Analysis of interatomic Contacts of Structural Units in PDB entry:
5J3D

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 5J3D entry

There are 12 chains in PDB entry 5J3D (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	VAL 5	CYS 231
B	ASP 1	CYS 234
C	VAL 5	CYS 231
D	ASP 1	CYS 234
E	GLN 26	GLN 98
F	ALA 147	GLY 514
G	GLN 26	GLN 98
H	VAL 5	CYS 231
I	ALA 147	GLY 514
J	GLN 26	GLN 98
K	ALA 147	GLY 514
L	ASP 1	CYS 234

There are 50 helices in PDB entry 5J3D. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	29	37	Right-handed 310
Helix 2	AA2	A	95	99	Right-handed 310
Helix 3	AA3	A	171	173	Right-handed 310
Helix 4	AA4	A	200	204	Right-handed 310
Helix 5	AA5	A	216	219	Right-handed 310
Helix 6	AA6	B	95	99	Right-handed 310
Helix 7	AA7	B	141	146	Right-handed alpha
Helix 8	AA8	B	203	207	Right-handed alpha
Helix 9	AA9	C	29	37	Right-handed 310
Helix 10	AB1	C	95	99	Right-handed 310
Helix 11	AB2	C	171	173	Right-handed 310
Helix 12	AB3	C	200	204	Right-handed 310
Helix 13	AB4	D	95	99	Right-handed 310
Helix 14	AB5	D	141	146	Right-handed alpha
Helix 15	AB6	D	203	207	Right-handed alpha
Helix 16	AB7	E	77	95	Right-handed alpha
Helix 17	AB8	F	153	202	Right-handed alpha
Helix 18	AB9	F	202	227	Right-handed alpha
Helix 19	AC1	F	227	241	Right-handed alpha
Helix 20	AC2	F	253	262	Right-handed alpha
Helix 21	AC3	F	267	276	Right-handed alpha
Helix 22	AC4	F	277	284	Right-handed alpha
Helix 23	AC5	F	370	372	Right-handed 310
Helix 24	AC6	F	376	382	Right-handed 310
Helix 25	AC7	F	484	511	Right-handed alpha
Helix 26	AC8	G	77	95	Right-handed alpha
Helix 27	AC9	H	95	99	Right-handed 310
Helix 28	AD1	H	171	173	Right-handed 310
Helix 29	AD2	H	200	204	Right-handed 310
Helix 30	AD3	I	153	202	Right-handed alpha
Helix 31	AD4	I	202	227	Right-handed alpha
Helix 32	AD5	I	227	241	Right-handed alpha
Helix 33	AD6	I	253	262	Right-handed alpha
Helix 34	AD7	I	267	276	Right-handed alpha
Helix 35	AD8	I	277	284	Right-handed alpha
Helix 36	AD9	I	370	372	Right-handed 310
Helix 37	AE1	I	376	383	Right-handed 310
Helix 38	AE2	I	484	512	Right-handed alpha
Helix 39	AE3	J	77	95	Right-handed alpha
Helix 40	AE4	K	154	202	Right-handed alpha
Helix 41	AE5	K	202	227	Right-handed alpha
Helix 42	AE6	K	227	241	Right-handed alpha
Helix 43	AE7	K	253	262	Right-handed alpha
Helix 44	AE8	K	267	276	Right-handed alpha
Helix 45	AE9	K	277	284	Right-handed alpha
Helix 46	AF1	K	376	383	Right-handed 310
Helix 47	AF2	K	484	511	Right-handed alpha
Helix 48	AF3	L	95	99	Right-handed 310
Helix 49	AF4	L	141	146	Right-handed alpha
Helix 50	AF5	L	203	207	Right-handed alpha

There are 52 sheets in PDB entry 5J3D. 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,

