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

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 4RYD entry

There are 18 chains in PDB entry 4RYD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	VAL 109	ALA 574
B	TYR 110	ALA 574
C	VAL 109	ALA 574
D	TYR 110	ALA 574
E	TYR 110	ALA 574
F	TYR 110	ALA 574
H	ARG 2	ARG 2
H	ARG 4	ARG 4
I	ARG 2	ARG 2
I	ARG 4	ARG 4
J	ARG 2	ARG 2
J	ARG 4	ARG 4
K	ARG 2	ARG 2
K	ARG 4	ARG 4
L	ARG 2	ARG 2
L	ARG 4	ARG 4
N	ARG 2	ARG 2
N	ARG 4	ARG 4

There are 86 helices in PDB entry 4RYD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	117	121	Right-handed 310
Helix 2	2	A	133	140	Right-handed alpha
Helix 3	3	A	168	172	Right-handed 310
Helix 4	4	A	190	192	Right-handed 310
Helix 5	5	A	193	204	Right-handed alpha
Helix 6	6	A	232	241	Right-handed alpha
Helix 7	7	A	267	281	Right-handed alpha
Helix 8	8	A	282	285	Right-handed 310
Helix 9	9	A	296	300	Right-handed 310
Helix 10	10	A	302	306	Right-handed 310
Helix 11	11	A	366	385	Right-handed alpha
Helix 12	12	A	389	401	Right-handed alpha
Helix 13	13	A	430	441	Right-handed alpha
Helix 14	14	A	497	499	Right-handed 310
Helix 15	15	B	117	121	Right-handed 310
Helix 16	16	B	133	140	Right-handed alpha
Helix 17	17	B	163	167	Right-handed 310
Helix 18	18	B	168	172	Right-handed 310
Helix 19	19	B	190	192	Right-handed 310
Helix 20	20	B	193	204	Right-handed alpha
Helix 21	21	B	232	241	Right-handed alpha
Helix 22	22	B	267	281	Right-handed alpha
Helix 23	23	B	282	285	Right-handed 310
Helix 24	24	B	295	300	Right-handed 310
Helix 25	25	B	302	306	Right-handed 310
Helix 26	26	B	366	385	Right-handed alpha
Helix 27	27	B	389	401	Right-handed alpha
Helix 28	28	B	430	441	Right-handed alpha
Helix 29	29	B	497	499	Right-handed 310
Helix 30	30	C	117	121	Right-handed 310
Helix 31	31	C	133	140	Right-handed alpha
Helix 32	32	C	168	172	Right-handed 310
Helix 33	33	C	190	192	Right-handed 310
Helix 34	34	C	193	204	Right-handed alpha
Helix 35	35	C	232	241	Right-handed alpha
Helix 36	36	C	267	281	Right-handed alpha
Helix 37	37	C	282	285	Right-handed 310
Helix 38	38	C	295	300	Right-handed 310
Helix 39	39	C	302	306	Right-handed 310
Helix 40	40	C	366	385	Right-handed alpha
Helix 41	41	C	389	401	Right-handed alpha
Helix 42	42	C	430	441	Right-handed alpha
Helix 43	43	C	497	499	Right-handed 310
Helix 44	44	D	117	121	Right-handed 310
Helix 45	45	D	133	140	Right-handed alpha
Helix 46	46	D	168	172	Right-handed 310
Helix 47	47	D	190	192	Right-handed 310
Helix 48	48	D	193	204	Right-handed alpha
Helix 49	49	D	232	241	Right-handed alpha
Helix 50	50	D	267	281	Right-handed alpha
Helix 51	51	D	282	285	Right-handed 310
Helix 52	52	D	296	300	Right-handed 310
Helix 53	53	D	302	306	Right-handed 310
Helix 54	54	D	366	385	Right-handed alpha
Helix 55	55	D	389	401	Right-handed alpha
Helix 56	56	D	430	441	Right-handed alpha
Helix 57	57	D	497	499	Right-handed 310
Helix 58	58	E	117	121	Right-handed 310
Helix 59	59	E	133	140	Right-handed alpha
Helix 60	60	E	168	172	Right-handed 310
Helix 61	61	E	190	192	Right-handed 310
Helix 62	62	E	193	204	Right-handed alpha
Helix 63	63	E	232	241	Right-handed alpha
Helix 64	64	E	267	281	Right-handed alpha
Helix 65	65	E	282	285	Right-handed 310
Helix 66	66	E	296	300	Right-handed 310
Helix 67	67	E	302	306	Right-handed 310
Helix 68	68	E	366	385	Right-handed alpha
Helix 69	69	E	389	401	Right-handed alpha
Helix 70	70	E	430	441	Right-handed alpha
Helix 71	71	E	497	499	Right-handed 310
Helix 72	72	F	117	121	Right-handed 310
Helix 73	73	F	133	140	Right-handed alpha
Helix 74	74	F	163	167	Right-handed 310
Helix 75	75	F	168	172	Right-handed 310
Helix 76	76	F	190	192	Right-handed 310
Helix 77	77	F	193	204	Right-handed alpha
Helix 78	78	F	232	241	Right-handed alpha
Helix 79	79	F	267	281	Right-handed alpha
Helix 80	80	F	282	285	Right-handed 310
Helix 81	81	F	296	300	Right-handed 310
Helix 82	82	F	302	306	Right-handed 310
Helix 83	83	F	366	385	Right-handed alpha
Helix 84	84	F	389	401	Right-handed alpha
Helix 85	85	F	430	441	Right-handed alpha
Helix 86	86	F	497	499	Right-handed 310

