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

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 4DPM entry

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

Chain ID	Initial residue	Terminal residue
A	ARG 6	LYS 359
B	ARG 6	LYS 359
C	ARG 6	LYS 359
D	ARG 6	LEU 235

There are 96 helices in PDB entry 4DPM. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	19	28	Right-handed alpha
Helix 2	2	A	47	52	Right-handed alpha
Helix 3	3	A	61	66	Right-handed alpha
Helix 4	4	A	73	77	Right-handed 310
Helix 5	5	A	91	102	Right-handed alpha
Helix 6	6	A	127	131	Right-handed 310
Helix 7	7	A	132	142	Right-handed alpha
Helix 8	8	A	152	169	Right-handed alpha
Helix 9	9	A	181	186	Right-handed 310
Helix 10	10	A	191	195	Right-handed 310
Helix 11	11	A	203	221	Right-handed alpha
Helix 12	12	A	229	233	Right-handed 310
Helix 13	13	A	261	271	Right-handed alpha
Helix 14	14	A	274	279	Right-handed alpha
Helix 15	15	A	299	304	Right-handed alpha
Helix 16	16	A	340	354	Right-handed alpha
Helix 17	17	B	19	28	Right-handed alpha
Helix 18	18	B	47	52	Right-handed alpha
Helix 19	19	B	61	66	Right-handed alpha
Helix 20	20	B	73	77	Right-handed 310
Helix 21	21	B	91	102	Right-handed alpha
Helix 22	22	B	110	114	Right-handed 310
Helix 23	23	B	127	132	Right-handed 310
Helix 24	24	B	133	142	Right-handed alpha
Helix 25	25	B	152	169	Right-handed alpha
Helix 26	26	B	182	186	Right-handed 310
Helix 27	27	B	191	195	Right-handed 310
Helix 28	28	B	203	219	Right-handed alpha
Helix 29	29	B	229	233	Right-handed 310
Helix 30	30	B	261	271	Right-handed alpha
Helix 31	31	B	274	279	Right-handed alpha
Helix 32	32	B	299	304	Right-handed alpha
Helix 33	33	B	340	354	Right-handed alpha
Helix 34	34	C	19	29	Right-handed alpha
Helix 35	35	C	47	52	Right-handed alpha
Helix 36	36	C	61	66	Right-handed alpha
Helix 37	37	C	91	102	Right-handed alpha
Helix 38	38	C	110	114	Right-handed 310
Helix 39	39	C	127	132	Right-handed 310
Helix 40	40	C	133	142	Right-handed alpha
Helix 41	41	C	152	169	Right-handed alpha
Helix 42	42	C	181	186	Right-handed 310
Helix 43	43	C	191	195	Right-handed 310
Helix 44	44	C	202	219	Right-handed alpha
Helix 45	45	C	229	233	Right-handed 310
Helix 46	46	C	261	271	Right-handed alpha
Helix 47	47	C	274	279	Right-handed alpha
Helix 48	48	C	299	304	Right-handed alpha
Helix 49	49	C	340	354	Right-handed alpha
Helix 50	50	D	19	29	Right-handed alpha
Helix 51	51	D	47	52	Right-handed alpha
Helix 52	52	D	61	66	Right-handed alpha
Helix 53	53	D	91	102	Right-handed alpha
Helix 54	54	D	110	114	Right-handed 310
Helix 55	55	D	127	132	Right-handed 310
Helix 56	56	D	133	142	Right-handed alpha
Helix 57	57	D	152	169	Right-handed alpha
Helix 58	58	D	182	186	Right-handed 310
Helix 59	59	D	191	196	Right-handed alpha
Helix 60	60	D	202	219	Right-handed alpha
Helix 61	61	D	229	233	Right-handed 310
Helix 62	62	D	261	271	Right-handed alpha
Helix 63	63	D	274	279	Right-handed alpha
Helix 64	64	D	299	304	Right-handed alpha
Helix 65	65	D	340	354	Right-handed alpha
Helix 66	66	E	19	28	Right-handed alpha
Helix 67	67	E	47	52	Right-handed alpha
Helix 68	68	E	61	66	Right-handed alpha
Helix 69	69	E	91	102	Right-handed alpha
Helix 70	70	E	127	132	Right-handed 310
Helix 71	71	E	133	142	Right-handed alpha
Helix 72	72	E	152	169	Right-handed alpha
Helix 73	73	E	182	186	Right-handed 310
Helix 74	74	E	191	195	Right-handed 310
Helix 75	75	E	203	221	Right-handed alpha
Helix 76	76	E	229	233	Right-handed 310
Helix 77	77	E	261	271	Right-handed alpha
Helix 78	78	E	274	279	Right-handed alpha
Helix 79	79	E	299	304	Right-handed alpha
Helix 80	80	E	340	354	Right-handed alpha
Helix 81	81	F	19	28	Right-handed alpha
Helix 82	82	F	47	52	Right-handed alpha
Helix 83	83	F	61	66	Right-handed alpha
Helix 84	84	F	91	102	Right-handed alpha
Helix 85	85	F	110	114	Right-handed 310
Helix 86	86	F	127	132	Right-handed 310
Helix 87	87	F	133	142	Right-handed alpha
Helix 88	88	F	152	169	Right-handed alpha
Helix 89	89	F	182	186	Right-handed 310
Helix 90	90	F	191	196	Right-handed alpha
Helix 91	91	F	202	219	Right-handed alpha
Helix 92	92	F	229	233	Right-handed 310
Helix 93	93	F	261	271	Right-handed alpha
Helix 94	94	F	274	279	Right-handed alpha
Helix 95	95	F	299	304	Right-handed alpha
Helix 96	96	F	340	354	Right-handed alpha

