Analysis of interatomic Contacts of Structural Units in PDB entry:
4YDD

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 4YDD entry

There are 6 chains in PDB entry 4YDD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ILE 5	PHE 899
B	MET 5	THR 333
C	ALA 8	PHE 899
D	LYS 6	THR 333
E	ALA 8	PHE 899
F	LYS 6	THR 333

There are172 helices in PDB entry 4YDD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	11	22	Right-handed alpha
Helix 2	AA2	A	76	80	Right-handed 310
Helix 3	AA3	A	81	86	Right-handed alpha
Helix 4	AA4	A	109	128	Right-handed alpha
Helix 5	AA5	A	129	131	Right-handed 310
Helix 6	AA6	A	139	142	Right-handed 310
Helix 7	AA7	A	143	158	Right-handed alpha
Helix 8	AA8	A	172	180	Right-handed alpha
Helix 9	AA9	A	187	194	Right-handed 310
Helix 10	AB1	A	203	208	Right-handed alpha
Helix 11	AB2	A	209	211	Right-handed 310
Helix 12	AB3	A	212	221	Right-handed alpha
Helix 13	AB4	A	233	239	Right-handed 310
Helix 14	AB5	A	249	264	Right-handed alpha
Helix 15	AB6	A	268	276	Right-handed alpha
Helix 16	AB7	A	291	296	Right-handed alpha
Helix 17	AB8	A	338	342	Right-handed 310
Helix 18	AB9	A	375	387	Right-handed alpha
Helix 19	AC1	A	388	397	Right-handed alpha
Helix 20	AC2	A	399	413	Right-handed alpha
Helix 21	AC3	A	421	426	Right-handed alpha
Helix 22	AC4	A	429	445	Right-handed alpha
Helix 23	AC5	A	465	474	Right-handed alpha
Helix 24	AC6	A	477	481	Right-handed 310
Helix 25	AC7	A	485	494	Right-handed alpha
Helix 26	AC8	A	506	517	Right-handed alpha
Helix 27	AC9	A	524	528	Right-handed 310
Helix 28	AD1	A	539	544	Right-handed alpha
Helix 29	AD2	A	546	554	Right-handed alpha
Helix 30	AD3	A	555	558	Right-handed 310
Helix 31	AD4	A	569	574	Right-handed alpha
Helix 32	AD5	A	583	587	Right-handed 310
Helix 33	AD6	A	614	633	Right-handed alpha
Helix 34	AD7	A	641	644	Right-handed 310
Helix 35	AD8	A	651	658	Right-handed alpha
Helix 36	AD9	A	664	675	Right-handed alpha
Helix 37	AE1	A	683	690	Right-handed alpha
Helix 38	AE2	A	711	716	Right-handed alpha
Helix 39	AE3	A	734	740	Right-handed alpha
Helix 40	AE4	A	776	782	Right-handed alpha
Helix 41	AE5	A	792	797	Right-handed alpha
Helix 42	AE6	A	798	800	Right-handed 310
Helix 43	AE7	A	847	852	Right-handed 310
Helix 44	AE8	A	857	862	Right-handed 310
Helix 45	AE9	B	25	36	Right-handed alpha
Helix 46	AF1	B	60	64	Right-handed 310
Helix 47	AF2	B	80	85	Right-handed alpha
Helix 48	AF3	B	91	98	Right-handed alpha
Helix 49	AF4	B	143	149	Right-handed alpha
Helix 50	AF5	B	174	180	Right-handed alpha
Helix 51	AF6	B	200	206	Right-handed alpha
Helix 52	AF7	B	210	215	Right-handed alpha
