Analysis of interatomic Contacts of Structural Units in PDB entry:
1YKP

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 1YKP entry

There are 18 chains in PDB entry 1YKP (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	PRO 1	PHE 200
B	PRO 301	ARG 428
B	LEU 430	CYS 538
C	PRO 1	PHE 200
D	PRO 301	ARG 428
D	LEU 430	CYS 538
E	PRO 1	PHE 200
F	PRO 301	ARG 428
F	LEU 430	CYS 538
G	PRO 1	PHE 200
H	PRO 301	ARG 428
H	LEU 430	CYS 538
I	PRO 1	PHE 200
J	PRO 301	ARG 428
J	LEU 430	CYS 538
K	PRO 1	PHE 200
L	PRO 301	ARG 428
L	LEU 430	CYS 538

There are 59 helices in PDB entry 1YKP. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	16	22	Right-handed alpha
Helix 2	2	A	148	153	Right-handed alpha
Helix 3	3	A	157	161	Right-handed 310
Helix 4	4	A	163	168	Right-handed alpha
Helix 5	5	B	324	328	Right-handed 310
Helix 6	6	B	342	347	Right-handed alpha
Helix 7	7	B	485	489	Right-handed 310
Helix 8	8	B	497	503	Right-handed alpha
Helix 9	9	B	510	513	Right-handed 310
Helix 10	10	C	14	16	Right-handed 310
Helix 11	11	C	17	22	Right-handed alpha
Helix 12	12	C	148	154	Right-handed alpha
Helix 13	13	C	157	161	Right-handed 310
Helix 14	14	C	163	168	Right-handed alpha
Helix 15	15	D	324	328	Right-handed 310
Helix 16	16	D	342	347	Right-handed alpha
Helix 17	17	D	485	489	Right-handed 310
Helix 18	18	D	491	495	Right-handed 310
Helix 19	19	D	497	502	Right-handed alpha
Helix 20	20	D	510	513	Right-handed 310
Helix 21	21	E	16	22	Right-handed alpha
Helix 22	22	E	23	27	Right-handed 310
Helix 23	23	E	148	154	Right-handed alpha
Helix 24	24	E	157	161	Right-handed 310
Helix 25	25	E	163	168	Right-handed alpha
Helix 26	26	F	324	328	Right-handed 310
Helix 27	27	F	342	347	Right-handed alpha
Helix 28	28	F	485	489	Right-handed 310
Helix 29	29	F	491	495	Right-handed 310
Helix 30	30	F	497	503	Right-handed alpha
Helix 31	31	G	17	22	Right-handed alpha
Helix 32	32	G	23	27	Right-handed 310
Helix 33	33	G	148	153	Right-handed alpha
Helix 34	34	G	157	161	Right-handed 310
Helix 35	35	G	163	168	Right-handed alpha
Helix 36	36	H	324	328	Right-handed 310
Helix 37	37	H	342	347	Right-handed alpha
Helix 38	38	H	485	489	Right-handed 310
Helix 39	39	H	497	504	Right-handed alpha
Helix 40	40	H	510	513	Right-handed 310
Helix 41	41	I	14	16	Right-handed 310
Helix 42	42	I	17	22	Right-handed alpha
Helix 43	43	I	148	155	Right-handed alpha
Helix 44	44	I	157	161	Right-handed 310
Helix 45	45	I	163	169	Right-handed alpha
Helix 46	46	J	324	328	Right-handed 310
Helix 47	47	J	342	347	Right-handed alpha
Helix 48	48	J	485	489	Right-handed 310
Helix 49	49	J	491	495	Right-handed 310
Helix 50	50	J	497	502	Right-handed alpha
Helix 51	51	K	16	22	Right-handed alpha
Helix 52	52	K	148	155	Right-handed alpha
Helix 53	53	K	157	161	Right-handed 310
Helix 54	54	K	163	169	Right-handed alpha
Helix 55	55	L	324	329	Right-handed 310
Helix 56	56	L	342	347	Right-handed alpha
Helix 57	57	L	485	489	Right-handed 310
Helix 58	58	L	491	495	Right-handed 310
Helix 59	59	L	497	503	Right-handed alpha