There are 36 sheets in PDB entry 4RYD. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, AA, AB, AC, AD, AE, AF, AG, AH, AI, AJ,

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	173	174	first strand
Strand 2	A	220	225	parallel
Strand 3	A	148	153	parallel
Strand 4	A	249	252	parallel
Strand 5	A	288	292	parallel
Strand 6	A	314	320	parallel
Strand 7	A	338	341	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	351	355	first strand
Strand 2	A	359	364	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	412	413	first strand
Strand 2	A	419	420	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	448	453	first strand
Strand 2	A	561	573	anti-parallel
Strand 3	A	459	460	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	448	453	first strand
Strand 2	A	561	573	anti-parallel
Strand 3	A	483	495	anti-parallel
Strand 4	A	528	535	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	464	471	first strand
Strand 2	A	545	553	anti-parallel
Strand 3	A	501	506	anti-parallel
Strand 4	A	512	516	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	173	174	first strand
Strand 2	B	220	225	parallel
Strand 3	B	148	153	parallel
Strand 4	B	249	252	parallel
Strand 5	B	288	292	parallel
Strand 6	B	314	320	parallel
Strand 7	B	338	341	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	351	355	first strand
Strand 2	B	359	364	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	412	413	first strand
Strand 2	B	419	420	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	448	453	first strand
Strand 2	B	561	573	anti-parallel
Strand 3	B	459	460	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	448	453	first strand
Strand 2	B	561	573	anti-parallel
Strand 3	B	483	495	anti-parallel
Strand 4	B	528	535	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	464	471	first strand
Strand 2	B	545	553	anti-parallel
Strand 3	B	501	506	anti-parallel
Strand 4	B	512	516	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	173	174	first strand
Strand 2	C	220	225	parallel
Strand 3	C	148	153	parallel
Strand 4	C	249	252	parallel
Strand 5	C	288	292	parallel
Strand 6	C	314	320	parallel
Strand 7	C	338	341	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	351	355	first strand
Strand 2	C	359	364	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	412	413	first strand
Strand 2	C	419	420	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	448	453	first strand
Strand 2	C	561	573	anti-parallel
Strand 3	C	459	460	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	448	453	first strand
Strand 2	C	561	573	anti-parallel
Strand 3	C	483	495	anti-parallel
Strand 4	C	528	535	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	464	471	first strand
Strand 2	C	545	553	anti-parallel
Strand 3	C	501	506	anti-parallel
Strand 4	C	512	516	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	173	174	first strand
Strand 2	D	220	225	parallel
Strand 3	D	148	153	parallel
Strand 4	D	249	252	parallel
Strand 5	D	288	292	parallel
Strand 6	D	314	320	parallel
Strand 7	D	338	341	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	351	355	first strand
Strand 2	D	359	364	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	412	413	first strand
Strand 2	D	419	420	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	448	453	first strand
Strand 2	D	561	573	anti-parallel
Strand 3	D	459	460	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	448	453	first strand
Strand 2	D	561	573	anti-parallel
Strand 3	D	483	495	anti-parallel
Strand 4	D	528	535	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	464	471	first strand
Strand 2	D	545	553	anti-parallel
Strand 3	D	501	506	anti-parallel
Strand 4	D	512	516	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	173	174	first strand
Strand 2	E	220	225	parallel
Strand 3	E	148	153	parallel
Strand 4	E	249	252	parallel
Strand 5	E	288	292	parallel
Strand 6	E	314	320	parallel
Strand 7	E	338	341	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	351	355	first strand
Strand 2	E	359	364	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	412	413	first strand
Strand 2	E	419	420	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	448	453	first strand
Strand 2	E	561	573	anti-parallel
Strand 3	E	459	460	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	448	453	first strand
Strand 2	E	561	573	anti-parallel
Strand 3	E	483	495	anti-parallel
Strand 4	E	528	535	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	464	471	first strand
Strand 2	E	545	553	anti-parallel
Strand 3	E	501	506	anti-parallel
Strand 4	E	512	516	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	173	174	first strand
Strand 2	F	220	225	parallel
Strand 3	F	148	153	parallel
Strand 4	F	249	252	parallel
Strand 5	F	288	292	parallel
Strand 6	F	314	320	parallel
Strand 7	F	338	341	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	351	355	first strand
Strand 2	F	359	364	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	412	413	first strand
Strand 2	F	419	420	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	448	453	first strand
Strand 2	F	561	573	anti-parallel
Strand 3	F	459	460	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	448	453	first strand
Strand 2	F	561	573	anti-parallel
Strand 3	F	483	495	anti-parallel
Strand 4	F	528	535	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	464	471	first strand
Strand 2	F	545	553	anti-parallel
Strand 3	F	501	506	anti-parallel
Strand 4	F	512	516	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: 4RYD

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