Analysis of interatomic Contacts of Structural Units in PDB entry:
9VDP

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 9VDP entry

There are 12 chains in PDB entry 9VDP (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ASP 5	GLU 506
I	C 5	A 9
B	ASP 5	GLU 506
C	C 5	A 9
D	ASP 5	GLU 506
E	C 5	A 9
F	ASP 5	GLU 506
G	C 5	A 9
H	ASP 5	GLU 506
J	C 5	A 9
K	ASP 5	GLU 506
L	C 5	A 9

There are144 helices in PDB entry 9VDP. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	5	17	Right-handed alpha
Helix 2	AA2	A	40	50	Right-handed alpha
Helix 3	AA3	A	81	95	Right-handed alpha
Helix 4	AA4	A	95	100	Right-handed alpha
Helix 5	AA5	A	101	103	Right-handed 310
Helix 6	AA6	A	127	139	Right-handed alpha
Helix 7	AA7	A	160	168	Right-handed alpha
Helix 8	AA8	A	168	176	Right-handed alpha
Helix 9	AA9	A	186	199	Right-handed alpha
Helix 10	AB1	A	210	231	Right-handed alpha
Helix 11	AB2	A	248	266	Right-handed alpha
Helix 12	AB3	A	286	295	Right-handed alpha
Helix 13	AB4	A	311	329	Right-handed alpha
Helix 14	AB5	A	333	343	Right-handed alpha
Helix 15	AB6	A	350	365	Right-handed alpha
Helix 16	AB7	A	366	374	Right-handed 310
Helix 17	AB8	A	385	402	Right-handed alpha
Helix 18	AB9	A	403	417	Right-handed alpha
Helix 19	AC1	A	422	433	Right-handed alpha
Helix 20	AC2	A	434	445	Right-handed alpha
Helix 21	AC3	A	447	462	Right-handed alpha
Helix 22	AC4	A	463	469	Right-handed alpha
Helix 23	AC5	A	470	480	Right-handed alpha
Helix 24	AC6	A	490	498	Right-handed alpha
Helix 25	AC7	B	6	17	Right-handed alpha
Helix 26	AC8	B	40	50	Right-handed alpha
Helix 27	AC9	B	81	95	Right-handed alpha
Helix 28	AD1	B	95	100	Right-handed alpha
Helix 29	AD2	B	101	103	Right-handed 310
Helix 30	AD3	B	127	139	Right-handed alpha
Helix 31	AD4	B	160	168	Right-handed alpha
Helix 32	AD5	B	168	176	Right-handed alpha
Helix 33	AD6	B	186	199	Right-handed alpha
Helix 34	AD7	B	210	231	Right-handed alpha
Helix 35	AD8	B	248	266	Right-handed alpha
Helix 36	AD9	B	286	295	Right-handed alpha
Helix 37	AE1	B	311	329	Right-handed alpha
Helix 38	AE2	B	333	343	Right-handed alpha
Helix 39	AE3	B	350	365	Right-handed alpha
Helix 40	AE4	B	366	374	Right-handed 310
Helix 41	AE5	B	385	402	Right-handed alpha
Helix 42	AE6	B	403	417	Right-handed alpha
Helix 43	AE7	B	422	433	Right-handed alpha
Helix 44	AE8	B	434	445	Right-handed alpha
Helix 45	AE9	B	447	462	Right-handed alpha
Helix 46	AF1	B	463	469	Right-handed alpha
Helix 47	AF2	B	470	480	Right-handed alpha
Helix 48	AF3	B	490	498	Right-handed alpha
Helix 49	AF4	D	6	17	Right-handed alpha
Helix 50	AF5	D	40	50	Right-handed alpha
Helix 51	AF6	D	81	95	Right-handed alpha
Helix 52	AF7	D	95	100	Right-handed alpha
Helix 53	AF8	D	101	103	Right-handed 310
Helix 54	AF9	D	127	139	Right-handed alpha
Helix 55	AG1	D	160	168	Right-handed alpha
Helix 56	AG2	D	168	176	Right-handed alpha
Helix 57	AG3	D	186	199	Right-handed alpha
Helix 58	AG4	D	210	231	Right-handed alpha
Helix 59	AG5	D	248	266	Right-handed alpha
Helix 60	AG6	D	286	295	Right-handed alpha
Helix 61	AG7	D	311	329	Right-handed alpha
Helix 62	AG8	D	333	343	Right-handed alpha
Helix 63	AG9	D	350	365	Right-handed alpha
Helix 64	AH1	D	366	374	Right-handed 310
Helix 65	AH2	D	385	402	Right-handed alpha
Helix 66	AH3	D	403	417	Right-handed alpha
Helix 67	AH4	D	422	433	Right-handed alpha
Helix 68	AH5	D	434	445	Right-handed alpha
Helix 69	AH6	D	447	462	Right-handed alpha
Helix 70	AH7	D	463	469	Right-handed alpha
Helix 71	AH8	D	470	480	Right-handed alpha
Helix 72	AH9	D	490	498	Right-handed alpha
Helix 73	AI1	F	6	17	Right-handed alpha
Helix 74	AI2	F	40	50	Right-handed alpha
Helix 75	AI3	F	81	95	Right-handed alpha
Helix 76	AI4	F	95	100	Right-handed alpha
Helix 77	AI5	F	101	103	Right-handed 310
Helix 78	AI6	F	127	139	Right-handed alpha
Helix 79	AI7	F	160	168	Right-handed alpha
Helix 80	AI8	F	168	176	Right-handed alpha
Helix 81	AI9	F	186	199	Right-handed alpha
Helix 82	AJ1	F	210	231	Right-handed alpha
Helix 83	AJ2	F	248	266	Right-handed alpha
Helix 84	AJ3	F	286	295	Right-handed alpha
Helix 85	AJ4	F	311	329	Right-handed alpha
Helix 86	AJ5	F	333	343	Right-handed alpha
Helix 87	AJ6	F	350	365	Right-handed alpha
Helix 88	AJ7	F	366	374	Right-handed 310
Helix 89	AJ8	F	385	402	Right-handed alpha
Helix 90	AJ9	F	403	417	Right-handed alpha
Helix 91	AK1	F	422	433	Right-handed alpha
Helix 92	AK2	F	434	445	Right-handed alpha
Helix 93	AK3	F	447	462	Right-handed alpha
Helix 94	AK4	F	463	469	Right-handed alpha
Helix 95	AK5	F	470	480	Right-handed alpha
Helix 96	AK6	F	490	498	Right-handed alpha
Helix 97	AK7	H	6	17	Right-handed alpha
Helix 98	AK8	H	40	50	Right-handed alpha
Helix 99	AK9	H	81	95	Right-handed alpha
Helix 100	AL1	H	95	100	Right-handed alpha
Helix 101	AL2	H	101	103	Right-handed 310
Helix 102	AL3	H	127	139	Right-handed alpha
Helix 103	AL4	H	160	168	Right-handed alpha
Helix 104	AL5	H	168	176	Right-handed alpha
Helix 105	AL6	H	186	199	Right-handed alpha
Helix 106	AL7	H	210	231	Right-handed alpha
Helix 107	AL8	H	248	266	Right-handed alpha
Helix 108	AL9	H	286	295	Right-handed alpha
Helix 109	AM1	H	311	329	Right-handed alpha
Helix 110	AM2	H	333	343	Right-handed alpha
Helix 111	AM3	H	350	365	Right-handed alpha
Helix 112	AM4	H	366	374	Right-handed 310
Helix 113	AM5	H	385	402	Right-handed alpha
Helix 114	AM6	H	403	417	Right-handed alpha
Helix 115	AM7	H	422	433	Right-handed alpha
Helix 116	AM8	H	434	445	Right-handed alpha
Helix 117	AM9	H	447	462	Right-handed alpha
Helix 118	AN1	H	463	469	Right-handed alpha
Helix 119	AN2	H	470	480	Right-handed alpha
Helix 120	AN3	H	490	498	Right-handed alpha
Helix 121	AN4	K	6	17	Right-handed alpha
Helix 122	AN5	K	40	50	Right-handed alpha
Helix 123	AN6	K	81	95	Right-handed alpha
Helix 124	AN7	K	95	100	Right-handed alpha
Helix 125	AN8	K	101	103	Right-handed 310
Helix 126	AN9	K	127	139	Right-handed alpha
Helix 127	AO1	K	160	168	Right-handed alpha
Helix 128	AO2	K	168	176	Right-handed alpha
Helix 129	AO3	K	186	199	Right-handed alpha
Helix 130	AO4	K	210	231	Right-handed alpha
Helix 131	AO5	K	248	266	Right-handed alpha
Helix 132	AO6	K	286	295	Right-handed alpha
Helix 133	AO7	K	311	329	Right-handed alpha
Helix 134	AO8	K	333	343	Right-handed alpha
Helix 135	AO9	K	350	365	Right-handed alpha
Helix 136	AP1	K	366	374	Right-handed 310
Helix 137	AP2	K	385	402	Right-handed alpha
Helix 138	AP3	K	403	417	Right-handed alpha
Helix 139	AP4	K	422	433	Right-handed alpha
Helix 140	AP5	K	434	445	Right-handed alpha
Helix 141	AP6	K	447	462	Right-handed alpha
Helix 142	AP7	K	463	469	Right-handed alpha
Helix 143	AP8	K	470	480	Right-handed alpha
Helix 144	AP9	K	490	498	Right-handed alpha