There are 14 sheets in PDB entry 4DPM. 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,

There are 5 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	33	38	first strand
Strand 2	A	8	12	parallel
Strand 3	A	82	85	parallel
Strand 4	A	105	108	parallel
Strand 5	A	146	149	parallel

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There are 7 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	200	201	first strand
Strand 2	A	234	241	anti-parallel
Strand 3	A	171	180	parallel
Strand 4	A	248	256	anti-parallel
Strand 5	A	326	333	anti-parallel
Strand 6	A	314	323	anti-parallel
Strand 7	A	289	291	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	70	71	first strand
Strand 2	B	33	40	parallel
Strand 3	B	8	12	parallel
Strand 4	B	82	85	parallel
Strand 5	B	105	108	parallel
Strand 6	B	146	149	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	234	238	first strand
Strand 2	B	171	179	parallel
Strand 3	B	248	256	anti-parallel
Strand 4	B	326	333	anti-parallel
Strand 5	B	314	323	anti-parallel
Strand 6	B	289	291	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	200	201	first strand
Strand 2	B	240	241	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	70	71	first strand
Strand 2	C	33	40	parallel
Strand 3	C	8	12	parallel
Strand 4	C	82	85	parallel
Strand 5	C	105	108	parallel
Strand 6	C	146	149	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	C	200	201	first strand
Strand 2	C	234	241	anti-parallel
Strand 3	C	171	180	parallel
Strand 4	C	248	256	anti-parallel
Strand 5	C	326	333	anti-parallel
Strand 6	C	314	323	anti-parallel
Strand 7	C	289	291	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	70	71	first strand
Strand 2	D	33	40	parallel
Strand 3	D	8	12	parallel
Strand 4	D	82	85	parallel
Strand 5	D	105	108	parallel
Strand 6	D	146	149	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	200	201	first strand
Strand 2	D	234	241	anti-parallel
Strand 3	D	171	180	parallel
Strand 4	D	248	256	anti-parallel
Strand 5	D	326	333	anti-parallel
Strand 6	D	314	323	anti-parallel
Strand 7	D	289	291	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	70	71	first strand
Strand 2	E	33	40	parallel
Strand 3	E	8	12	parallel
Strand 4	E	82	85	parallel
Strand 5	E	105	108	parallel
Strand 6	E	146	149	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	234	238	first strand
Strand 2	E	171	179	parallel
Strand 3	E	248	256	anti-parallel
Strand 4	E	326	333	anti-parallel
Strand 5	E	314	323	anti-parallel
Strand 6	E	289	291	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	E	200	201	first strand
Strand 2	E	240	241	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	70	71	first strand
Strand 2	F	33	40	parallel
Strand 3	F	8	12	parallel
Strand 4	F	82	85	parallel
Strand 5	F	105	108	parallel
Strand 6	F	146	149	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	F	200	201	first strand
Strand 2	F	234	241	anti-parallel
Strand 3	F	171	180	parallel
Strand 4	F	248	256	anti-parallel
Strand 5	F	326	333	anti-parallel
Strand 6	F	314	323	anti-parallel
Strand 7	F	289	292	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: 4DPM

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