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

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 3DKB entry

There are 6 chains in PDB entry 3DKB (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	GLU 6003	GLN 6362
B	GLU 1003	GLN 1362
C	GLU 2003	GLN 2362
D	GLU 3003	GLN 3362
E	GLU 4003	GLN 4362
F	GLU 5003	GLN 5362

There are 90 helices in PDB entry 3DKB. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	6009	6013	Right-handed 310
Helix 2	2	A	6014	6028	Right-handed alpha
Helix 3	3	A	6042	6046	Right-handed 310
Helix 4	4	A	6057	6069	Right-handed alpha
Helix 5	5	A	6070	6080	Right-handed alpha
Helix 6	6	A	6102	6114	Right-handed alpha
Helix 7	7	A	6120	6133	Right-handed alpha
Helix 8	8	A	6135	6148	Right-handed alpha
Helix 9	9	A	6165	6175	Right-handed alpha
Helix 10	10	A	6192	6203	Right-handed alpha
Helix 11	11	A	6292	6298	Right-handed alpha
Helix 12	12	A	6298	6307	Right-handed alpha
Helix 13	13	A	6336	6339	Right-handed 310
Helix 14	14	A	6340	6358	Right-handed alpha
Helix 15	15	A	6359	6362	Right-handed 310
Helix 16	16	B	1009	1013	Right-handed 310
Helix 17	17	B	1014	1028	Right-handed alpha
Helix 18	18	B	1042	1046	Right-handed 310
Helix 19	19	B	1057	1069	Right-handed alpha
Helix 20	20	B	1070	1080	Right-handed alpha
Helix 21	21	B	1102	1114	Right-handed alpha
Helix 22	22	B	1120	1133	Right-handed alpha
Helix 23	23	B	1135	1148	Right-handed alpha
Helix 24	24	B	1163	1175	Right-handed alpha
Helix 25	25	B	1192	1203	Right-handed alpha
Helix 26	26	B	1292	1298	Right-handed alpha
Helix 27	27	B	1298	1307	Right-handed alpha
Helix 28	28	B	1336	1339	Right-handed 310
Helix 29	29	B	1340	1358	Right-handed alpha
Helix 30	30	B	1359	1362	Right-handed 310
Helix 31	31	C	2009	2013	Right-handed 310
Helix 32	32	C	2014	2028	Right-handed alpha
Helix 33	33	C	2042	2046	Right-handed 310
Helix 34	34	C	2057	2069	Right-handed alpha
Helix 35	35	C	2070	2080	Right-handed alpha
Helix 36	36	C	2102	2114	Right-handed alpha
Helix 37	37	C	2120	2133	Right-handed alpha
Helix 38	38	C	2135	2148	Right-handed alpha
Helix 39	39	C	2163	2175	Right-handed alpha
Helix 40	40	C	2192	2204	Right-handed alpha
Helix 41	41	C	2292	2298	Right-handed alpha
Helix 42	42	C	2298	2307	Right-handed alpha
Helix 43	43	C	2336	2339	Right-handed 310
Helix 44	44	C	2340	2358	Right-handed alpha
Helix 45	45	C	2359	2362	Right-handed 310
Helix 46	46	D	3009	3013	Right-handed 310
Helix 47	47	D	3014	3028	Right-handed alpha
Helix 48	48	D	3042	3046	Right-handed 310
Helix 49	49	D	3057	3069	Right-handed alpha
Helix 50	50	D	3070	3080	Right-handed alpha
Helix 51	51	D	3102	3114	Right-handed alpha
Helix 52	52	D	3120	3133	Right-handed alpha
Helix 53	53	D	3135	3148	Right-handed alpha
Helix 54	54	D	3163	3175	Right-handed alpha
Helix 55	55	D	3192	3203	Right-handed alpha
Helix 56	56	D	3292	3298	Right-handed alpha
Helix 57	57	D	3298	3307	Right-handed alpha
Helix 58	58	D	3336	3339	Right-handed 310
Helix 59	59	D	3340	3358	Right-handed alpha
Helix 60	60	D	3359	3362	Right-handed 310
Helix 61	61	E	4009	4013	Right-handed 310
Helix 62	62	E	4014	4028	Right-handed alpha
Helix 63	63	E	4042	4046	Right-handed 310
Helix 64	64	E	4057	4069	Right-handed alpha
Helix 65	65	E	4070	4080	Right-handed alpha
Helix 66	66	E	4102	4114	Right-handed alpha
Helix 67	67	E	4120	4133	Right-handed alpha
Helix 68	68	E	4135	4148	Right-handed alpha
Helix 69	69	E	4166	4175	Right-handed alpha
Helix 70	70	E	4192	4204	Right-handed alpha
Helix 71	71	E	4292	4298	Right-handed alpha
Helix 72	72	E	4298	4307	Right-handed alpha
Helix 73	73	E	4336	4339	Right-handed 310
Helix 74	74	E	4340	4358	Right-handed alpha
Helix 75	75	E	4359	4362	Right-handed 310
Helix 76	76	F	5009	5013	Right-handed 310
Helix 77	77	F	5014	5028	Right-handed alpha
Helix 78	78	F	5042	5046	Right-handed 310
Helix 79	79	F	5057	5069	Right-handed alpha
Helix 80	80	F	5070	5080	Right-handed alpha
Helix 81	81	F	5102	5114	Right-handed alpha
Helix 82	82	F	5120	5133	Right-handed alpha
Helix 83	83	F	5135	5148	Right-handed alpha
Helix 84	84	F	5166	5175	Right-handed alpha
Helix 85	85	F	5192	5204	Right-handed alpha
Helix 86	86	F	5292	5298	Right-handed alpha
Helix 87	87	F	5298	5307	Right-handed alpha
Helix 88	88	F	5336	5339	Right-handed 310
Helix 89	89	F	5340	5358	Right-handed alpha
Helix 90	90	F	5359	5362	Right-handed 310