Helix 53	AF8	B	231	238	Right-handed alpha
Helix 54	AF9	B	247	251	Right-handed 310
Helix 55	AG1	B	281	290	Right-handed alpha
Helix 56	AG2	B	292	309	Right-handed alpha
Helix 57	AG3	B	313	321	Right-handed alpha
Helix 58	AG4	B	323	327	Right-handed 310
Helix 59	AG5	C	11	22	Right-handed alpha
Helix 60	AG6	C	76	80	Right-handed 310
Helix 61	AG7	C	81	86	Right-handed alpha
Helix 62	AG8	C	109	128	Right-handed alpha
Helix 63	AG9	C	129	131	Right-handed 310
Helix 64	AH1	C	139	142	Right-handed 310
Helix 65	AH2	C	143	158	Right-handed alpha
Helix 66	AH3	C	172	180	Right-handed alpha
Helix 67	AH4	C	187	194	Right-handed 310
Helix 68	AH5	C	203	208	Right-handed alpha
Helix 69	AH6	C	209	211	Right-handed 310
Helix 70	AH7	C	212	221	Right-handed alpha
Helix 71	AH8	C	233	239	Right-handed 310
Helix 72	AH9	C	249	264	Right-handed alpha
Helix 73	AI1	C	268	276	Right-handed alpha
Helix 74	AI2	C	291	296	Right-handed alpha
Helix 75	AI3	C	338	342	Right-handed 310
Helix 76	AI4	C	375	387	Right-handed alpha
Helix 77	AI5	C	388	397	Right-handed alpha
Helix 78	AI6	C	399	413	Right-handed alpha
Helix 79	AI7	C	421	426	Right-handed alpha
Helix 80	AI8	C	429	445	Right-handed alpha
Helix 81	AI9	C	465	474	Right-handed alpha
Helix 82	AJ1	C	477	481	Right-handed 310
Helix 83	AJ2	C	485	494	Right-handed alpha
Helix 84	AJ3	C	506	517	Right-handed alpha
Helix 85	AJ4	C	524	528	Right-handed 310
Helix 86	AJ5	C	539	544	Right-handed alpha
Helix 87	AJ6	C	546	554	Right-handed alpha
Helix 88	AJ7	C	555	558	Right-handed 310
Helix 89	AJ8	C	569	574	Right-handed alpha
Helix 90	AJ9	C	583	587	Right-handed 310
Helix 91	AK1	C	614	633	Right-handed alpha
Helix 92	AK2	C	641	644	Right-handed 310
Helix 93	AK3	C	651	658	Right-handed alpha
Helix 94	AK4	C	664	675	Right-handed alpha
Helix 95	AK5	C	683	690	Right-handed alpha
Helix 96	AK6	C	711	716	Right-handed alpha
Helix 97	AK7	C	734	740	Right-handed alpha
Helix 98	AK8	C	776	782	Right-handed alpha
Helix 99	AK9	C	792	797	Right-handed alpha
Helix 100	AL1	C	847	852	Right-handed 310
Helix 101	AL2	C	857	862	Right-handed 310
Helix 102	AL3	D	25	35	Right-handed alpha
Helix 103	AL4	D	60	64	Right-handed 310
Helix 104	AL5	D	80	85	Right-handed alpha
Helix 105	AL6	D	91	98	Right-handed alpha
Helix 106	AL7	D	143	149	Right-handed alpha
Helix 107	AL8	D	174	180	Right-handed alpha
Helix 108	AL9	D	200	205	Right-handed alpha
Helix 109	AM1	D	210	215	Right-handed alpha
Helix 110	AM2	D	231	238	Right-handed alpha
Helix 111	AM3	D	247	251	Right-handed 310
Helix 112	AM4	D	281	290	Right-handed alpha
