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

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 1YKM entry

There are 18 chains in PDB entry 1YKM (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 54 helices in PDB entry 1YKM. Click on helix of interest for CSU analysis.

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

There are 54 sheets in PDB entry 1YKM. 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, AT, AU, AV, AW, AX, AY, AZ, BA, BB,

There are 4 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	104	109	first strand
Strand 2	A	48	53	anti-parallel
Strand 3	A	180	184	parallel
Strand 4	A	175	177	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 5 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	92	96	first strand
Strand 2	A	67	71	anti-parallel
Strand 3	A	126	131	anti-parallel
Strand 4	A	139	145	anti-parallel
Strand 5	A	171	172	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	114	115	first strand
Strand 2	A	121	122	anti-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	A	198	199	first strand
Strand 2	B	337	338	parallel

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There are 2 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	307	308	first strand
Strand 2	B	530	531	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	460	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 H 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	460	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 I 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 4 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	104	109	first strand
Strand 2	C	48	53	anti-parallel
Strand 3	C	180	184	parallel
Strand 4	C	175	177	anti-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	55	56	first strand
Strand 2	C	187	188	parallel

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There are 5 strands in L 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	125	131	anti-parallel
Strand 4	C	139	145	anti-parallel
Strand 5	C	171	172	parallel

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There are 2 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	114	115	first strand
Strand 2	C	121	122	anti-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	198	199	first strand
Strand 2	D	337	338	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	307	308	first strand
Strand 2	D	530	531	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	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 Q 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 R sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	447	448	first strand
Strand 2	D	456	457	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	104	109	first strand
Strand 2	E	48	53	anti-parallel
Strand 3	E	180	184	parallel
Strand 4	E	175	177	anti-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	E	55	56	first strand
Strand 2	E	187	188	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	92	96	first strand
Strand 2	E	67	71	anti-parallel
Strand 3	E	126	131	anti-parallel
Strand 4	E	139	145	anti-parallel
Strand 5	E	171	172	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	E	114	115	first strand
Strand 2	E	121	122	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	307	308	first strand
Strand 2	F	530	531	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	447	448	first strand
Strand 2	F	456	457	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	104	109	first strand
Strand 2	G	48	53	anti-parallel
Strand 3	G	180	184	parallel
Strand 4	G	175	177	anti-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	G	55	56	first strand
Strand 2	G	187	188	parallel

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There are 5 strands in AD 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	67	71	anti-parallel
Strand 3	G	125	131	anti-parallel
Strand 4	G	139	145	anti-parallel
Strand 5	G	171	172	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	G	114	115	first strand
Strand 2	G	121	122	anti-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	G	198	199	first strand
Strand 2	H	337	338	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	H	307	308	first strand
Strand 2	H	530	531	anti-parallel

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There are 8 strands in AH 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 AI 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 AJ 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 4 strands in AK sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	104	109	first strand
Strand 2	I	48	53	anti-parallel
Strand 3	I	180	184	parallel
Strand 4	I	175	177	anti-parallel

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There are 2 strands in AL 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 5 strands in AM 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	172	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	I	114	115	first strand
Strand 2	I	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	I	198	199	first strand
Strand 2	J	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	J	307	308	first strand
Strand 2	J	530	531	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	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 AR 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 AS sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	447	448	first strand
Strand 2	J	456	457	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	104	109	first strand
Strand 2	K	48	53	anti-parallel
Strand 3	K	180	184	parallel
Strand 4	K	175	177	anti-parallel

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There are 2 strands in AU 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 5 strands in AV 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	172	parallel

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There are 2 strands in AW 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 AX 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 AY sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	307	308	first strand
Strand 2	L	530	531	anti-parallel

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There are 8 strands in AZ 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	401	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	386	parallel
Strand 8	L	436	442	anti-parallel

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There are 8 strands in BA 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	401	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	386	parallel
Strand 8	L	525	527	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	447	449	first strand
Strand 2	L	455	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: 1YKM

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