Analysis of interatomic Contacts of Structural Units in PDB entry:
1PD5

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 1PD5 entry

There are 12 chains in PDB entry 1PD5 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	THR 6	GLY 218
B	LYS 3	GLY 218
C	THR 6	GLY 218
D	THR 6	GLY 218
E	LYS 3	GLY 217
F	THR 6	GLY 217
G	THR 6	GLY 218
H	LYS 4	ALA 219
I	LYS 4	GLY 217
J	THR 6	GLN 216
K	LYS 4	TRP 215
L	THR 6	TRP 215

There are 83 helices in PDB entry 1PD5. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	12	16	Right-handed 310
Helix 2	2	A	18	28	Right-handed alpha
Helix 3	3	A	41	52	Right-handed alpha
Helix 4	4	A	54	68	Right-handed alpha
Helix 5	5	A	70	73	Right-handed 310
Helix 6	6	A	112	128	Right-handed alpha
Helix 7	7	A	197	215	Right-handed alpha
Helix 8	8	B	12	16	Right-handed 310
Helix 9	9	B	18	26	Right-handed alpha
Helix 10	10	B	41	51	Right-handed alpha
Helix 11	11	B	54	68	Right-handed alpha
Helix 12	12	B	69	73	Right-handed 310
Helix 13	13	B	112	128	Right-handed alpha
Helix 14	14	B	197	214	Right-handed alpha
Helix 15	15	C	12	16	Right-handed 310
Helix 16	16	C	18	28	Right-handed alpha
Helix 17	17	C	41	51	Right-handed alpha
Helix 18	18	C	54	68	Right-handed alpha
Helix 19	19	C	69	73	Right-handed 310
Helix 20	20	C	112	128	Right-handed alpha
Helix 21	21	C	197	215	Right-handed alpha
Helix 22	22	D	12	16	Right-handed 310
Helix 23	23	D	18	26	Right-handed alpha
Helix 24	24	D	41	51	Right-handed alpha
Helix 25	25	D	54	68	Right-handed alpha
Helix 26	26	D	69	73	Right-handed 310
Helix 27	27	D	112	128	Right-handed alpha
Helix 28	28	D	197	215	Right-handed alpha
Helix 29	29	E	18	27	Right-handed alpha
Helix 30	30	E	41	51	Right-handed alpha
Helix 31	31	E	54	68	Right-handed alpha
Helix 32	32	E	69	73	Right-handed 310
Helix 33	33	E	112	128	Right-handed alpha
Helix 34	34	E	197	215	Right-handed alpha
Helix 35	35	F	12	16	Right-handed 310
Helix 36	36	F	18	26	Right-handed alpha
Helix 37	37	F	41	51	Right-handed alpha
Helix 38	38	F	54	68	Right-handed alpha
Helix 39	39	F	69	73	Right-handed 310
Helix 40	40	F	112	128	Right-handed alpha
Helix 41	41	F	197	215	Right-handed alpha
Helix 42	42	G	12	16	Right-handed 310
Helix 43	43	G	18	27	Right-handed alpha
Helix 44	44	G	41	51	Right-handed alpha
Helix 45	45	G	54	68	Right-handed alpha
Helix 46	46	G	69	73	Right-handed 310
Helix 47	47	G	112	128	Right-handed alpha
Helix 48	48	G	197	215	Right-handed alpha
Helix 49	49	H	12	16	Right-handed 310
Helix 50	50	H	18	26	Right-handed alpha
Helix 51	51	H	41	51	Right-handed alpha
Helix 52	52	H	54	68	Right-handed alpha
Helix 53	53	H	69	69	Right-handed 310
Helix 54	54	H	70	73	Right-handed 310
Helix 55	55	H	112	128	Right-handed alpha
Helix 56	56	H	197	215	Right-handed alpha
Helix 57	57	I	12	16	Right-handed 310
Helix 58	58	I	18	27	Right-handed alpha
Helix 59	59	I	41	51	Right-handed alpha
Helix 60	60	I	54	68	Right-handed alpha
Helix 61	61	I	70	73	Right-handed 310
Helix 62	62	I	112	128	Right-handed alpha
Helix 63	63	I	197	215	Right-handed alpha
Helix 64	64	J	12	16	Right-handed 310
Helix 65	65	J	18	27	Right-handed alpha
Helix 66	66	J	41	51	Right-handed alpha
Helix 67	67	J	54	68	Right-handed alpha
Helix 68	68	J	69	73	Right-handed 310
Helix 69	69	J	112	128	Right-handed alpha
Helix 70	70	J	197	215	Right-handed alpha
Helix 71	71	K	18	27	Right-handed alpha
Helix 72	72	K	41	51	Right-handed alpha
Helix 73	73	K	54	70	Right-handed alpha
Helix 74	74	K	71	73	Right-handed 310
Helix 75	75	K	112	128	Right-handed alpha
Helix 76	76	K	197	215	Right-handed alpha
Helix 77	77	L	12	16	Right-handed 310
Helix 78	78	L	18	27	Right-handed alpha
Helix 79	79	L	41	51	Right-handed alpha
Helix 80	80	L	54	68	Right-handed alpha
Helix 81	81	L	69	73	Right-handed 310
Helix 82	82	L	112	128	Right-handed alpha
Helix 83	83	L	197	215	Right-handed alpha

