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

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 9YML entry

There are 18 chains in PDB entry 9YML (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
G	VAL 2	SER 112
H	GLN 1	VAL 111
I	ALA 3	VAL 106
L	SER 1	THR 105
A	ASN 33	VAL 506
B	SER 519	ASP 664
J	VAL 2	SER 112
K	GLN 1	VAL 111
M	ALA 3	VAL 106
N	SER 1	THR 105
C	ASN 33	VAL 506
D	SER 519	ASP 664
O	VAL 2	SER 112
P	GLN 1	VAL 111
Q	ALA 3	VAL 106
R	SER 1	THR 105
E	ASN 33	VAL 506
F	SER 519	ASP 664

There are 45 helices in PDB entry 9YML. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	G	28	32	Right-handed 310
Helix 2	AA2	G	61	64	Right-handed 310
Helix 3	AA3	H	63	67	Right-handed 310
Helix 4	AA4	H	83	87	Right-handed 310
Helix 5	AA5	A	98	117	Right-handed alpha
Helix 6	AA6	A	335	353	Right-handed alpha
Helix 7	AA7	A	368	373	Right-handed alpha
Helix 8	AA8	A	425	429	Right-handed 310
Helix 9	AA9	A	475	481	Right-handed alpha
Helix 10	AB1	B	529	534	Right-handed alpha
Helix 11	AB2	B	536	543	Right-handed alpha
Helix 12	AB3	B	571	596	Right-handed alpha
Helix 13	AB4	B	618	625	Right-handed alpha
Helix 14	AB5	B	627	635	Right-handed alpha
Helix 15	AB6	B	638	662	Right-handed alpha
Helix 16	AB7	J	28	32	Right-handed 310
Helix 17	AB8	J	61	64	Right-handed 310
Helix 18	AB9	K	63	67	Right-handed 310
Helix 19	AC1	K	83	87	Right-handed 310
Helix 20	AC2	C	98	117	Right-handed alpha
Helix 21	AC3	C	335	353	Right-handed alpha
Helix 22	AC4	C	368	373	Right-handed alpha
Helix 23	AC5	C	425	429	Right-handed 310
Helix 24	AC6	C	475	481	Right-handed alpha
Helix 25	AC7	D	529	534	Right-handed alpha
Helix 26	AC8	D	536	543	Right-handed alpha
Helix 27	AC9	D	571	596	Right-handed alpha
Helix 28	AD1	D	618	625	Right-handed alpha
Helix 29	AD2	D	627	635	Right-handed alpha
Helix 30	AD3	D	638	662	Right-handed alpha
Helix 31	AD4	O	28	32	Right-handed 310
Helix 32	AD5	O	61	64	Right-handed 310
Helix 33	AD6	P	63	67	Right-handed 310
Helix 34	AD7	P	83	87	Right-handed 310
Helix 35	AD8	E	98	117	Right-handed alpha
Helix 36	AD9	E	335	353	Right-handed alpha
Helix 37	AE1	E	368	373	Right-handed alpha
Helix 38	AE2	E	425	429	Right-handed 310
Helix 39	AE3	E	475	481	Right-handed alpha
Helix 40	AE4	F	529	534	Right-handed alpha
Helix 41	AE5	F	536	543	Right-handed alpha
Helix 42	AE6	F	571	596	Right-handed alpha
Helix 43	AE7	F	618	625	Right-handed alpha
Helix 44	AE8	F	627	635	Right-handed alpha
Helix 45	AE9	F	638	662	Right-handed alpha

There are 57 sheets in PDB entry 9YML. 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, AD1, AD2, AD3, AD4, AD5, AD6, AD7, AD8, AD9, AE1, AE2, AE3, AE4, AE5, AE6, AE7, AE8, AE9, AF1, AF2, AF3, AF4, AF5, AF6, AF7, AF8, AF9, AG1, AG2, AG3,

There are 4 strands in AA1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	3	6	first strand
Strand 2	G	17	25	anti-parallel
Strand 3	G	77	82	anti-parallel
Strand 4	G	67	72	anti-parallel

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There are 5 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	57	59	first strand
Strand 2	G	45	51	anti-parallel
Strand 3	G	34	39	anti-parallel
Strand 4	G	88	95	anti-parallel
Strand 5	G	100	102	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	G	57	59	first strand
Strand 2	G	45	51	anti-parallel
Strand 3	G	34	39	anti-parallel
Strand 4	G	88	95	anti-parallel
Strand 5	G	108	109	anti-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	H	21	23	first strand
Strand 2	H	77	79	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	H	50	51	first strand
Strand 2	H	34	39	anti-parallel
Strand 3	H	88	95	anti-parallel
Strand 4	H	108	109	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	H	97	99	first strand
Strand 2	H	100	100	anti-parallel