There are 24 sheets in PDB entry 3DKB. 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,

There are 2 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	6029	6030	first strand
Strand 2	A	6039	6040	anti-parallel

Back to list of sheets
Back to top of page

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	6092	6094	first strand
Strand 2	A	6257	6262	anti-parallel
Strand 3	A	6248	6252	anti-parallel
Strand 4	A	6207	6211	parallel
Strand 5	A	6231	6233	anti-parallel

Back to list of sheets
Back to top of page

There are 3 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	6272	6274	first strand
Strand 2	A	6322	6329	anti-parallel
Strand 3	A	6309	6315	anti-parallel

Back to list of sheets
Back to top of page

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	6276	6278	first strand
Strand 2	A	6283	6285	anti-parallel

Back to list of sheets
Back to top of page

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	1029	1030	first strand
Strand 2	B	1039	1040	anti-parallel

Back to list of sheets
Back to top of page

There are 5 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	1092	1094	first strand
Strand 2	B	1257	1262	anti-parallel
Strand 3	B	1248	1252	anti-parallel
Strand 4	B	1207	1211	parallel
Strand 5	B	1231	1233	anti-parallel

Back to list of sheets
Back to top of page

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	1272	1274	first strand
Strand 2	B	1322	1329	anti-parallel
Strand 3	B	1309	1315	anti-parallel

Back to list of sheets
Back to top of page

There are 2 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	1276	1278	first strand
Strand 2	B	1283	1285	anti-parallel

Back to list of sheets
Back to top of page

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	C	2029	2030	first strand
Strand 2	C	2039	2040	anti-parallel

Back to list of sheets
Back to top of page

There are 5 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	2092	2094	first strand
Strand 2	C	2257	2262	anti-parallel
Strand 3	C	2248	2252	anti-parallel
Strand 4	C	2207	2211	parallel
Strand 5	C	2231	2233	anti-parallel

Back to list of sheets
Back to top of page

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	C	2272	2274	first strand
Strand 2	C	2322	2329	anti-parallel
Strand 3	C	2309	2315	anti-parallel

Back to list of sheets
Back to top of page

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	C	2276	2278	first strand
Strand 2	C	2283	2285	anti-parallel

Back to list of sheets
Back to top of page

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	D	3029	3030	first strand
Strand 2	D	3039	3040	anti-parallel

Back to list of sheets
Back to top of page

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	D	3092	3094	first strand
Strand 2	D	3257	3262	anti-parallel
Strand 3	D	3248	3252	anti-parallel
Strand 4	D	3207	3211	parallel
Strand 5	D	3231	3233	anti-parallel

Back to list of sheets
Back to top of page

There are 3 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	3272	3274	first strand
Strand 2	D	3322	3329	anti-parallel
Strand 3	D	3309	3315	anti-parallel

Back to list of sheets
Back to top of page

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	D	3276	3278	first strand
Strand 2	D	3283	3285	anti-parallel

Back to list of sheets
Back to top of page

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	E	4029	4030	first strand
Strand 2	E	4039	4040	anti-parallel

Back to list of sheets
Back to top of page

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	E	4092	4094	first strand
Strand 2	E	4257	4262	anti-parallel
Strand 3	E	4248	4252	anti-parallel
Strand 4	E	4207	4211	parallel
Strand 5	E	4231	4233	anti-parallel

Back to list of sheets
Back to top of page

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	E	4272	4274	first strand
Strand 2	E	4322	4329	anti-parallel
Strand 3	E	4309	4315	anti-parallel

Back to list of sheets
Back to top of page

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	4276	4278	first strand
Strand 2	E	4283	4285	anti-parallel

Back to list of sheets
Back to top of page

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	5029	5030	first strand
Strand 2	F	5039	5040	anti-parallel

Back to list of sheets
Back to top of page

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	F	5092	5094	first strand
Strand 2	F	5257	5262	anti-parallel
Strand 3	F	5248	5252	anti-parallel
Strand 4	F	5207	5211	parallel
Strand 5	F	5231	5233	anti-parallel

Back to list of sheets
Back to top of page

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	5272	5274	first strand
Strand 2	F	5322	5329	anti-parallel
Strand 3	F	5309	5315	anti-parallel

Back to list of sheets
Back to top of page

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	5276	5278	first strand
Strand 2	F	5283	5285	anti-parallel

Back to list of sheets
Back to top of page

Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il

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

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