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

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 4JDM entry

There are 6 chains in PDB entry 4JDM (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	GLY 2	ALA 264
B	MSE 1	ASN 263
C	GLY -4	ALA 264
D	GLY 2	ALA 264
E	MSE 1	ASN 263
F	GLY -4	ALA 264

There are 20 helices in PDB entry 4JDM. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	73	85	Right-handed alpha
Helix 2	2	A	86	111	Right-handed alpha
Helix 3	3	A	243	247	Right-handed 310
Helix 4	4	B	49	53	Right-handed 310
Helix 5	5	B	73	84	Right-handed alpha
Helix 6	6	B	86	109	Right-handed alpha
Helix 7	7	B	243	247	Right-handed 310
Helix 8	8	C	73	111	Right-handed alpha
Helix 9	9	C	243	247	Right-handed 310
Helix 10	10	D	73	85	Right-handed alpha
Helix 11	11	D	86	111	Right-handed alpha
Helix 12	12	D	243	247	Right-handed 310
Helix 13	13	E	49	53	Right-handed 310
Helix 14	14	E	73	84	Right-handed alpha
Helix 15	15	E	87	109	Right-handed alpha
Helix 16	16	E	243	247	Right-handed 310
Helix 17	17	F	73	84	Right-handed alpha
Helix 18	18	F	84	95	Right-handed alpha
Helix 19	19	F	98	111	Right-handed alpha
Helix 20	20	F	243	247	Right-handed 310

There are 32 sheets in PDB entry 4JDM. 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,

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	5	9	first strand
Strand 2	A	12	17	anti-parallel
Strand 3	C	19	22	parallel

Back to list of sheets
Back to top of page

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	21	22	first strand
Strand 2	B	12	17	parallel
Strand 3	B	5	9	anti-parallel

Back to list of sheets
Back to top of page

There are 8 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	56	57	first strand
Strand 2	A	66	69	anti-parallel
Strand 3	C	43	49	parallel
Strand 4	C	33	37	anti-parallel
Strand 5	A	33	36	anti-parallel
Strand 6	A	43	49	anti-parallel
Strand 7	B	66	70	parallel
Strand 8	B	54	57	anti-parallel

Back to list of sheets
Back to top of page

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	120	125	first strand
Strand 2	A	251	258	anti-parallel
Strand 3	A	162	172	anti-parallel
Strand 4	A	233	235	anti-parallel
Strand 5	A	129	131	anti-parallel

Back to list of sheets
Back to top of page

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	120	125	first strand
Strand 2	A	251	258	anti-parallel
Strand 3	A	162	172	anti-parallel
Strand 4	A	203	212	anti-parallel

Back to list of sheets
Back to top of page

There are 3 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	134	135	first strand
Strand 2	A	219	228	parallel
Strand 3	A	147	154	anti-parallel

Back to list of sheets
Back to top of page

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	134	135	first strand
Strand 2	A	219	228	parallel
Strand 3	A	176	184	anti-parallel
Strand 4	A	192	198	anti-parallel

Back to list of sheets
Back to top of page

There are 3 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	19	22	first strand
Strand 2	C	12	17	parallel
Strand 3	C	5	9	anti-parallel

Back to list of sheets
Back to top of page

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	33	36	first strand
Strand 2	B	43	48	anti-parallel
Strand 3	C	66	70	parallel
Strand 4	C	54	57	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	B	120	125	first strand
Strand 2	B	251	258	anti-parallel
Strand 3	B	162	173	anti-parallel
Strand 4	B	233	235	anti-parallel
Strand 5	B	129	131	anti-parallel

Back to list of sheets
Back to top of page

There are 4 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	120	125	first strand
Strand 2	B	251	258	anti-parallel
Strand 3	B	162	173	anti-parallel
Strand 4	B	203	212	anti-parallel

Back to list of sheets
Back to top of page

There are 4 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	147	154	first strand
Strand 2	B	219	227	anti-parallel
Strand 3	B	176	184	anti-parallel
Strand 4	B	192	198	anti-parallel

