Analysis of interatomic Contacts of Structural Units in PDB entry:
9GUP

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 9GUP entry

There are 33 chains in PDB entry 9GUP (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	A 1	G 515
A	G 517	C 526
A	C 528	U 965
A	A 968	G 1206
A	C 1208	G 1401
A	C 1403	U 1406
A	A 1408	G 1497
A	A 1499	G 1515
A	G 1517	G 1517
A	C 1520	U 1541
B	MET 1	ILE 174
C	ALA 2	GLN 227
D	GLY 2	ALA 212
E	ALA 2	LYS 206
F	GLU 10	LEU 165
G	MET 1	LYS 104
H	PRO 2	PHE 151
I	SER 2	ALA 130
J	GLU 3	ARG 130
K	ASN 3	GLY 103
L	ARG 13	VAL 129
M	ALA 2	LYS 88
M	LEU 90	LYS 123
N	ALA 2	ILE 116
O	ALA 2	TRP 101
P	SER 2	ARG 89
Q	MET 1	ALA 82
R	LYS 4	VAL 83
S	LYS 9	GLN 75
T	PRO 2	ALA 84
U	ALA 2	ALA 87
V	PRO 2	TYR 71
X	A 4	U 20

There are 97 helices in PDB entry 9GUP. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	B	4	16	Right-handed alpha
Helix 2	AA2	B	51	54	Right-handed 310
Helix 3	AA3	B	86	105	Right-handed alpha
Helix 4	AA4	B	134	136	Right-handed 310
Helix 5	AA5	B	144	148	Right-handed 310
Helix 6	AA6	B	161	164	Right-handed 310
Helix 7	AA7	C	5	13	Right-handed alpha
Helix 8	AA8	C	21	23	Right-handed 310
Helix 9	AA9	C	24	29	Right-handed 310
Helix 10	AB1	C	42	63	Right-handed alpha
Helix 11	AB2	C	76	86	Right-handed alpha
Helix 12	AB3	C	103	122	Right-handed alpha
Helix 13	AB4	C	131	149	Right-handed alpha
Helix 14	AB5	C	169	179	Right-handed alpha
Helix 15	AB6	C	206	227	Right-handed alpha
Helix 16	AB7	D	6	12	Right-handed alpha
Helix 17	AB8	D	25	47	Right-handed alpha
Helix 18	AB9	D	72	78	Right-handed alpha
Helix 19	AC1	D	81	96	Right-handed alpha
Helix 20	AC2	D	108	111	Right-handed 310
Helix 21	AC3	D	112	126	Right-handed alpha
Helix 22	AC4	D	129	145	Right-handed alpha
Helix 23	AC5	D	156	160	Right-handed 310
Helix 24	AC6	E	7	16	Right-handed alpha
Helix 25	AC7	E	27	32	Right-handed alpha
Helix 26	AC8	E	49	66	Right-handed alpha
Helix 27	AC9	E	68	82	Right-handed alpha
Helix 28	AD1	E	85	97	Right-handed alpha
Helix 29	AD2	E	97	106	Right-handed alpha
Helix 30	AD3	E	110	120	Right-handed alpha
Helix 31	AD4	E	146	151	Right-handed alpha
Helix 32	AD5	E	152	165	Right-handed alpha
Helix 33	AD6	E	196	206	Right-handed alpha
Helix 34	AD7	F	55	69	Right-handed alpha
Helix 35	AD8	F	108	119	Right-handed alpha
Helix 36	AD9	F	132	146	Right-handed alpha
Helix 37	AE1	F	149	158	Right-handed alpha
Helix 38	AE2	F	160	165	Right-handed alpha
Helix 39	AE3	G	12	15	Right-handed 310
Helix 40	AE4	G	17	32	Right-handed alpha
Helix 41	AE5	G	67	81	Right-handed alpha
Helix 42	AE6	H	20	31	Right-handed alpha
Helix 43	AE7	H	35	55	Right-handed alpha
Helix 44	AE8	H	57	70	Right-handed alpha
Helix 45	AE9	H	92	110	Right-handed alpha
Helix 46	AF1	H	115	129	Right-handed alpha
Helix 47	AF2	H	132	148	Right-handed alpha
Helix 48	AF3	I	5	20	Right-handed alpha
Helix 49	AF4	I	30	44	Right-handed alpha
Helix 50	AF5	I	88	92	Right-handed 310
Helix 51	AF6	I	94	99	Right-handed 310
Helix 52	AF7	I	113	120	Right-handed alpha
Helix 53	AF8	J	35	39	Right-handed alpha
Helix 54	AF9	J	41	55	Right-handed alpha
Helix 55	AG1	J	71	92	Right-handed alpha
Helix 56	AG2	J	94	102	Right-handed alpha
Helix 57	AG3	K	14	32	Right-handed alpha
Helix 58	AG4	K	80	89	Right-handed alpha
Helix 59	AG5	L	47	51	Right-handed alpha
Helix 60	AG6	L	59	74	Right-handed alpha
Helix 61	AG7	L	75	78	Right-handed 310
Helix 62	AG8	L	93	104	Right-handed alpha
Helix 63	AG9	M	3	10	Right-handed alpha
Helix 64	AH1	M	21	25	Right-handed 310
Helix 65	AH2	N	14	20	Right-handed alpha
Helix 66	AH3	N	26	37	Right-handed alpha
Helix 67	AH4	N	44	48	Right-handed 310
Helix 68	AH5	N	49	62	Right-handed alpha
Helix 69	AH6	N	65	84	Right-handed alpha
Helix 70	AH7	N	85	94	Right-handed alpha
Helix 71	AH8	N	106	111	Right-handed alpha
Helix 72	AH9	O	3	20	Right-handed alpha
Helix 73	AI1	O	20	33	Right-handed alpha
Helix 74	AI2	O	37	51	Right-handed alpha
Helix 75	AI3	O	52	60	Right-handed 310
Helix 76	AI4	O	80	91	Right-handed alpha
Helix 77	AI5	P	4	16	Right-handed alpha
Helix 78	AI6	P	24	46	Right-handed alpha
Helix 79	AI7	P	49	74	Right-handed alpha
Helix 80	AI8	P	74	86	Right-handed alpha
Helix 81	AI9	Q	53	63	Right-handed alpha
Helix 82	AJ1	Q	68	82	Right-handed alpha
Helix 83	AJ2	R	48	52	Right-handed 310
Helix 84	AJ3	S	13	17	Right-handed 310
Helix 85	AJ4	S	25	33	Right-handed alpha
Helix 86	AJ5	S	41	46	Right-handed alpha
Helix 87	AJ6	S	48	65	Right-handed alpha
Helix 88	AJ7	T	12	26	Right-handed alpha
Helix 89	AJ8	T	41	45	Right-handed 310
Helix 90	AJ9	T	63	67	Right-handed 310
Helix 91	AK1	T	70	75	Right-handed 310
Helix 92	AK2	U	4	42	Right-handed alpha
Helix 93	AK3	U	44	65	Right-handed alpha
Helix 94	AK4	U	68	86	Right-handed alpha
Helix 95	AK5	V	11	27	Right-handed alpha
Helix 96	AK6	V	27	35	Right-handed alpha
Helix 97	AK7	V	40	66	Right-handed alpha