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There are 3 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	19	24	first strand
Strand 2	I	70	75	anti-parallel
Strand 3	I	62	67	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	I	45	48	first strand
Strand 2	I	33	38	anti-parallel
Strand 3	I	85	91	anti-parallel
Strand 4	I	96	98	anti-parallel

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There are 3 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	23	24	first strand
Strand 2	L	70	73	anti-parallel
Strand 3	L	64	67	anti-parallel

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There are 3 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	44	48	first strand
Strand 2	L	34	38	anti-parallel
Strand 3	L	85	89	anti-parallel

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There are 3 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	494	499	first strand
Strand 2	A	35	40	anti-parallel
Strand 3	B	603	609	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	A	45	47	first strand
Strand 2	A	486	491	anti-parallel
Strand 3	A	223	228	anti-parallel
Strand 4	A	242	245	anti-parallel
Strand 5	A	83	86	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	A	75	76	first strand
Strand 2	A	53	56	parallel
Strand 3	A	216	218	anti-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	91	94	first strand
Strand 2	A	236	239	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	A	169	177	first strand
Strand 2	A	154	162	anti-parallel
Strand 3	A	129	133	anti-parallel
Strand 4	A	190	193	anti-parallel
Strand 5	A	181	183	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	200	203	first strand
Strand 2	A	432	435	parallel
Strand 3	A	423	424	anti-parallel

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There are 7 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	259	261	first strand
Strand 2	A	443	456	anti-parallel
Strand 3	A	284	298	anti-parallel
Strand 4	A	329	334	anti-parallel
Strand 5	A	413	421	anti-parallel
Strand 6	A	381	385	anti-parallel
Strand 7	A	374	378	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	A	271	274	first strand
Strand 2	A	284	298	anti-parallel
Strand 3	A	443	456	anti-parallel
Strand 4	A	467	470	anti-parallel
Strand 5	A	360	361	parallel
Strand 6	A	393	394	anti-parallel

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There are 2 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	302	312	first strand
Strand 2	A	315	323	anti-parallel

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There are 4 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	3	6	first strand
Strand 2	J	17	25	anti-parallel
Strand 3	J	77	82	anti-parallel
Strand 4	J	67	72	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	J	57	59	first strand
Strand 2	J	45	51	anti-parallel
Strand 3	J	34	39	anti-parallel
Strand 4	J	88	95	anti-parallel
Strand 5	J	100	102	anti-parallel

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There are 5 strands in AC4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	57	59	first strand
Strand 2	J	45	51	anti-parallel
Strand 3	J	34	39	anti-parallel
Strand 4	J	88	95	anti-parallel
Strand 5	J	108	109	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	K	21	23	first strand
Strand 2	K	77	79	anti-parallel

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There are 4 strands in AC6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	50	51	first strand
Strand 2	K	34	39	anti-parallel
Strand 3	K	88	95	anti-parallel
Strand 4	K	108	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	K	97	99	first strand
Strand 2	K	100	100	anti-parallel

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There are 3 strands in AC8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	M	19	24	first strand
Strand 2	M	70	75	anti-parallel
Strand 3	M	62	67	anti-parallel

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There are 4 strands in AC9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	M	45	48	first strand
Strand 2	M	33	38	anti-parallel
Strand 3	M	85	91	anti-parallel
Strand 4	M	96	98	anti-parallel

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There are 3 strands in AD1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	N	23	24	first strand
Strand 2	N	70	73	anti-parallel
Strand 3	N	64	67	anti-parallel

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There are 3 strands in AD2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	N	44	48	first strand
Strand 2	N	34	38	anti-parallel
Strand 3	N	85	89	anti-parallel

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There are 3 strands in AD3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	494	499	first strand
Strand 2	C	35	40	anti-parallel
Strand 3	D	603	609	anti-parallel

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There are 5 strands in AD4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	45	47	first strand
Strand 2	C	486	491	anti-parallel
Strand 3	C	223	228	anti-parallel
Strand 4	C	242	245	anti-parallel
Strand 5	C	83	86	anti-parallel

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There are 3 strands in AD5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	75	76	first strand
Strand 2	C	53	56	parallel
Strand 3	C	216	218	anti-parallel

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There are 2 strands in AD6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	91	94	first strand
Strand 2	C	236	239	anti-parallel

