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

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 3QDK entry

There are 4 chains in PDB entry 3QDK (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	LYS 5	LYS 553
B	LYS 5	LYS 553
C	LYS 5	ARG 558
D	LYS 5	ARG 558

There are 98 helices in PDB entry 3QDK. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	61	79	Right-handed alpha
Helix 2	2	A	108	112	Right-handed 310
Helix 3	3	A	114	122	Right-handed 310
Helix 4	4	A	131	146	Right-handed alpha
Helix 5	5	A	149	154	Right-handed 310
Helix 6	6	A	161	173	Right-handed alpha
Helix 7	7	A	173	180	Right-handed alpha
Helix 8	8	A	186	196	Right-handed alpha
Helix 9	9	A	202	209	Right-handed alpha
Helix 10	10	A	219	225	Right-handed alpha
Helix 11	11	A	227	231	Right-handed 310
Helix 12	12	A	232	236	Right-handed 310
Helix 13	13	A	253	261	Right-handed alpha
Helix 14	14	A	277	282	Right-handed alpha
Helix 15	15	A	335	346	Right-handed alpha
Helix 16	16	A	348	358	Right-handed alpha
Helix 17	17	A	361	371	Right-handed alpha
Helix 18	18	A	410	435	Right-handed alpha
Helix 19	19	A	448	453	Right-handed alpha
Helix 20	20	A	453	465	Right-handed alpha
Helix 21	21	A	475	490	Right-handed alpha
Helix 22	22	A	498	507	Right-handed alpha
Helix 23	23	A	517	540	Right-handed alpha
Helix 24	24	A	544	553	Right-handed alpha
Helix 25	25	B	62	79	Right-handed alpha
Helix 26	26	B	108	112	Right-handed 310
Helix 27	27	B	118	122	Right-handed 310
Helix 28	28	B	131	146	Right-handed alpha
Helix 29	29	B	148	153	Right-handed alpha
Helix 30	30	B	161	173	Right-handed alpha
Helix 31	31	B	173	180	Right-handed alpha
Helix 32	32	B	186	196	Right-handed alpha
Helix 33	33	B	202	208	Right-handed alpha
Helix 34	34	B	219	227	Right-handed alpha
Helix 35	35	B	228	231	Right-handed 310
Helix 36	36	B	232	236	Right-handed 310
Helix 37	37	B	253	261	Right-handed alpha
Helix 38	38	B	277	282	Right-handed alpha
Helix 39	39	B	335	346	Right-handed alpha
Helix 40	40	B	348	358	Right-handed alpha
Helix 41	41	B	361	372	Right-handed alpha
Helix 42	42	B	410	434	Right-handed alpha
Helix 43	43	B	448	453	Right-handed alpha
Helix 44	44	B	453	465	Right-handed alpha
Helix 45	45	B	475	488	Right-handed alpha
Helix 46	46	B	498	507	Right-handed alpha
Helix 47	47	B	517	540	Right-handed alpha
Helix 48	48	B	544	552	Right-handed alpha
Helix 49	49	C	62	79	Right-handed alpha
Helix 50	50	C	108	112	Right-handed 310
Helix 51	51	C	131	146	Right-handed alpha
Helix 52	52	C	148	153	Right-handed alpha
Helix 53	53	C	161	173	Right-handed alpha
Helix 54	54	C	173	180	Right-handed alpha
Helix 55	55	C	186	196	Right-handed alpha
Helix 56	56	C	202	209	Right-handed alpha
Helix 57	57	C	219	227	Right-handed alpha
Helix 58	58	C	228	231	Right-handed 310
Helix 59	59	C	232	236	Right-handed 310
Helix 60	60	C	253	261	Right-handed alpha
Helix 61	61	C	274	282	Right-handed alpha
Helix 62	62	C	335	346	Right-handed alpha
Helix 63	63	C	348	358	Right-handed alpha
Helix 64	64	C	361	372	Right-handed alpha
Helix 65	65	C	410	434	Right-handed alpha
Helix 66	66	C	448	453	Right-handed alpha
Helix 67	67	C	453	465	Right-handed alpha
Helix 68	68	C	475	490	Right-handed alpha
Helix 69	69	C	491	494	Right-handed 310
Helix 70	70	C	498	507	Right-handed alpha
Helix 71	71	C	517	540	Right-handed alpha
Helix 72	72	C	544	557	Right-handed alpha
Helix 73	73	D	62	79	Right-handed alpha
Helix 74	74	D	83	85	Right-handed 310
Helix 75	75	D	108	112	Right-handed 310
Helix 76	76	D	118	122	Right-handed 310
Helix 77	77	D	131	146	Right-handed alpha
Helix 78	78	D	149	154	Right-handed 310
Helix 79	79	D	161	173	Right-handed alpha
Helix 80	80	D	173	180	Right-handed alpha
Helix 81	81	D	186	196	Right-handed alpha
Helix 82	82	D	202	209	Right-handed alpha
Helix 83	83	D	219	227	Right-handed alpha
Helix 84	84	D	228	231	Right-handed 310
Helix 85	85	D	232	236	Right-handed 310
Helix 86	86	D	253	261	Right-handed alpha
Helix 87	87	D	274	282	Right-handed alpha
Helix 88	88	D	335	346	Right-handed alpha
Helix 89	89	D	348	356	Right-handed alpha
Helix 90	90	D	361	371	Right-handed alpha
Helix 91	91	D	410	434	Right-handed alpha
Helix 92	92	D	448	453	Right-handed alpha
Helix 93	93	D	453	465	Right-handed alpha
Helix 94	94	D	475	490	Right-handed alpha
Helix 95	95	D	491	494	Right-handed 310
Helix 96	96	D	498	507	Right-handed alpha
Helix 97	97	D	517	540	Right-handed alpha
Helix 98	98	D	544	557	Right-handed alpha

