Analysis of interatomic Contacts of Structural Units in PDB entry:
3KD9

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 3KD9 entry

There are 3 chains in PDB entry 3KD9 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	SER 2	GLY 443
B	SER 2	GLY 443
C	SER 2	GLY 443

There are 34 helices in PDB entry 3KD9. 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	26	Right-handed alpha
Helix 2	2	A	67	72	Right-handed alpha
Helix 3	3	A	133	144	Right-handed alpha
Helix 4	4	A	157	170	Right-handed alpha
Helix 5	5	A	189	201	Right-handed alpha
Helix 6	6	A	246	252	Right-handed alpha
Helix 7	7	A	297	313	Right-handed alpha
Helix 8	8	A	341	348	Right-handed alpha
Helix 9	9	A	395	408	Right-handed alpha
Helix 10	10	A	411	417	Right-handed alpha
Helix 11	11	A	431	442	Right-handed alpha
Helix 12	12	B	12	26	Right-handed alpha
Helix 13	13	B	68	73	Right-handed alpha
Helix 14	14	B	132	144	Right-handed alpha
Helix 15	15	B	157	169	Right-handed alpha
Helix 16	16	B	189	201	Right-handed alpha
Helix 17	17	B	246	251	Right-handed alpha
Helix 18	18	B	279	282	Right-handed 310
Helix 19	19	B	297	313	Right-handed alpha
Helix 20	20	B	341	348	Right-handed alpha
Helix 21	21	B	395	409	Right-handed alpha
Helix 22	22	B	411	417	Right-handed alpha
Helix 23	23	B	431	442	Right-handed alpha
Helix 24	24	C	12	26	Right-handed alpha
Helix 25	25	C	66	71	Right-handed 310
Helix 26	26	C	132	144	Right-handed alpha
Helix 27	27	C	157	169	Right-handed alpha
Helix 28	28	C	189	201	Right-handed alpha
Helix 29	29	C	246	251	Right-handed alpha
Helix 30	30	C	297	313	Right-handed alpha
Helix 31	31	C	341	349	Right-handed alpha
Helix 32	32	C	395	409	Right-handed alpha
Helix 33	33	C	411	417	Right-handed alpha
Helix 34	34	C	431	442	Right-handed alpha

There are 21 sheets in PDB entry 3KD9. 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,

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	75	77	first strand
Strand 2	A	30	34	parallel
Strand 3	A	5	9	parallel
Strand 4	A	105	108	parallel
Strand 5	A	275	277	parallel

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There are 3 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	81	85	first strand
Strand 2	A	89	93	anti-parallel
Strand 3	A	98	102	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	112	114	first strand
Strand 2	A	242	244	anti-parallel

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There are 5 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	127	128	first strand
Strand 2	A	235	238	parallel
Strand 3	A	150	154	parallel
Strand 4	A	173	178	parallel
Strand 5	A	205	208	parallel

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There are 3 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	212	216	first strand
Strand 2	A	223	226	anti-parallel
Strand 3	A	229	232	anti-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	A	284	285	first strand
Strand 2	A	292	293	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	326	330	first strand
Strand 2	A	333	339	anti-parallel
Strand 3	A	385	392	anti-parallel
Strand 4	A	371	379	anti-parallel
Strand 5	A	352	360	anti-parallel

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There are 5 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	75	78	first strand
Strand 2	B	30	35	parallel
Strand 3	B	5	9	parallel
Strand 4	B	105	108	parallel
Strand 5	B	275	277	parallel

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There are 3 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	80	86	first strand
Strand 2	B	89	94	anti-parallel
Strand 3	B	97	102	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	B	112	114	first strand
Strand 2	B	242	244	anti-parallel

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There are 5 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	127	129	first strand
Strand 2	B	236	238	parallel
Strand 3	B	151	154	parallel
Strand 4	B	174	177	parallel
Strand 5	B	205	207	parallel

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There are 3 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	212	214	first strand
Strand 2	B	223	226	anti-parallel
Strand 3	B	229	232	anti-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	B	284	285	first strand
Strand 2	B	292	293	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	326	330	first strand
Strand 2	B	333	339	anti-parallel
Strand 3	B	384	392	anti-parallel
Strand 4	B	371	379	anti-parallel
Strand 5	B	352	360	anti-parallel

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There are 5 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	75	78	first strand
Strand 2	C	30	35	parallel
Strand 3	C	5	9	parallel
Strand 4	C	105	108	parallel
Strand 5	C	275	277	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	80	85	first strand
Strand 2	C	89	94	anti-parallel
Strand 3	C	97	102	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	C	112	114	first strand
Strand 2	C	242	244	anti-parallel

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There are 5 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	127	128	first strand
Strand 2	C	235	238	parallel
Strand 3	C	150	154	parallel
Strand 4	C	173	178	parallel
Strand 5	C	205	208	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	C	212	217	first strand
Strand 2	C	221	226	anti-parallel
Strand 3	C	229	232	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	C	284	285	first strand
Strand 2	C	292	293	anti-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	C	326	330	first strand
Strand 2	C	333	339	anti-parallel
Strand 3	C	385	392	anti-parallel
Strand 4	C	371	379	anti-parallel
Strand 5	C	352	360	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: 3KD9

Analysis of interatomic Contacts of Structural Units in PDB entry:
3KD9