There are 45 sheets in PDB entry 1YKP. 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, AK, AL, AM, AN, AO, AP, AQ, AR, AS,

There are 8 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	92	96	first strand
Strand 2	A	66	71	anti-parallel
Strand 3	A	125	132	anti-parallel
Strand 4	A	139	145	anti-parallel
Strand 5	A	171	176	parallel
Strand 6	A	181	184	anti-parallel
Strand 7	A	48	53	parallel
Strand 8	A	104	109	anti-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	55	56	first strand
Strand 2	A	187	188	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	114	115	first strand
Strand 2	A	121	122	anti-parallel

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There are 2 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	198	199	first strand
Strand 2	B	337	338	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	306	308	first strand
Strand 2	B	530	532	anti-parallel

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There are 8 strands in F sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	426	430	first strand
Strand 2	B	396	400	anti-parallel
Strand 3	B	461	465	anti-parallel
Strand 4	B	474	480	anti-parallel
Strand 5	B	505	508	parallel
Strand 6	B	519	522	anti-parallel
Strand 7	B	377	386	parallel
Strand 8	B	436	442	anti-parallel

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There are 8 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	426	430	first strand
Strand 2	B	396	400	anti-parallel
Strand 3	B	461	465	anti-parallel
Strand 4	B	474	480	anti-parallel
Strand 5	B	505	508	parallel
Strand 6	B	519	522	anti-parallel
Strand 7	B	377	386	parallel
Strand 8	B	525	527	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	447	449	first strand
Strand 2	B	455	457	anti-parallel

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There are 8 strands in I sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	92	96	first strand
Strand 2	C	67	71	anti-parallel
Strand 3	C	126	131	anti-parallel
Strand 4	C	139	145	anti-parallel
Strand 5	C	171	177	parallel
Strand 6	C	180	184	anti-parallel
Strand 7	C	48	53	parallel
Strand 8	C	104	109	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	55	56	first strand
Strand 2	C	187	188	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	198	199	first strand
Strand 2	D	337	338	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	306	308	first strand
Strand 2	D	530	532	anti-parallel

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There are 8 strands in M sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	426	430	first strand
Strand 2	D	396	400	anti-parallel
Strand 3	D	460	465	anti-parallel
Strand 4	D	474	480	anti-parallel
Strand 5	D	505	508	parallel
Strand 6	D	519	522	anti-parallel
Strand 7	D	377	386	parallel
Strand 8	D	436	442	anti-parallel

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There are 8 strands in N sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	426	430	first strand
Strand 2	D	396	400	anti-parallel
Strand 3	D	460	465	anti-parallel
Strand 4	D	474	480	anti-parallel
Strand 5	D	505	508	parallel
Strand 6	D	519	522	anti-parallel
Strand 7	D	377	386	parallel
Strand 8	D	525	527	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	D	447	449	first strand
Strand 2	D	455	457	anti-parallel

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There are 8 strands in P sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	92	97	first strand
Strand 2	E	66	71	anti-parallel
Strand 3	E	125	132	anti-parallel
Strand 4	E	139	145	anti-parallel
Strand 5	E	171	177	parallel
Strand 6	E	180	184	anti-parallel
Strand 7	E	48	53	parallel
Strand 8	E	104	109	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	55	56	first strand
Strand 2	E	187	188	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	198	199	first strand
Strand 2	F	337	338	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	306	308	first strand
Strand 2	F	530	532	anti-parallel

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There are 8 strands in T sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	426	430	first strand
Strand 2	F	396	400	anti-parallel
Strand 3	F	460	465	anti-parallel
Strand 4	F	474	480	anti-parallel
Strand 5	F	505	508	parallel
Strand 6	F	519	522	anti-parallel
Strand 7	F	377	386	parallel
Strand 8	F	436	442	anti-parallel

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There are 8 strands in U sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	426	430	first strand
Strand 2	F	396	400	anti-parallel
Strand 3	F	460	465	anti-parallel
Strand 4	F	474	480	anti-parallel
Strand 5	F	505	508	parallel
Strand 6	F	519	522	anti-parallel
Strand 7	F	377	386	parallel
Strand 8	F	525	527	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	447	449	first strand
Strand 2	F	455	457	anti-parallel