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There are 5 strands in AD7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	169	177	first strand
Strand 2	C	154	162	anti-parallel
Strand 3	C	129	133	anti-parallel
Strand 4	C	190	193	anti-parallel
Strand 5	C	181	183	anti-parallel

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There are 3 strands in AD8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	200	203	first strand
Strand 2	C	432	435	parallel
Strand 3	C	423	424	anti-parallel

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There are 7 strands in AD9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	259	261	first strand
Strand 2	C	443	456	anti-parallel
Strand 3	C	284	298	anti-parallel
Strand 4	C	329	334	anti-parallel
Strand 5	C	413	421	anti-parallel
Strand 6	C	381	385	anti-parallel
Strand 7	C	374	378	anti-parallel

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There are 6 strands in AE1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	271	274	first strand
Strand 2	C	284	298	anti-parallel
Strand 3	C	443	456	anti-parallel
Strand 4	C	467	470	anti-parallel
Strand 5	C	360	361	parallel
Strand 6	C	393	394	anti-parallel

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There are 2 strands in AE2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	302	312	first strand
Strand 2	C	315	323	anti-parallel

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There are 4 strands in AE3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	O	3	6	first strand
Strand 2	O	17	25	anti-parallel
Strand 3	O	77	82	anti-parallel
Strand 4	O	67	72	anti-parallel

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There are 5 strands in AE4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	O	57	59	first strand
Strand 2	O	45	51	anti-parallel
Strand 3	O	34	39	anti-parallel
Strand 4	O	88	95	anti-parallel
Strand 5	O	100	102	anti-parallel

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There are 5 strands in AE5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	O	57	59	first strand
Strand 2	O	45	51	anti-parallel
Strand 3	O	34	39	anti-parallel
Strand 4	O	88	95	anti-parallel
Strand 5	O	108	109	anti-parallel

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There are 2 strands in AE6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	P	21	23	first strand
Strand 2	P	77	79	anti-parallel

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There are 4 strands in AE7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	P	50	51	first strand
Strand 2	P	34	39	anti-parallel
Strand 3	P	88	95	anti-parallel
Strand 4	P	108	109	anti-parallel

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There are 2 strands in AE8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	P	97	99	first strand
Strand 2	P	100	100	anti-parallel

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There are 3 strands in AE9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	Q	19	24	first strand
Strand 2	Q	70	75	anti-parallel
Strand 3	Q	62	67	anti-parallel

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There are 4 strands in AF1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	Q	45	48	first strand
Strand 2	Q	33	38	anti-parallel
Strand 3	Q	85	91	anti-parallel
Strand 4	Q	96	98	anti-parallel

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There are 3 strands in AF2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	R	23	24	first strand
Strand 2	R	70	73	anti-parallel
Strand 3	R	64	67	anti-parallel

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There are 3 strands in AF3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	R	44	48	first strand
Strand 2	R	34	38	anti-parallel
Strand 3	R	85	89	anti-parallel

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There are 3 strands in AF4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	494	499	first strand
Strand 2	E	35	40	anti-parallel
Strand 3	F	603	609	anti-parallel

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There are 5 strands in AF5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	45	47	first strand
Strand 2	E	486	491	anti-parallel
Strand 3	E	223	228	anti-parallel
Strand 4	E	242	245	anti-parallel
Strand 5	E	83	86	anti-parallel

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There are 3 strands in AF6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	75	76	first strand
Strand 2	E	53	56	parallel
Strand 3	E	216	218	anti-parallel

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There are 2 strands in AF7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	91	94	first strand
Strand 2	E	236	239	anti-parallel

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There are 5 strands in AF8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	169	177	first strand
Strand 2	E	154	162	anti-parallel
Strand 3	E	129	133	anti-parallel
Strand 4	E	190	193	anti-parallel
Strand 5	E	181	183	anti-parallel

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There are 3 strands in AF9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	200	203	first strand
Strand 2	E	432	435	parallel
Strand 3	E	423	424	anti-parallel

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There are 7 strands in AG1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	259	261	first strand
Strand 2	E	443	456	anti-parallel
Strand 3	E	284	298	anti-parallel
Strand 4	E	329	334	anti-parallel
Strand 5	E	413	421	anti-parallel
Strand 6	E	381	385	anti-parallel
Strand 7	E	374	378	anti-parallel

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There are 6 strands in AG2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	271	274	first strand
Strand 2	E	284	298	anti-parallel
Strand 3	E	443	456	anti-parallel
Strand 4	E	467	470	anti-parallel
Strand 5	E	360	361	parallel
Strand 6	E	393	394	anti-parallel

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There are 2 strands in AG3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	302	312	first strand
Strand 2	E	315	323	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: 9YML

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