Analysis of interatomic Contacts of Structural Units in PDB entry:
5VNJ

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 5VNJ entry

There are 2 chains in PDB entry 5VNJ (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	THR 3	ALA 764
B	GLU 346	ASN 932

There are 59 helices in PDB entry 5VNJ. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	3	16	Right-handed alpha
Helix 2	AA2	A	27	32	Right-handed alpha
Helix 3	AA3	A	95	99	Right-handed 310
Helix 4	AA4	A	107	114	Right-handed 310
Helix 5	AA5	A	140	156	Right-handed alpha
Helix 6	AA6	A	196	205	Right-handed alpha
Helix 7	AA7	A	236	247	Right-handed alpha
Helix 8	AA8	A	263	279	Right-handed alpha
Helix 9	AA9	A	312	318	Right-handed alpha
Helix 10	AB1	A	323	342	Right-handed alpha
Helix 11	AB2	A	356	361	Right-handed alpha
Helix 12	AB3	A	361	367	Right-handed alpha
Helix 13	AB4	A	379	389	Right-handed alpha
Helix 14	AB5	A	505	507	Right-handed 310
Helix 15	AB6	A	508	516	Right-handed alpha
Helix 16	AB7	A	518	535	Right-handed alpha
Helix 17	AB8	A	542	558	Right-handed alpha
Helix 18	AB9	A	564	568	Right-handed 310
Helix 19	AC1	A	576	587	Right-handed alpha
Helix 20	AC2	A	596	608	Right-handed alpha
Helix 21	AC3	A	611	620	Right-handed alpha
Helix 22	AC4	A	638	642	Right-handed 310
Helix 23	AC5	A	680	699	Right-handed alpha
Helix 24	AC6	A	712	714	Right-handed 310
Helix 25	AC7	A	715	722	Right-handed alpha
Helix 26	AC8	A	748	761	Right-handed alpha
Helix 27	AC9	B	353	357	Right-handed alpha
Helix 28	AD1	B	373	378	Right-handed alpha
Helix 29	AD2	B	396	404	Right-handed alpha
Helix 30	AD3	B	462	466	Right-handed 310
Helix 31	AD4	B	476	484	Right-handed 310
Helix 32	AD5	B	493	497	Right-handed 310
Helix 33	AD6	B	513	520	Right-handed alpha
Helix 34	AD7	B	520	532	Right-handed alpha
Helix 35	AD8	B	591	606	Right-handed alpha
Helix 36	AD9	B	615	628	Right-handed alpha
Helix 37	AE1	B	671	683	Right-handed alpha
Helix 38	AE2	B	698	703	Right-handed alpha
Helix 39	AE3	B	703	708	Right-handed alpha
Helix 40	AE4	B	724	741	Right-handed alpha
Helix 41	AE5	B	830	837	Right-handed alpha
Helix 42	AE6	B	839	858	Right-handed alpha
Helix 43	AE7	B	859	880	Right-handed alpha
Helix 44	AE8	B	895	897	Right-handed 310
Helix 45	AE9	B	898	909	Right-handed alpha
Helix 46	AF1	B	919	933	Right-handed alpha
Helix 47	AF2	B	934	943	Right-handed alpha
Helix 48	AF3	B	974	978	Right-handed 310
Helix 49	AF4	B	1001	1008	Right-handed alpha
Helix 50	AF5	B	1013	1017	Right-handed 310
Helix 51	AF6	B	1029	1044	Right-handed alpha
Helix 52	AF7	B	1065	1069	Right-handed 310
Helix 53	AF8	B	1079	1092	Right-handed alpha
Helix 54	AF9	C	30	44	Right-handed alpha
Helix 55	AG1	C	80	100	Right-handed alpha
Helix 56	AG2	C	102	106	Right-handed 310
Helix 57	AG3	C	112	114	Right-handed 310
Helix 58	AG4	C	115	124	Right-handed alpha
Helix 59	AG5	C	153	157	Right-handed alpha

There are 14 sheets in PDB entry 5VNJ. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2, AB3, AB4, AB5,

There are 3 strands in AA1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	23	24	first strand
Strand 2	A	492	503	parallel
Strand 3	A	116	121	anti-parallel

Back to list of sheets
Back to top of page

There are 6 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	23	24	first strand
Strand 2	A	492	503	parallel
Strand 3	A	477	486	anti-parallel
Strand 4	A	401	410	anti-parallel
Strand 5	A	445	451	anti-parallel
Strand 6	A	424	425	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AA3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	39	42	first strand
Strand 2	A	457	463	anti-parallel
Strand 3	A	414	420	anti-parallel
Strand 4	A	440	441	anti-parallel

Back to list of sheets
Back to top of page

There are 3 strands in AA4 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	82	84	anti-parallel
Strand 3	A	91	93	anti-parallel

Back to list of sheets
Back to top of page

There are 8 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	231	232	first strand
Strand 2	A	163	169	anti-parallel
Strand 3	A	172	176	anti-parallel
Strand 4	A	185	190	anti-parallel
Strand 5	B	566	570	parallel
Strand 6	B	553	557	anti-parallel
Strand 7	B	543	549	anti-parallel
Strand 8	B	586	587	anti-parallel

Back to list of sheets
Back to top of page

There are 14 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	371	374	first strand
Strand 2	A	344	350	parallel
Strand 3	A	284	290	parallel
Strand 4	A	130	136	parallel
Strand 5	A	163	169	parallel
Strand 6	A	172	176	anti-parallel
Strand 7	A	185	190	anti-parallel
Strand 8	B	566	570	parallel
Strand 9	B	553	557	anti-parallel
Strand 10	B	543	549	anti-parallel
Strand 11	B	505	511	parallel
Strand 12	B	632	638	parallel
Strand 13	B	685	691	parallel
Strand 14	B	714	715	parallel

Back to list of sheets
Back to top of page

There are 5 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	633	634	first strand
Strand 2	A	622	626	anti-parallel
Strand 3	A	647	651	anti-parallel
Strand 4	A	655	660	anti-parallel
Strand 5	A	704	709	parallel

Back to list of sheets
Back to top of page

There are 2 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	350	352	first strand
Strand 2	B	891	893	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	386	388	first strand
Strand 2	B	408	411	anti-parallel
Strand 3	B	785	791	anti-parallel
Strand 4	B	757	763	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	393	394	first strand
Strand 2	B	816	828	parallel
Strand 3	B	487	491	anti-parallel
Strand 4	B	422	423	parallel

Back to list of sheets
Back to top of page

There are 6 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	393	394	first strand
Strand 2	B	816	828	parallel
Strand 3	B	800	811	anti-parallel
Strand 4	B	744	753	anti-parallel
Strand 5	B	774	779	anti-parallel
Strand 6	B	767	768	anti-parallel

Back to list of sheets
Back to top of page

There are 3 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	443	444	first strand
Strand 2	B	449	451	anti-parallel
Strand 3	B	458	460	anti-parallel

Back to list of sheets
Back to top of page

There are 4 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	945	948	first strand
Strand 2	B	983	987	anti-parallel
Strand 3	B	991	996	anti-parallel
Strand 4	B	1051	1053	parallel

Back to list of sheets
Back to top of page

There are 6 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	15	19	first strand
Strand 2	C	5	9	anti-parallel
Strand 3	C	69	76	anti-parallel
Strand 4	C	59	66	anti-parallel
Strand 5	C	51	56	anti-parallel
Strand 6	C	150	152	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: 5VNJ

Analysis of interatomic Contacts of Structural Units in PDB entry:
5VNJ