Back to list of sheets
Back to top of page

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	120	125	first strand
Strand 2	C	251	258	anti-parallel
Strand 3	C	162	173	anti-parallel
Strand 4	C	233	235	anti-parallel
Strand 5	C	129	131	anti-parallel

Back to list of sheets
Back to top of page

There are 4 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	120	125	first strand
Strand 2	C	251	258	anti-parallel
Strand 3	C	162	173	anti-parallel
Strand 4	C	203	212	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	C	134	135	first strand
Strand 2	C	219	228	parallel
Strand 3	C	147	154	anti-parallel

Back to list of sheets
Back to top of page

There are 4 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	134	135	first strand
Strand 2	C	219	228	parallel
Strand 3	C	176	184	anti-parallel
Strand 4	C	192	198	anti-parallel

Back to list of sheets
Back to top of page

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	5	9	first strand
Strand 2	D	12	17	anti-parallel
Strand 3	F	19	22	parallel

Back to list of sheets
Back to top of page

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	21	22	first strand
Strand 2	E	12	17	parallel
Strand 3	E	5	9	anti-parallel

Back to list of sheets
Back to top of page

There are 8 strands in S sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	56	57	first strand
Strand 2	D	66	69	anti-parallel
Strand 3	F	43	49	parallel
Strand 4	F	33	37	anti-parallel
Strand 5	D	33	36	anti-parallel
Strand 6	D	43	49	anti-parallel
Strand 7	E	66	70	parallel
Strand 8	E	54	57	anti-parallel

Back to list of sheets
Back to top of page

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	120	125	first strand
Strand 2	D	251	258	anti-parallel
Strand 3	D	162	173	anti-parallel
Strand 4	D	233	235	anti-parallel
Strand 5	D	129	131	anti-parallel

Back to list of sheets
Back to top of page

There are 4 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	120	125	first strand
Strand 2	D	251	258	anti-parallel
Strand 3	D	162	173	anti-parallel
Strand 4	D	203	212	anti-parallel

Back to list of sheets
Back to top of page

There are 3 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	134	135	first strand
Strand 2	D	219	228	parallel
Strand 3	D	147	154	anti-parallel

Back to list of sheets
Back to top of page

There are 4 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	134	135	first strand
Strand 2	D	219	228	parallel
Strand 3	D	176	184	anti-parallel
Strand 4	D	192	198	anti-parallel

Back to list of sheets
Back to top of page

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	19	22	first strand
Strand 2	F	12	17	parallel
Strand 3	F	5	9	anti-parallel

Back to list of sheets
Back to top of page

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	33	36	first strand
Strand 2	E	43	48	anti-parallel
Strand 3	F	66	70	parallel
Strand 4	F	54	57	anti-parallel

Back to list of sheets
Back to top of page

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	120	125	first strand
Strand 2	E	251	258	anti-parallel
Strand 3	E	162	173	anti-parallel
Strand 4	E	233	235	anti-parallel
Strand 5	E	129	131	anti-parallel

Back to list of sheets
Back to top of page

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	E	120	125	first strand
Strand 2	E	251	258	anti-parallel
Strand 3	E	162	173	anti-parallel
Strand 4	E	203	212	anti-parallel

Back to list of sheets
Back to top of page

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	147	154	first strand
Strand 2	E	219	227	anti-parallel
Strand 3	E	176	184	anti-parallel
Strand 4	E	190	198	anti-parallel

Back to list of sheets
Back to top of page

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	120	125	first strand
Strand 2	F	251	258	anti-parallel
Strand 3	F	162	173	anti-parallel
Strand 4	F	233	235	anti-parallel
Strand 5	F	129	131	anti-parallel

Back to list of sheets
Back to top of page

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	120	125	first strand
Strand 2	F	251	258	anti-parallel
Strand 3	F	162	173	anti-parallel
Strand 4	F	203	212	anti-parallel

Back to list of sheets
Back to top of page

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	134	135	first strand
Strand 2	F	219	228	parallel
Strand 3	F	147	154	anti-parallel

Back to list of sheets
Back to top of page

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	F	134	135	first strand
Strand 2	F	219	228	parallel
Strand 3	F	176	184	anti-parallel
Strand 4	F	192	198	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: 4JDM

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