There are 12 sheets in PDB entry 9VDP. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2, AB3,

There are 2 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	63	68	first strand
Strand 2	A	74	79	anti-parallel

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There are 4 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	234	238	first strand
Strand 2	A	241	246	anti-parallel
Strand 3	A	144	149	anti-parallel
Strand 4	A	276	279	anti-parallel

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There are 2 strands in AA3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	63	68	first strand
Strand 2	B	74	79	anti-parallel

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There are 4 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	234	238	first strand
Strand 2	B	241	246	anti-parallel
Strand 3	B	144	149	anti-parallel
Strand 4	B	276	279	anti-parallel

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There are 2 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	63	68	first strand
Strand 2	D	74	79	anti-parallel

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There are 4 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	234	238	first strand
Strand 2	D	241	246	anti-parallel
Strand 3	D	144	149	anti-parallel
Strand 4	D	276	279	anti-parallel

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There are 2 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	63	68	first strand
Strand 2	F	74	79	anti-parallel

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There are 4 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	234	238	first strand
Strand 2	F	241	246	anti-parallel
Strand 3	F	144	149	anti-parallel
Strand 4	F	276	279	anti-parallel

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There are 2 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	63	68	first strand
Strand 2	H	74	79	anti-parallel

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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	H	234	238	first strand
Strand 2	H	241	246	anti-parallel
Strand 3	H	144	149	anti-parallel
Strand 4	H	276	279	anti-parallel

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There are 2 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	63	68	first strand
Strand 2	K	74	79	anti-parallel

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There are 4 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	234	238	first strand
Strand 2	K	241	246	anti-parallel
Strand 3	K	144	149	anti-parallel
Strand 4	K	276	279	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: 9VDP

Analysis of interatomic Contacts of Structural Units in PDB entry:
9VDP