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

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 5NDF entry

There are 6 chains in PDB entry 5NDF (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	LYS 75	LEU 569
B	LYS 75	LEU 569
C	LYS 75	LEU 569
D	LYS 75	LEU 569
E	LYS 75	THR 566
F	LYS 75	LEU 569

There are122 helices in PDB entry 5NDF. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	77	81	Right-handed 310
Helix 2	AA2	A	82	88	Right-handed alpha
Helix 3	AA3	A	105	111	Right-handed alpha
Helix 4	AA4	A	123	129	Right-handed alpha
Helix 5	AA5	A	148	163	Right-handed alpha
Helix 6	AA6	A	164	166	Right-handed 310
Helix 7	AA7	A	181	188	Right-handed alpha
Helix 8	AA8	A	202	215	Right-handed alpha
Helix 9	AA9	A	234	244	Right-handed alpha
Helix 10	AB1	A	286	294	Right-handed alpha
Helix 11	AB2	A	315	321	Right-handed alpha
Helix 12	AB3	A	333	345	Right-handed alpha
Helix 13	AB4	A	372	389	Right-handed alpha
Helix 14	AB5	A	392	400	Right-handed alpha
Helix 15	AB6	A	401	406	Right-handed 310
Helix 16	AB7	A	411	422	Right-handed alpha
Helix 17	AB8	A	425	433	Right-handed alpha
Helix 18	AB9	A	477	481	Right-handed 310
Helix 19	AC1	A	517	520	Right-handed 310
Helix 20	AC2	A	544	548	Right-handed 310
Helix 21	AC3	A	558	562	Right-handed 310
Helix 22	AC4	B	77	81	Right-handed 310
Helix 23	AC5	B	82	88	Right-handed alpha
Helix 24	AC6	B	105	111	Right-handed alpha
Helix 25	AC7	B	123	129	Right-handed alpha
Helix 26	AC8	B	148	163	Right-handed alpha
Helix 27	AC9	B	164	166	Right-handed 310
Helix 28	AD1	B	181	188	Right-handed alpha
Helix 29	AD2	B	202	215	Right-handed alpha
Helix 30	AD3	B	234	244	Right-handed alpha
Helix 31	AD4	B	286	293	Right-handed alpha
Helix 32	AD5	B	315	321	Right-handed alpha
Helix 33	AD6	B	333	345	Right-handed alpha
Helix 34	AD7	B	372	389	Right-handed alpha
Helix 35	AD8	B	392	400	Right-handed alpha
Helix 36	AD9	B	401	406	Right-handed 310
Helix 37	AE1	B	411	422	Right-handed alpha
Helix 38	AE2	B	425	433	Right-handed alpha
Helix 39	AE3	B	477	481	Right-handed 310
Helix 40	AE4	B	517	520	Right-handed 310
Helix 41	AE5	B	558	562	Right-handed 310
Helix 42	AE6	C	77	81	Right-handed 310
Helix 43	AE7	C	82	88	Right-handed alpha
Helix 44	AE8	C	105	111	Right-handed alpha
Helix 45	AE9	C	123	128	Right-handed alpha
Helix 46	AF1	C	148	163	Right-handed alpha
Helix 47	AF2	C	164	166	Right-handed 310
Helix 48	AF3	C	181	188	Right-handed alpha
Helix 49	AF4	C	202	215	Right-handed alpha
Helix 50	AF5	C	234	244	Right-handed alpha
Helix 51	AF6	C	286	293	Right-handed alpha
Helix 52	AF7	C	315	321	Right-handed alpha
Helix 53	AF8	C	333	345	Right-handed alpha
Helix 54	AF9	C	372	389	Right-handed alpha
Helix 55	AG1	C	392	400	Right-handed alpha
Helix 56	AG2	C	401	406	Right-handed 310
Helix 57	AG3	C	411	422	Right-handed alpha
Helix 58	AG4	C	425	433	Right-handed alpha
Helix 59	AG5	C	477	481	Right-handed 310
Helix 60	AG6	C	517	520	Right-handed 310
Helix 61	AG7	C	558	562	Right-handed 310
Helix 62	AG8	D	77	81	Right-handed 310
Helix 63	AG9	D	82	88	Right-handed alpha
Helix 64	AH1	D	105	111	Right-handed alpha
Helix 65	AH2	D	123	129	Right-handed alpha
Helix 66	AH3	D	148	163	Right-handed alpha
Helix 67	AH4	D	164	166	Right-handed 310
Helix 68	AH5	D	181	188	Right-handed alpha
Helix 69	AH6	D	202	215	Right-handed alpha
Helix 70	AH7	D	234	244	Right-handed alpha
Helix 71	AH8	D	286	293	Right-handed alpha
Helix 72	AH9	D	315	321	Right-handed alpha
Helix 73	AI1	D	333	345	Right-handed alpha
Helix 74	AI2	D	372	389	Right-handed alpha
Helix 75	AI3	D	392	400	Right-handed alpha
Helix 76	AI4	D	401	406	Right-handed 310
Helix 77	AI5	D	411	422	Right-handed alpha
Helix 78	AI6	D	425	433	Right-handed alpha
Helix 79	AI7	D	477	481	Right-handed 310
Helix 80	AI8	D	517	520	Right-handed 310
Helix 81	AI9	D	544	548	Right-handed 310
Helix 82	AJ1	D	558	562	Right-handed 310
Helix 83	AJ2	E	77	81	Right-handed 310
Helix 84	AJ3	E	82	88	Right-handed alpha
Helix 85	AJ4	E	105	111	Right-handed alpha
Helix 86	AJ5	E	123	129	Right-handed alpha
Helix 87	AJ6	E	148	163	Right-handed alpha
Helix 88	AJ7	E	164	166	Right-handed 310
Helix 89	AJ8	E	181	188	Right-handed alpha
Helix 90	AJ9	E	202	215	Right-handed alpha
Helix 91	AK1	E	234	244	Right-handed alpha
Helix 92	AK2	E	286	293	Right-handed alpha
Helix 93	AK3	E	315	321	Right-handed alpha
Helix 94	AK4	E	333	345	Right-handed alpha
Helix 95	AK5	E	372	389	Right-handed alpha
Helix 96	AK6	E	392	400	Right-handed alpha
Helix 97	AK7	E	401	406	Right-handed 310
Helix 98	AK8	E	411	422	Right-handed alpha
Helix 99	AK9	E	425	433	Right-handed alpha
Helix 100	AL1	E	477	481	Right-handed 310
Helix 101	AL2	E	517	520	Right-handed 310
Helix 102	AL3	E	558	562	Right-handed 310
Helix 103	AL4	F	77	81	Right-handed 310
Helix 104	AL5	F	82	88	Right-handed alpha
Helix 105	AL6	F	105	111	Right-handed alpha
Helix 106	AL7	F	123	129	Right-handed alpha
Helix 107	AL8	F	148	163	Right-handed alpha
Helix 108	AL9	F	164	166	Right-handed 310
Helix 109	AM1	F	181	188	Right-handed alpha
Helix 110	AM2	F	202	215	Right-handed alpha
Helix 111	AM3	F	234	244	Right-handed alpha
Helix 112	AM4	F	286	293	Right-handed alpha
Helix 113	AM5	F	315	321	Right-handed alpha
Helix 114	AM6	F	333	345	Right-handed alpha
Helix 115	AM7	F	372	389	Right-handed alpha
Helix 116	AM8	F	392	400	Right-handed alpha
Helix 117	AM9	F	401	406	Right-handed 310
Helix 118	AN1	F	411	422	Right-handed alpha
Helix 119	AN2	F	425	433	Right-handed alpha
Helix 120	AN3	F	477	481	Right-handed 310
Helix 121	AN4	F	517	520	Right-handed 310
Helix 122	AN5	F	558	562	Right-handed 310