There are 36 sheets in PDB entry 1PD5. 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 3 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	8	10	first strand
Strand 2	A	81	85	anti-parallel
Strand 3	A	75	78	anti-parallel

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There are 6 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	101	106	first strand
Strand 2	A	89	96	anti-parallel
Strand 3	A	142	147	parallel
Strand 4	A	170	173	parallel
Strand 5	A	182	192	anti-parallel
Strand 6	A	177	179	anti-parallel

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There are 7 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	101	106	first strand
Strand 2	A	89	96	anti-parallel
Strand 3	A	142	147	parallel
Strand 4	A	170	173	parallel
Strand 5	A	182	192	anti-parallel
Strand 6	A	31	40	anti-parallel
Strand 7	C	155	160	anti-parallel

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There are 7 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	155	160	first strand
Strand 2	B	31	40	anti-parallel
Strand 3	B	182	192	anti-parallel
Strand 4	B	170	173	anti-parallel
Strand 5	B	142	147	parallel
Strand 6	B	89	96	parallel
Strand 7	B	101	106	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	155	160	first strand
Strand 2	B	31	40	anti-parallel
Strand 3	B	182	192	anti-parallel
Strand 4	B	177	179	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	B	4	5	first strand
Strand 2	I	8	10	anti-parallel
Strand 3	I	81	85	anti-parallel
Strand 4	I	75	78	anti-parallel

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There are 3 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	8	10	first strand
Strand 2	B	81	85	anti-parallel
Strand 3	B	75	78	anti-parallel

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There are 7 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	155	160	first strand
Strand 2	C	31	40	anti-parallel
Strand 3	C	182	192	anti-parallel
Strand 4	C	170	173	anti-parallel
Strand 5	C	142	147	parallel
Strand 6	C	89	96	parallel
Strand 7	C	101	106	anti-parallel

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There are 4 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	155	160	first strand
Strand 2	C	31	40	anti-parallel
Strand 3	C	182	192	anti-parallel
Strand 4	C	177	179	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	C	8	10	first strand
Strand 2	C	81	85	anti-parallel
Strand 3	C	75	78	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	8	10	first strand
Strand 2	D	81	85	anti-parallel
Strand 3	D	75	78	anti-parallel

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There are 6 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	101	106	first strand
Strand 2	D	89	96	anti-parallel
Strand 3	D	142	147	parallel
Strand 4	D	170	173	parallel
Strand 5	D	182	192	anti-parallel
Strand 6	D	177	179	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	D	101	106	first strand
Strand 2	D	89	96	anti-parallel
Strand 3	D	142	147	parallel
Strand 4	D	170	173	parallel
Strand 5	D	182	192	anti-parallel
Strand 6	D	31	40	anti-parallel
Strand 7	F	155	160	anti-parallel

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There are 7 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	155	160	first strand
Strand 2	E	31	40	anti-parallel
Strand 3	E	182	192	anti-parallel
Strand 4	E	170	173	anti-parallel
Strand 5	E	142	147	parallel
Strand 6	E	89	96	parallel
Strand 7	E	101	106	anti-parallel

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There are 4 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	155	160	first strand
Strand 2	E	31	40	anti-parallel
Strand 3	E	182	192	anti-parallel
Strand 4	E	177	179	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	E	8	10	first strand
Strand 2	E	81	85	anti-parallel
Strand 3	E	75	78	anti-parallel