There are 23 sheets in PDB entry 9GUP. 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,

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	B	47	49	first strand
Strand 2	B	35	39	anti-parallel
Strand 3	B	23	31	anti-parallel
Strand 4	B	67	74	anti-parallel
Strand 5	B	83	85	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	B	151	154	first strand
Strand 2	B	108	115	anti-parallel
Strand 3	B	119	124	anti-parallel
Strand 4	B	127	132	anti-parallel
Strand 5	B	165	167	parallel
Strand 6	B	158	160	anti-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	16	19	first strand
Strand 2	C	38	41	anti-parallel
Strand 3	C	31	34	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	C	90	92	first strand
Strand 2	C	67	70	parallel
Strand 3	C	160	164	parallel
Strand 4	C	183	187	parallel
Strand 5	C	198	201	parallel

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There are 3 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	52	58	first strand
Strand 2	D	64	70	anti-parallel
Strand 3	D	99	105	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	D	165	171	first strand
Strand 2	D	148	154	anti-parallel
Strand 3	D	194	206	anti-parallel
Strand 4	D	180	191	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	E	128	129	first strand
Strand 2	E	123	125	anti-parallel
Strand 3	E	142	145	anti-parallel
Strand 4	E	179	182	anti-parallel
Strand 5	E	171	174	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	F	12	25	first strand
Strand 2	F	28	40	anti-parallel
Strand 3	F	45	53	anti-parallel
Strand 4	F	72	73	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	F	85	89	first strand
Strand 2	F	92	98	anti-parallel
Strand 3	F	123	129	anti-parallel
Strand 4	F	105	106	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	G	35	45	first strand
Strand 2	G	57	65	anti-parallel
Strand 3	G	3	10	anti-parallel
Strand 4	G	84	92	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	H	73	79	first strand
Strand 2	H	84	90	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	I	24	28	first strand
Strand 2	I	58	63	anti-parallel
Strand 3	I	46	52	anti-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	I	74	77	first strand
Strand 2	I	123	130	anti-parallel
Strand 3	I	86	87	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	I	74	77	first strand
Strand 2	I	123	130	anti-parallel
Strand 3	I	101	106	anti-parallel
Strand 4	I	109	112	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	6	12	first strand
Strand 2	J	15	23	anti-parallel
Strand 3	J	61	68	anti-parallel
Strand 4	J	28	30	parallel
Strand 5	J	33	34	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	K	35	36	first strand
Strand 2	K	62	77	anti-parallel
Strand 3	K	6	12	anti-parallel
Strand 4	K	96	102	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	K	40	52	first strand
Strand 2	K	62	77	anti-parallel
Strand 3	O	97	98	anti-parallel

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There are 6 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	41	46	first strand
Strand 2	L	30	36	anti-parallel
Strand 3	L	18	25	anti-parallel
Strand 4	L	81	87	parallel
Strand 5	L	106	112	parallel
Strand 6	V	3	5	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	M	29	40	first strand
Strand 2	M	50	57	anti-parallel
Strand 3	M	62	66	anti-parallel
Strand 4	M	93	97	parallel
Strand 5	M	79	84	anti-parallel
Strand 6	M	29	40	anti-parallel

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There are 2 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	N	3	4	first strand
Strand 2	N	7	8	anti-parallel

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There are 5 strands in AC3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	Q	50	52	first strand
Strand 2	Q	34	39	anti-parallel
Strand 3	Q	14	23	anti-parallel
Strand 4	Q	2	11	anti-parallel
Strand 5	Q	66	67	parallel

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There are 6 strands in AC4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	R	8	17	first strand
Strand 2	R	20	30	anti-parallel
Strand 3	R	37	47	anti-parallel
Strand 4	R	73	79	parallel
Strand 5	R	58	63	anti-parallel
Strand 6	R	8	17	anti-parallel

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There are 3 strands in AC5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	T	31	33	first strand
Strand 2	T	47	52	parallel
Strand 3	T	57	62	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: 9GUP

Analysis of interatomic Contacts of Structural Units in PDB entry:
9GUP