There are 26 sheets in PDB entry 3QDK. 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,

There are 6 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	29	36	first strand
Strand 2	A	16	23	anti-parallel
Strand 3	A	6	12	anti-parallel
Strand 4	A	87	94	parallel
Strand 5	A	267	269	parallel
Strand 6	A	248	251	anti-parallel

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There are 5 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	29	36	first strand
Strand 2	A	16	23	anti-parallel
Strand 3	A	6	12	anti-parallel
Strand 4	A	87	94	parallel
Strand 5	A	272	273	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	59	60	first strand
Strand 2	A	123	124	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	99	102	first strand
Strand 2	A	182	185	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	200	201	first strand
Strand 2	A	242	243	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	A	315	318	first strand
Strand 2	A	326	332	anti-parallel
Strand 3	A	298	304	anti-parallel
Strand 4	A	288	294	anti-parallel
Strand 5	A	440	447	parallel
Strand 6	A	468	470	parallel

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There are 4 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	381	383	first strand
Strand 2	A	400	405	anti-parallel
Strand 3	B	400	405	anti-parallel
Strand 4	B	381	383	anti-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	B	29	36	first strand
Strand 2	B	16	23	anti-parallel
Strand 3	B	6	12	anti-parallel
Strand 4	B	87	94	parallel
Strand 5	B	267	269	parallel
Strand 6	B	248	251	anti-parallel

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There are 5 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	29	36	first strand
Strand 2	B	16	23	anti-parallel
Strand 3	B	6	12	anti-parallel
Strand 4	B	87	94	parallel
Strand 5	B	272	273	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	59	60	first strand
Strand 2	B	123	124	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	B	99	102	first strand
Strand 2	B	182	185	anti-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	B	200	201	first strand
Strand 2	B	242	243	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	B	315	318	first strand
Strand 2	B	326	332	anti-parallel
Strand 3	B	298	304	anti-parallel
Strand 4	B	288	294	anti-parallel
Strand 5	B	440	447	parallel
Strand 6	B	468	470	parallel

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There are 6 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	29	36	first strand
Strand 2	C	16	23	anti-parallel
Strand 3	C	6	12	anti-parallel
Strand 4	C	87	94	parallel
Strand 5	C	267	269	parallel
Strand 6	C	248	251	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	29	36	first strand
Strand 2	C	16	23	anti-parallel
Strand 3	C	6	12	anti-parallel
Strand 4	C	87	94	parallel
Strand 5	C	272	273	parallel

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There are 2 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	59	60	first strand
Strand 2	C	123	124	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	99	102	first strand
Strand 2	C	182	185	anti-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	C	200	201	first strand
Strand 2	C	242	243	parallel

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There are 6 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	315	318	first strand
Strand 2	C	326	332	anti-parallel
Strand 3	C	298	304	anti-parallel
Strand 4	C	288	294	anti-parallel
Strand 5	C	440	446	parallel
Strand 6	C	468	470	parallel

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There are 4 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	381	383	first strand
Strand 2	C	400	405	anti-parallel
Strand 3	D	400	405	anti-parallel
Strand 4	D	381	383	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	D	29	36	first strand
Strand 2	D	16	23	anti-parallel
Strand 3	D	6	12	anti-parallel
Strand 4	D	87	94	parallel
Strand 5	D	267	269	parallel
Strand 6	D	248	251	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	29	36	first strand
Strand 2	D	16	23	anti-parallel
Strand 3	D	6	12	anti-parallel
Strand 4	D	87	94	parallel
Strand 5	D	272	273	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	D	59	60	first strand
Strand 2	D	123	124	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	D	99	102	first strand
Strand 2	D	182	185	anti-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	D	200	201	first strand
Strand 2	D	242	243	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	315	318	first strand
Strand 2	D	326	332	anti-parallel
Strand 3	D	298	304	anti-parallel
Strand 4	D	288	294	anti-parallel
Strand 5	D	440	446	parallel
Strand 6	D	468	470	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: 3QDK

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