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There are 8 strands in W sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	92	96	first strand
Strand 2	G	66	71	anti-parallel
Strand 3	G	125	132	anti-parallel
Strand 4	G	139	145	anti-parallel
Strand 5	G	171	176	parallel
Strand 6	G	181	184	anti-parallel
Strand 7	G	48	53	parallel
Strand 8	G	104	109	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	55	56	first strand
Strand 2	G	187	188	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	198	199	first strand
Strand 2	H	337	338	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	H	306	308	first strand
Strand 2	H	530	532	anti-parallel

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There are 8 strands in AA sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	426	430	first strand
Strand 2	H	396	400	anti-parallel
Strand 3	H	460	465	anti-parallel
Strand 4	H	474	480	anti-parallel
Strand 5	H	505	508	parallel
Strand 6	H	519	522	anti-parallel
Strand 7	H	377	386	parallel
Strand 8	H	436	442	anti-parallel

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There are 8 strands in AB sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	426	430	first strand
Strand 2	H	396	400	anti-parallel
Strand 3	H	460	465	anti-parallel
Strand 4	H	474	480	anti-parallel
Strand 5	H	505	508	parallel
Strand 6	H	519	522	anti-parallel
Strand 7	H	377	386	parallel
Strand 8	H	525	527	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	447	449	first strand
Strand 2	H	455	457	anti-parallel

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There are 8 strands in AD sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	92	96	first strand
Strand 2	I	67	71	anti-parallel
Strand 3	I	125	131	anti-parallel
Strand 4	I	139	145	anti-parallel
Strand 5	I	171	177	parallel
Strand 6	I	180	184	anti-parallel
Strand 7	I	48	53	parallel
Strand 8	I	104	109	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	55	56	first strand
Strand 2	I	187	188	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	I	114	115	first strand
Strand 2	I	121	122	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	I	198	199	first strand
Strand 2	J	337	338	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	306	308	first strand
Strand 2	J	530	532	anti-parallel

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There are 8 strands in AI sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	426	430	first strand
Strand 2	J	396	400	anti-parallel
Strand 3	J	460	465	anti-parallel
Strand 4	J	474	480	anti-parallel
Strand 5	J	505	508	parallel
Strand 6	J	519	522	anti-parallel
Strand 7	J	377	386	parallel
Strand 8	J	436	442	anti-parallel

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There are 8 strands in AJ sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	426	430	first strand
Strand 2	J	396	400	anti-parallel
Strand 3	J	460	465	anti-parallel
Strand 4	J	474	480	anti-parallel
Strand 5	J	505	508	parallel
Strand 6	J	519	522	anti-parallel
Strand 7	J	377	386	parallel
Strand 8	J	525	527	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	447	449	first strand
Strand 2	J	455	457	anti-parallel

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There are 8 strands in AL sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	92	96	first strand
Strand 2	K	67	71	anti-parallel
Strand 3	K	125	131	anti-parallel
Strand 4	K	139	145	anti-parallel
Strand 5	K	171	177	parallel
Strand 6	K	180	184	anti-parallel
Strand 7	K	48	53	parallel
Strand 8	K	104	109	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	55	56	first strand
Strand 2	K	187	188	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	114	115	first strand
Strand 2	K	121	122	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	198	199	first strand
Strand 2	L	337	338	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	306	308	first strand
Strand 2	L	530	532	anti-parallel

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There are 8 strands in AQ sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	426	430	first strand
Strand 2	L	396	400	anti-parallel
Strand 3	L	460	465	anti-parallel
Strand 4	L	474	480	anti-parallel
Strand 5	L	505	508	parallel
Strand 6	L	519	522	anti-parallel
Strand 7	L	377	385	parallel
Strand 8	L	436	442	anti-parallel

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There are 8 strands in AR sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	426	430	first strand
Strand 2	L	396	400	anti-parallel
Strand 3	L	460	465	anti-parallel
Strand 4	L	474	480	anti-parallel
Strand 5	L	505	508	parallel
Strand 6	L	519	522	anti-parallel
Strand 7	L	377	385	parallel
Strand 8	L	525	526	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	447	448	first strand
Strand 2	L	456	457	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: 1YKP

Analysis of interatomic Contacts of Structural Units in PDB entry:
1YKP