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	A	6	7	first strand
Strand 2	A	18	24	anti-parallel
Strand 3	A	86	92	anti-parallel
Strand 4	A	76	77	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	A	6	7	first strand
Strand 2	A	18	24	anti-parallel
Strand 3	A	86	92	anti-parallel
Strand 4	A	80	81	anti-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	A	11	13	first strand
Strand 2	A	122	126	parallel
Strand 3	A	100	106	anti-parallel
Strand 4	A	39	44	anti-parallel
Strand 5	A	51	56	anti-parallel
Strand 6	A	65	67	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	A	11	13	first strand
Strand 2	A	122	126	parallel
Strand 3	A	100	106	anti-parallel
Strand 4	A	117	118	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	A	135	139	first strand
Strand 2	A	151	160	anti-parallel
Strand 3	A	191	199	anti-parallel
Strand 4	A	178	180	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	A	135	139	first strand
Strand 2	A	151	160	anti-parallel
Strand 3	A	191	199	anti-parallel
Strand 4	A	184	185	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	A	166	169	first strand
Strand 2	A	210	215	anti-parallel
Strand 3	A	220	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	B	4	7	first strand
Strand 2	B	20	25	anti-parallel
Strand 3	B	86	91	anti-parallel
Strand 4	B	76	83	anti-parallel

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There are 6 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	10	14	first strand
Strand 2	B	122	127	parallel
Strand 3	B	101	106	anti-parallel
Strand 4	B	39	44	anti-parallel
Strand 5	B	51	55	anti-parallel
Strand 6	B	66	67	anti-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	B	10	14	first strand
Strand 2	B	122	127	parallel
Strand 3	B	101	106	anti-parallel
Strand 4	B	117	118	anti-parallel

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There are 4 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	134	138	first strand
Strand 2	B	149	159	anti-parallel
Strand 3	B	193	202	anti-parallel
Strand 4	B	179	180	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	B	164	170	first strand
Strand 2	B	211	218	anti-parallel
Strand 3	B	225	230	anti-parallel

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There are 6 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	11	13	first strand
Strand 2	C	122	126	parallel
Strand 3	C	100	106	anti-parallel
Strand 4	C	39	44	anti-parallel
Strand 5	C	51	56	anti-parallel
Strand 6	C	65	67	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	C	11	13	first strand
Strand 2	C	122	126	parallel
Strand 3	C	100	106	anti-parallel
Strand 4	C	117	118	anti-parallel

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There are 3 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	19	24	first strand
Strand 2	C	86	91	anti-parallel
Strand 3	C	76	81	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	C	135	139	first strand
Strand 2	C	151	160	anti-parallel
Strand 3	C	191	199	anti-parallel
Strand 4	C	178	180	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	C	135	139	first strand
Strand 2	C	151	160	anti-parallel
Strand 3	C	191	199	anti-parallel
Strand 4	C	184	185	anti-parallel

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There are 3 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	166	169	first strand
Strand 2	C	210	215	anti-parallel
Strand 3	C	220	225	anti-parallel

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There are 4 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	4	7	first strand
Strand 2	D	19	25	anti-parallel
Strand 3	D	86	91	anti-parallel
Strand 4	D	76	83	anti-parallel

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There are 6 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	10	14	first strand
Strand 2	D	122	127	parallel
Strand 3	D	101	106	anti-parallel
Strand 4	D	39	44	anti-parallel
Strand 5	D	51	55	anti-parallel
Strand 6	D	66	67	anti-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	D	10	14	first strand
Strand 2	D	122	127	parallel
Strand 3	D	101	106	anti-parallel
Strand 4	D	117	118	anti-parallel

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There are 4 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	134	138	first strand
Strand 2	D	149	159	anti-parallel
Strand 3	D	193	202	anti-parallel
Strand 4	D	179	180	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	D	164	170	first strand
Strand 2	D	211	218	anti-parallel
Strand 3	D	225	230	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	F	358	361	first strand
Strand 2	F	364	368	anti-parallel
Strand 3	E	38	60	parallel
Strand 4	I	467	469	parallel

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There are 5 strands in AC7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	29	33	first strand
Strand 2	E	38	60	anti-parallel
Strand 3	F	296	318	anti-parallel
Strand 4	F	286	293	anti-parallel
Strand 5	F	243	244	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	F	296	318	first strand
Strand 2	F	340	344	anti-parallel
Strand 3	F	349	352	anti-parallel
Strand 4	F	373	375	anti-parallel

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There are 2 strands in AC9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	334	336	first strand
Strand 2	F	395	397	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	F	404	408	first strand
Strand 2	F	411	416	anti-parallel
Strand 3	F	438	443	anti-parallel

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There are 4 strands in AD2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	430	434	first strand
Strand 2	F	422	426	anti-parallel
Strand 3	F	449	452	anti-parallel
Strand 4	F	455	458	anti-parallel