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There are 7 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	155	160	first strand
Strand 2	F	31	40	anti-parallel
Strand 3	F	182	192	anti-parallel
Strand 4	F	170	173	anti-parallel
Strand 5	F	142	147	parallel
Strand 6	F	89	96	parallel
Strand 7	F	101	106	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	E	155	160	first strand
Strand 2	F	31	40	anti-parallel
Strand 3	F	182	192	anti-parallel
Strand 4	F	177	179	anti-parallel

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There are 3 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	8	10	first strand
Strand 2	F	81	85	anti-parallel
Strand 3	F	75	78	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	8	10	first strand
Strand 2	G	81	85	anti-parallel
Strand 3	G	75	78	anti-parallel

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There are 6 strands in U sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	101	106	first strand
Strand 2	G	89	96	anti-parallel
Strand 3	G	142	147	parallel
Strand 4	G	170	173	parallel
Strand 5	G	182	192	anti-parallel
Strand 6	G	177	179	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	101	106	first strand
Strand 2	G	89	96	anti-parallel
Strand 3	G	142	147	parallel
Strand 4	G	170	173	parallel
Strand 5	G	182	192	anti-parallel
Strand 6	G	31	40	anti-parallel
Strand 7	I	155	160	anti-parallel

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There are 7 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	155	160	first strand
Strand 2	H	31	40	anti-parallel
Strand 3	H	182	192	anti-parallel
Strand 4	H	170	173	anti-parallel
Strand 5	H	142	147	parallel
Strand 6	H	89	96	parallel
Strand 7	H	101	106	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	G	155	160	first strand
Strand 2	H	31	40	anti-parallel
Strand 3	H	182	192	anti-parallel
Strand 4	H	177	179	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	8	10	first strand
Strand 2	H	81	85	anti-parallel
Strand 3	H	75	78	anti-parallel

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There are 7 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	155	160	first strand
Strand 2	I	31	40	anti-parallel
Strand 3	I	182	192	anti-parallel
Strand 4	I	170	173	anti-parallel
Strand 5	I	142	147	parallel
Strand 6	I	89	96	parallel
Strand 7	I	101	106	anti-parallel

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There are 4 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	155	160	first strand
Strand 2	I	31	40	anti-parallel
Strand 3	I	182	192	anti-parallel
Strand 4	I	177	179	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	J	8	10	first strand
Strand 2	J	81	85	anti-parallel
Strand 3	J	75	78	anti-parallel

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There are 6 strands in AC sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	101	106	first strand
Strand 2	J	89	96	anti-parallel
Strand 3	J	142	147	parallel
Strand 4	J	170	173	parallel
Strand 5	J	182	192	anti-parallel
Strand 6	J	177	179	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	101	106	first strand
Strand 2	J	89	96	anti-parallel
Strand 3	J	142	147	parallel
Strand 4	J	170	173	parallel
Strand 5	J	182	192	anti-parallel
Strand 6	J	31	40	anti-parallel
Strand 7	L	155	160	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	J	155	160	first strand
Strand 2	K	31	40	anti-parallel
Strand 3	K	182	192	anti-parallel
Strand 4	K	170	173	anti-parallel
Strand 5	K	142	147	parallel
Strand 6	K	89	96	parallel
Strand 7	K	101	106	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	155	160	first strand
Strand 2	K	31	40	anti-parallel
Strand 3	K	182	192	anti-parallel
Strand 4	K	177	179	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	8	10	first strand
Strand 2	K	81	85	anti-parallel
Strand 3	K	75	78	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	155	160	first strand
Strand 2	L	31	40	anti-parallel
Strand 3	L	182	192	anti-parallel
Strand 4	L	170	173	anti-parallel
Strand 5	L	142	147	parallel
Strand 6	L	89	96	parallel
Strand 7	L	101	106	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	K	155	160	first strand
Strand 2	L	31	40	anti-parallel
Strand 3	L	182	192	anti-parallel
Strand 4	L	177	179	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	8	10	first strand
Strand 2	L	81	85	anti-parallel
Strand 3	L	75	78	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: 1PD5

Analysis of interatomic Contacts of Structural Units in PDB entry:
1PD5