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


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).
For CSU analysis of other PDB entry

This page provides analyses of contacts formed by:
For analysis of ligand-protein contacts, use: 3D structure can be seen in additional window with STING software for 9VMD entry

There are 4 chains in PDB entry 9VMD (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
O
 PRO 2LYS 181
P
 GLN 3GLY 129
Q
 SER 1GLY 107
R
 G 1 C 83
Residue contacts

1. List of contacts for up to 10 consecutive residues:
Chain ID from residue number to residue number


2. Detailed analyses of contacts for any single residue:
Residue number chain ID
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There are 6 helices in PDB entry 9VMD. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
AA1
O
3 14Right-handed alpha
Helix 2
AA2
O
38 42Right-handed 310
Helix 3
AA3
O
86 90Right-handed 310
Helix 4
AA4
P
89 93Right-handed 310
Helix 5
AA5
Q
26 30Right-handed 310
Helix 6
AA6
Q
78 82Right-handed 310
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There are 8 sheets in PDB entry 9VMD. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8,

There are 7 strands in AA1 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
O
15 20first strand
Strand 2
O
23 31anti-parallel
Strand 3
O
34 37anti-parallel
Strand 4
O
68 77anti-parallel
Strand 5
O
52 64anti-parallel
Strand 6
O
46 49anti-parallel
Strand 7
O
15 20anti-parallel
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There are 8 strands in AA2 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
O
119 120first strand
Strand 2
O
134 138anti-parallel
Strand 3
O
167 172anti-parallel
Strand 4
O
155 163anti-parallel
Strand 5
O
149 152anti-parallel
Strand 6
O
100 105anti-parallel
Strand 7
O
108 113anti-parallel
Strand 8
P
105 107anti-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
O
123 126first strand
Strand 2
O
129 132anti-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
P
5 10first strand
Strand 2
P
20 27anti-parallel
Strand 3
P
80 85anti-parallel
Strand 4
P
70 75anti-parallel
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There are 6 strands in AA5 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
P
12 14first strand
Strand 2
P
122 126parallel
Strand 3
P
94 99anti-parallel
Strand 4
P
36 41anti-parallel
Strand 5
P
47 53anti-parallel
Strand 6
P
60 62anti-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
Q
4 5first strand
Strand 2
Q
18 24anti-parallel
Strand 3
Q
69 74anti-parallel
Strand 4
Q
61 66anti-parallel
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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
Q
9 11first strand
Strand 2
Q
101 104parallel
Strand 3
Q
84 91anti-parallel
Strand 4
Q
31 37anti-parallel
Strand 5
Q
44 47anti-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
Q
9 11first strand
Strand 2
Q
101 104parallel
Strand 3
Q
84 91anti-parallel
Strand 4
Q
94 97anti-parallel
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