There are 48 sheets in PDB entry 5NDF. 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,

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	A	193	197	first strand
Strand 2	A	168	175	parallel
Strand 3	A	138	144	parallel
Strand 4	A	219	223	parallel
Strand 5	A	311	314	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	227	229	first strand
Strand 2	A	348	360	anti-parallel
Strand 3	A	247	256	parallel
Strand 4	A	263	264	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	A	227	229	first strand
Strand 2	A	348	360	anti-parallel
Strand 3	A	301	302	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	A	270	274	first strand
Strand 2	A	280	284	anti-parallel

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There are 7 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	469	472	first strand
Strand 2	A	455	458	anti-parallel
Strand 3	A	446	452	anti-parallel
Strand 4	A	482	484	anti-parallel
Strand 5	A	490	492	anti-parallel
Strand 6	A	495	498	anti-parallel
Strand 7	A	509	512	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	469	472	first strand
Strand 2	A	455	458	anti-parallel
Strand 3	A	446	452	anti-parallel
Strand 4	A	564	568	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	A	522	525	first strand
Strand 2	A	530	533	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	A	538	541	first strand
Strand 2	A	551	554	anti-parallel

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There are 5 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	193	197	first strand
Strand 2	B	168	175	parallel
Strand 3	B	138	144	parallel
Strand 4	B	219	223	parallel
Strand 5	B	311	314	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	227	229	first strand
Strand 2	B	348	360	anti-parallel
Strand 3	B	247	256	parallel
Strand 4	B	263	264	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	B	227	229	first strand
Strand 2	B	348	360	anti-parallel
Strand 3	B	301	302	anti-parallel

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There are 2 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	270	274	first strand
Strand 2	B	280	284	anti-parallel

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There are 7 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	469	472	first strand
Strand 2	B	455	458	anti-parallel
Strand 3	B	446	452	anti-parallel
Strand 4	B	482	484	anti-parallel
Strand 5	B	490	492	anti-parallel
Strand 6	B	495	498	anti-parallel
Strand 7	B	509	512	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	B	469	472	first strand
Strand 2	B	455	458	anti-parallel
Strand 3	B	446	452	anti-parallel
Strand 4	B	564	568	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	B	522	525	first strand
Strand 2	B	530	533	anti-parallel