Helix 113	AM5	D	292	309	Right-handed alpha
Helix 114	AM6	D	313	321	Right-handed alpha
Helix 115	AM7	D	323	327	Right-handed 310
Helix 116	AM8	E	15	22	Right-handed alpha
Helix 117	AM9	E	76	80	Right-handed 310
Helix 118	AN1	E	81	86	Right-handed alpha
Helix 119	AN2	E	109	128	Right-handed alpha
Helix 120	AN3	E	129	131	Right-handed 310
Helix 121	AN4	E	139	142	Right-handed 310
Helix 122	AN5	E	143	158	Right-handed alpha
Helix 123	AN6	E	172	180	Right-handed alpha
Helix 124	AN7	E	187	194	Right-handed 310
Helix 125	AN8	E	203	208	Right-handed alpha
Helix 126	AN9	E	212	221	Right-handed alpha
Helix 127	AO1	E	233	239	Right-handed 310
Helix 128	AO2	E	249	264	Right-handed alpha
Helix 129	AO3	E	268	276	Right-handed alpha
Helix 130	AO4	E	291	296	Right-handed alpha
Helix 131	AO5	E	338	342	Right-handed 310
Helix 132	AO6	E	375	387	Right-handed alpha
Helix 133	AO7	E	388	397	Right-handed alpha
Helix 134	AO8	E	399	413	Right-handed alpha
Helix 135	AO9	E	421	426	Right-handed alpha
Helix 136	AP1	E	429	445	Right-handed alpha
Helix 137	AP2	E	465	474	Right-handed alpha
Helix 138	AP3	E	477	481	Right-handed 310
Helix 139	AP4	E	485	494	Right-handed alpha
Helix 140	AP5	E	506	517	Right-handed alpha
Helix 141	AP6	E	524	528	Right-handed 310
Helix 142	AP7	E	539	544	Right-handed alpha
Helix 143	AP8	E	546	554	Right-handed alpha
Helix 144	AP9	E	555	558	Right-handed 310
Helix 145	AQ1	E	569	574	Right-handed alpha
Helix 146	AQ2	E	583	587	Right-handed 310
Helix 147	AQ3	E	614	633	Right-handed alpha
Helix 148	AQ4	E	641	644	Right-handed 310
Helix 149	AQ5	E	651	658	Right-handed alpha
Helix 150	AQ6	E	664	675	Right-handed alpha
Helix 151	AQ7	E	683	690	Right-handed alpha
Helix 152	AQ8	E	711	716	Right-handed alpha
Helix 153	AQ9	E	734	740	Right-handed alpha
Helix 154	AR1	E	776	782	Right-handed alpha
Helix 155	AR2	E	792	797	Right-handed alpha
Helix 156	AR3	E	798	800	Right-handed 310
Helix 157	AR4	E	847	852	Right-handed 310
Helix 158	AR5	E	857	862	Right-handed 310
Helix 159	AR6	F	25	36	Right-handed alpha
Helix 160	AR7	F	60	64	Right-handed 310
Helix 161	AR8	F	80	85	Right-handed alpha
Helix 162	AR9	F	91	98	Right-handed alpha
Helix 163	AS1	F	143	149	Right-handed alpha
Helix 164	AS2	F	174	180	Right-handed alpha
Helix 165	AS3	F	200	205	Right-handed alpha
Helix 166	AS4	F	210	215	Right-handed alpha
Helix 167	AS5	F	231	238	Right-handed alpha
Helix 168	AS6	F	247	251	Right-handed 310
Helix 169	AS7	F	281	290	Right-handed alpha
Helix 170	AS8	F	292	309	Right-handed alpha
Helix 171	AS9	F	313	321	Right-handed alpha
Helix 172	AT1	F	323	327	Right-handed 310

