right-handed alpha
Helix 77	AI5	Y	101	116	Right-handed alpha
Helix 78	AI6	Y	117	120	Right-handed 310

There are 27 sheets in PDB entry 6YBS. 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,

There are 9 strands in AA1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	x	170	176	first strand
Strand 2	x	517	522	anti-parallel
Strand 3	x	506	508	anti-parallel
Strand 4	x	268	271	anti-parallel
Strand 5	x	277	281	anti-parallel
Strand 6	x	246	247	parallel
Strand 7	x	372	375	parallel
Strand 8	x	359	362	anti-parallel
Strand 9	x	195	197	anti-parallel

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There are 3 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	x	392	396	first strand
Strand 2	x	447	455	parallel
Strand 3	x	464	472	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	c	5	7	first strand
Strand 2	c	307	312	anti-parallel
Strand 3	c	297	301	anti-parallel
Strand 4	c	288	291	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	c	18	22	first strand
Strand 2	c	32	35	anti-parallel
Strand 3	c	40	44	anti-parallel
Strand 4	c	54	59	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	c	66	71	first strand
Strand 2	c	77	82	anti-parallel
Strand 3	c	87	91	anti-parallel
Strand 4	c	96	101	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	c	108	113	first strand
Strand 2	c	119	124	anti-parallel
Strand 3	c	129	133	anti-parallel
Strand 4	c	138	142	anti-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	151	155	first strand
Strand 2	c	164	169	anti-parallel
Strand 3	c	174	178	anti-parallel
Strand 4	c	183	188	anti-parallel
Strand 5	Z	224	225	anti-parallel

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There are 4 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	195	200	first strand
Strand 2	c	206	211	anti-parallel
Strand 3	c	215	220	anti-parallel
Strand 4	c	226	231	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	c	236	241	first strand
Strand 2	c	247	252	anti-parallel
Strand 3	c	255	260	anti-parallel
Strand 4	c	266	270	anti-parallel

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There are 6 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	n	55	58	first strand
Strand 2	n	10	20	anti-parallel
Strand 3	n	28	34	anti-parallel
Strand 4	n	42	47	anti-parallel
Strand 5	V	138	141	parallel
Strand 6	V	123	125	anti-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	X	39	40	first strand
Strand 2	Z	209	210	anti-parallel

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There are 3 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	51	55	first strand
Strand 2	h	77	91	anti-parallel
Strand 3	h	59	66	anti-parallel

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There are 4 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	h	51	55	first strand
Strand 2	h	77	91	anti-parallel
Strand 3	h	20	26	anti-parallel
Strand 4	h	110	116	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	o	267	273	first strand
Strand 2	o	276	286	anti-parallel
Strand 3	o	241	244	anti-parallel
Strand 4	o	312	313	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	o	302	305	first strand
Strand 2	o	308	310	anti-parallel

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There are 3 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	a	20	24	first strand
Strand 2	a	66	71	anti-parallel
Strand 3	a	58	62	anti-parallel

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There are 4 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	m	31	33	first strand
Strand 2	m	108	111	anti-parallel
Strand 3	m	49	52	anti-parallel
Strand 4	m	76	78	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	i	30	31	first strand
Strand 2	i	38	39	anti-parallel

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There are 3 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	b	76	78	first strand
Strand 2	b	93	97	parallel
Strand 3	b	102	106	anti-parallel

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There are 3 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	Z	34	41	first strand
Strand 2	Z	46	52	anti-parallel
Strand 3	Z	84	90	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	Z	148	155	first strand
Strand 2	Z	133	140	anti-parallel
Strand 3	Z	181	189	anti-parallel
Strand 4	Z	168	176	anti-parallel

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There are 2 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	81	85	first strand
Strand 2	d	88	93	anti-parallel

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There are 2 strands in AC5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	d	113	115	first strand
Strand 2	d	121	123	anti-parallel

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There are 2 strands in AC6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	e	99	102	first strand
Strand 2	e	107	109	anti-parallel

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There are 2 strands in AC7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	f	12	13	first strand
Strand 2	f	20	21	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	k	119	120	first strand
Strand 2	k	131	134	anti-parallel
Strand 3	k	138	140	anti-parallel
Strand 4	k	147	149	anti-parallel

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There are 5 strands in AC9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	Y	9	16	first strand
Strand 2	Y	19	27	anti-parallel
Strand 3	Y	66	73	anti-parallel
Strand 4	Y	31	34	parallel
Strand 5	Y	37	38	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: 6YBS

Analysis of interatomic Contacts of Structural Units in PDB entry:
6YBS