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There are 2 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	538	541	first strand
Strand 2	B	551	554	anti-parallel

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There are 5 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	193	197	first strand
Strand 2	C	168	175	parallel
Strand 3	C	138	144	parallel
Strand 4	C	219	223	parallel
Strand 5	C	311	314	anti-parallel

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There are 4 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	227	229	first strand
Strand 2	C	348	360	anti-parallel
Strand 3	C	247	256	parallel
Strand 4	C	263	264	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	C	227	229	first strand
Strand 2	C	348	360	anti-parallel
Strand 3	C	301	302	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	C	270	274	first strand
Strand 2	C	280	284	anti-parallel

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There are 7 strands in AC3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	469	472	first strand
Strand 2	C	455	458	anti-parallel
Strand 3	C	446	452	anti-parallel
Strand 4	C	482	484	anti-parallel
Strand 5	C	490	492	anti-parallel
Strand 6	C	495	498	anti-parallel
Strand 7	C	509	512	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	C	469	472	first strand
Strand 2	C	455	458	anti-parallel
Strand 3	C	446	452	anti-parallel
Strand 4	C	564	568	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	C	522	525	first strand
Strand 2	C	530	533	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	C	538	541	first strand
Strand 2	C	551	554	anti-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	D	193	197	first strand
Strand 2	D	168	175	parallel
Strand 3	D	138	144	parallel
Strand 4	D	219	223	parallel
Strand 5	D	311	314	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	D	227	229	first strand
Strand 2	D	348	360	anti-parallel
Strand 3	D	247	256	parallel
Strand 4	D	263	264	anti-parallel

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There are 3 strands in AC9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	227	229	first strand
Strand 2	D	348	360	anti-parallel
Strand 3	D	301	302	anti-parallel

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There are 2 strands in AD1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	270	274	first strand
Strand 2	D	280	284	anti-parallel

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There are 7 strands in AD2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	469	472	first strand
Strand 2	D	455	458	anti-parallel
Strand 3	D	446	452	anti-parallel
Strand 4	D	482	484	anti-parallel
Strand 5	D	490	492	anti-parallel
Strand 6	D	495	498	anti-parallel
Strand 7	D	509	512	anti-parallel

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There are 4 strands in AD3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	469	472	first strand
Strand 2	D	455	458	anti-parallel
Strand 3	D	446	452	anti-parallel
Strand 4	D	564	568	anti-parallel

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There are 2 strands in AD4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	522	525	first strand
Strand 2	D	530	533	anti-parallel

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There are 2 strands in AD5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	538	541	first strand
Strand 2	D	551	554	anti-parallel

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There are 5 strands in AD6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	193	197	first strand
Strand 2	E	168	175	parallel
Strand 3	E	138	144	parallel
Strand 4	E	219	223	parallel
Strand 5	E	311	314	anti-parallel

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There are 4 strands in AD7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	227	229	first strand
Strand 2	E	348	360	anti-parallel
Strand 3	E	247	256	parallel
Strand 4	E	263	264	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	E	227	229	first strand
Strand 2	E	348	360	anti-parallel
Strand 3	E	301	302	anti-parallel

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There are 2 strands in AD9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	270	274	first strand
Strand 2	E	280	284	anti-parallel

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There are 5 strands in AE1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	446	448	first strand
Strand 2	E	482	484	anti-parallel
Strand 3	E	490	492	anti-parallel
Strand 4	E	495	498	anti-parallel
Strand 5	E	509	512	anti-parallel

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There are 4 strands in AE2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	469	472	first strand
Strand 2	E	455	458	anti-parallel
Strand 3	E	450	452	anti-parallel
Strand 4	E	564	565	anti-parallel

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There are 2 strands in AE3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	522	525	first strand
Strand 2	E	530	533	anti-parallel

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There are 2 strands in AE4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	538	541	first strand
Strand 2	E	551	554	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	F	193	197	first strand
Strand 2	F	168	175	parallel
Strand 3	F	138	144	parallel
Strand 4	F	219	223	parallel
Strand 5	F	311	314	anti-parallel

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There are 4 strands in AE6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	227	229	first strand
Strand 2	F	348	360	anti-parallel
Strand 3	F	247	256	parallel
Strand 4	F	263	264	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	F	227	229	first strand
Strand 2	F	348	360	anti-parallel
Strand 3	F	301	302	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	F	270	274	first strand
Strand 2	F	280	284	anti-parallel

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There are 7 strands in AE9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	469	472	first strand
Strand 2	F	455	458	anti-parallel
Strand 3	F	446	452	anti-parallel
Strand 4	F	482	484	anti-parallel
Strand 5	F	490	492	anti-parallel
Strand 6	F	495	498	anti-parallel
Strand 7	F	509	512	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	F	469	472	first strand
Strand 2	F	455	458	anti-parallel
Strand 3	F	446	452	anti-parallel
Strand 4	F	564	568	anti-parallel

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There are 2 strands in AF2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	522	525	first strand
Strand 2	F	530	533	anti-parallel

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There are 2 strands in AF3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	538	541	first strand
Strand 2	F	551	554	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: 5NDF

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