There are 42 sheets in PDB entry 4YDD. 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,

There are 3 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	26	30	first strand
Strand 2	A	42	47	anti-parallel
Strand 3	A	50	56	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	A	105	107	first strand
Strand 2	A	94	96	anti-parallel
Strand 3	A	577	580	anti-parallel
Strand 4	A	560	565	parallel
Strand 5	A	532	536	parallel
Strand 6	A	133	136	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	A	241	243	first strand
Strand 2	A	224	228	parallel
Strand 3	A	196	200	parallel
Strand 4	A	416	420	parallel
Strand 5	A	453	456	parallel

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There are 3 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	281	283	first strand
Strand 2	A	369	374	anti-parallel
Strand 3	A	360	363	anti-parallel

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There are 2 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	306	308	first strand
Strand 2	A	313	315	anti-parallel

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There are 3 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	589	591	first strand
Strand 2	A	598	602	anti-parallel
Strand 3	A	692	693	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	637	640	first strand
Strand 2	A	645	648	anti-parallel

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There are 7 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	758	761	first strand
Strand 2	A	830	833	parallel
Strand 3	A	789	791	anti-parallel
Strand 4	A	815	822	parallel
Strand 5	A	806	810	anti-parallel
Strand 6	A	885	890	anti-parallel
Strand 7	A	758	761	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	B	221	225	first strand
Strand 2	B	12	17	anti-parallel
Strand 3	B	256	259	parallel
Strand 4	B	244	245	anti-parallel

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There are 2 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	48	52	first strand
Strand 2	B	131	135	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	B	68	69	first strand
Strand 2	B	72	73	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	154	156	first strand
Strand 2	B	163	165	anti-parallel

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There are 2 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	186	188	first strand
Strand 2	B	193	195	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	B	266	268	first strand
Strand 2	B	274	278	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	26	30	first strand
Strand 2	C	42	47	anti-parallel
Strand 3	C	50	56	anti-parallel

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There are 6 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	105	107	first strand
Strand 2	C	94	96	anti-parallel
Strand 3	C	577	580	anti-parallel
Strand 4	C	560	565	parallel
Strand 5	C	532	536	parallel
Strand 6	C	133	136	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	241	243	first strand
Strand 2	C	224	228	parallel
Strand 3	C	196	200	parallel
Strand 4	C	416	420	parallel
Strand 5	C	453	456	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	281	283	first strand
Strand 2	C	369	374	anti-parallel
Strand 3	C	360	363	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	C	306	307	first strand
Strand 2	C	314	315	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	C	589	591	first strand
Strand 2	C	598	602	anti-parallel
Strand 3	C	692	693	anti-parallel

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There are 2 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	637	640	first strand
Strand 2	C	645	648	anti-parallel

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There are 7 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	758	761	first strand
Strand 2	C	830	833	parallel
Strand 3	C	789	791	anti-parallel
Strand 4	C	814	822	parallel
Strand 5	C	806	811	anti-parallel
Strand 6	C	885	890	anti-parallel
Strand 7	C	758	761	anti-parallel

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There are 4 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	221	225	first strand
Strand 2	D	12	17	anti-parallel
Strand 3	D	256	259	parallel
Strand 4	D	244	245	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	D	48	52	first strand
Strand 2	D	131	135	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	D	68	69	first strand
Strand 2	D	72	73	anti-parallel

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There are 2 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	154	156	first strand
Strand 2	D	163	165	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	D	186	188	first strand
Strand 2	D	193	195	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	266	268	first strand
Strand 2	D	274	278	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	E	26	30	first strand
Strand 2	E	42	47	anti-parallel
Strand 3	E	50	56	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	E	105	107	first strand
Strand 2	E	94	96	anti-parallel
Strand 3	E	577	580	anti-parallel
Strand 4	E	560	565	parallel
Strand 5	E	532	536	parallel
Strand 6	E	133	136	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	E	241	243	first strand
Strand 2	E	224	228	parallel
Strand 3	E	196	200	parallel
Strand 4	E	416	420	parallel
Strand 5	E	453	456	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	E	281	283	first strand
Strand 2	E	370	374	anti-parallel
Strand 3	E	360	362	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	E	306	307	first strand
Strand 2	E	314	315	anti-parallel

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There are 3 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	589	591	first strand
Strand 2	E	598	602	anti-parallel
Strand 3	E	692	693	anti-parallel

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There are 2 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	637	640	first strand
Strand 2	E	645	648	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	E	758	761	first strand
Strand 2	E	830	833	parallel
Strand 3	E	789	791	anti-parallel
Strand 4	E	815	822	parallel
Strand 5	E	806	810	anti-parallel
Strand 6	E	885	890	anti-parallel
Strand 7	E	758	761	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	F	221	225	first strand
Strand 2	F	12	17	anti-parallel
Strand 3	F	256	259	parallel
Strand 4	F	244	245	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	F	48	52	first strand
Strand 2	F	131	135	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	F	68	69	first strand
Strand 2	F	72	73	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	F	154	156	first strand
Strand 2	F	163	165	anti-parallel

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There are 2 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	186	188	first strand
Strand 2	F	193	195	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	F	266	268	first strand
Strand 2	F	274	278	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: 4YDD

Analysis of interatomic Contacts of Structural Units in PDB entry:
4YDD