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There are 6 strands in AD3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	243	244	first strand
Strand 2	K	286	293	anti-parallel
Strand 3	K	296	318	anti-parallel
Strand 4	J	38	60	anti-parallel
Strand 5	K	364	368	parallel
Strand 6	K	358	361	anti-parallel

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There are 3 strands in AD4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	466	469	first strand
Strand 2	J	38	60	parallel
Strand 3	J	29	33	anti-parallel

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There are 4 strands in AD5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	296	318	first strand
Strand 2	K	340	343	anti-parallel
Strand 3	K	349	352	anti-parallel
Strand 4	K	373	375	anti-parallel

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There are 6 strands in AD6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	462	463	first strand
Strand 2	G	38	60	parallel
Strand 3	K	467	469	parallel
Strand 4	G	38	60	parallel
Strand 5	I	364	368	parallel
Strand 6	I	358	361	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	G	29	33	first strand
Strand 2	G	38	60	anti-parallel
Strand 3	I	296	318	anti-parallel
Strand 4	I	286	293	anti-parallel
Strand 5	I	243	244	anti-parallel

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There are 4 strands in AD8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	296	318	first strand
Strand 2	I	340	344	anti-parallel
Strand 3	I	349	352	anti-parallel
Strand 4	I	373	375	anti-parallel

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There are 6 strands in AD9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	11	13	first strand
Strand 2	H	122	126	parallel
Strand 3	H	100	106	anti-parallel
Strand 4	H	39	44	anti-parallel
Strand 5	H	51	56	anti-parallel
Strand 6	H	65	67	anti-parallel

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There are 4 strands in AE1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	11	13	first strand
Strand 2	H	122	126	parallel
Strand 3	H	100	106	anti-parallel
Strand 4	H	117	118	anti-parallel

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There are 3 strands in AE2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	18	24	first strand
Strand 2	H	86	92	anti-parallel
Strand 3	H	76	81	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	H	135	139	first strand
Strand 2	H	151	160	anti-parallel
Strand 3	H	191	199	anti-parallel
Strand 4	H	178	180	anti-parallel

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There are 4 strands in AE4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	135	139	first strand
Strand 2	H	151	160	anti-parallel
Strand 3	H	191	199	anti-parallel
Strand 4	H	184	185	anti-parallel

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There are 3 strands in AE5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	166	169	first strand
Strand 2	H	210	215	anti-parallel
Strand 3	H	220	225	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	I	334	336	first strand
Strand 2	I	395	397	anti-parallel

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There are 3 strands in AE7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	404	408	first strand
Strand 2	I	411	416	anti-parallel
Strand 3	I	438	443	anti-parallel

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There are 4 strands in AE8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	430	434	first strand
Strand 2	I	422	426	anti-parallel
Strand 3	I	449	452	anti-parallel
Strand 4	I	455	458	anti-parallel

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There are 2 strands in AE9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	335	336	first strand
Strand 2	K	395	396	anti-parallel

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There are 3 strands in AF1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	404	408	first strand
Strand 2	K	411	416	anti-parallel
Strand 3	K	438	443	anti-parallel

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There are 4 strands in AF2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	430	434	first strand
Strand 2	K	422	426	anti-parallel
Strand 3	K	449	452	anti-parallel
Strand 4	K	455	458	anti-parallel

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There are 4 strands in AF3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	4	7	first strand
Strand 2	L	19	25	anti-parallel
Strand 3	L	86	91	anti-parallel
Strand 4	L	76	83	anti-parallel

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There are 6 strands in AF4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	10	14	first strand
Strand 2	L	122	127	parallel
Strand 3	L	101	106	anti-parallel
Strand 4	L	39	44	anti-parallel
Strand 5	L	51	55	anti-parallel
Strand 6	L	66	67	anti-parallel

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There are 4 strands in AF5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	10	14	first strand
Strand 2	L	122	127	parallel
Strand 3	L	101	106	anti-parallel
Strand 4	L	117	118	anti-parallel

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There are 4 strands in AF6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	134	138	first strand
Strand 2	L	149	159	anti-parallel
Strand 3	L	193	202	anti-parallel
Strand 4	L	179	180	anti-parallel

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There are 3 strands in AF7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	165	170	first strand
Strand 2	L	211	217	anti-parallel
Strand 3	L	225	230	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: 5J3D

Analysis of interatomic Contacts of Structural Units in PDB entry:
5J3D