Contacts of the helix formed by residues 92 - 105 (chain B) in PDB entry 3VAS
Residue contacts within the protein 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). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 92 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A TYR* 3.9 15.7 - - - +
90B GLY 3.0 2.8 + - - +
91B ALA* 1.3 76.2 - - - +
93B ILE* 1.3 64.6 + - + +
94B GLN* 3.5 17.6 - - - +
95B GLY* 2.7 20.6 + - - -
96B LYS* 3.1 21.3 + - - +
119B MET* 3.2 28.3 - - - +
120B THR* 2.6 48.9 + - - +
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.0 30.5 - - + -
60A TYR* 3.9 29.9 - - + -
93A ILE* 4.2 19.1 - - + +
94A GLN* 4.1 28.5 - - + +
97A TYR* 4.4 15.7 - - + -
92B ASP* 1.3 73.7 - - + +
94B GLN* 1.3 85.5 + - - +
96B LYS* 3.3 7.5 + - + -
97B TYR* 2.9 27.9 + - - +
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Residues in contact with GLN 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ILE* 4.0 20.1 - - + +
17B LEU* 3.6 30.2 - - + +
53B GLN* 6.0 2.0 - - - +
60B TYR* 6.1 1.6 - - - -
92B ASP* 3.2 22.8 - - - +
93B ILE* 1.3 96.0 - - - +
95B GLY* 1.3 61.1 + - - +
97B TYR* 3.3 4.3 + - - +
98B ILE* 3.1 26.9 + - - +
119B MET* 5.4 1.2 - - - +
120B THR* 3.9 20.4 - - + +
122B LYS* 6.3 2.2 - - + -
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Residues in contact with GLY 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ILE* 3.6 29.9 - - - +
90B GLY 4.0 2.9 - - - -
92B ASP* 2.7 17.0 + - - -
94B GLN* 1.3 70.8 - - - +
96B LYS* 1.3 59.5 + - - +
98B ILE* 3.2 2.9 + - - +
99B LYS* 3.0 29.6 + - - +
120B THR* 3.2 16.5 + - - -
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Residues in contact with LYS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ASN* 4.7 6.1 - - - -
60A TYR* 3.1 32.5 + - + +
61A ILE* 4.7 8.0 - - - +
97A TYR* 3.2 36.5 + - + -
92B ASP 3.1 13.2 + - - +
93B ILE* 3.6 15.9 - - + +
94B GLN 3.3 0.2 - - - -
95B GLY* 1.3 75.5 - - - +
97B TYR* 1.3 58.1 + - - +
99B LYS* 3.8 29.2 - - + +
100B ASN* 3.0 37.9 + - - +
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Residues in contact with TYR 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 3.9 20.9 - - + -
96A LYS* 3.3 25.9 - - + -
97A TYR* 3.7 32.7 - + + -
100A ASN* 3.0 32.4 + - - -
17B LEU* 3.7 19.3 - - + -
60B TYR* 3.2 22.7 + - + -
61B ILE* 4.6 1.7 - - - +
62B ALA* 3.8 25.5 + - + -
93B ILE 2.9 17.7 + - - +
94B GLN 3.4 5.4 - - - +
96B LYS* 1.3 78.2 - - - +
98B ILE* 1.3 63.9 + - - +
100B ASN* 3.5 2.8 + - - +
101B ASP* 3.1 26.5 + - - +
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B PRO* 4.0 7.9 - - + +
16B LEU 3.6 36.3 - - - +
17B LEU* 3.8 8.7 - - + +
62B ALA* 4.0 20.0 - - + -
67B LEU* 3.9 27.4 - - + -
89B ILE* 4.4 4.7 - - + -
94B GLN 3.1 9.6 + - - +
95B GLY* 3.2 6.9 + - - +
97B TYR* 1.3 75.0 - - - +
99B LYS* 1.3 64.8 + - - +
101B ASP* 3.1 16.4 + - - +
102B CYS* 3.2 13.3 + - - -
111B PHE* 4.2 14.8 - - + -
120B THR* 3.9 22.4 - - + -
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Residues in contact with LYS 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 3.8 21.9 - - + +
95B GLY 3.0 15.9 + - - +
96B LYS* 3.8 29.0 - - + +
97B TYR 3.4 0.2 - - - -
98B ILE* 1.3 76.1 - - - +
100B ASN* 1.3 62.5 + - - +
102B CYS* 3.4 4.9 + - - +
103B SER* 3.3 27.2 + - - +
109B THR* 4.8 5.6 + - - +
111B PHE* 3.9 30.9 - - + -
113B ILE* 4.5 12.8 - - - +
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Residues in contact with ASN 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A TYR* 3.8 24.6 + - + -
100A ASN* 3.9 15.2 - - - +
101A ASP* 3.1 44.4 + - - +
104A ALA* 5.5 3.4 - - - +
96B LYS* 3.0 25.0 + - - +
97B TYR* 3.8 4.8 - - + +
99B LYS* 1.3 74.6 - - - +
101B ASP* 1.3 65.8 + - - +
103B SER* 3.4 9.5 + - - -
104B ALA* 3.1 22.9 + - - +
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Residues in contact with ASP 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ASN* 4.3 18.0 + - - +
62B ALA* 3.8 19.1 + - + +
71B LYS* 3.4 25.5 + - - +
97B TYR* 3.1 20.0 + - + +
98B ILE 3.1 11.5 + - - +
100B ASN* 1.3 77.9 + - - +
102B CYS* 1.3 64.2 + - - +
104B ALA* 3.6 7.0 + - - +
105B LEU* 3.5 30.4 + - - +
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Residues in contact with CYS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ALA* 6.3 0.2 - - - -
67B LEU* 3.8 34.5 - - - -
71B LYS* 5.9 2.2 - - - -
98B ILE 3.2 18.0 + - - -
99B LYS 3.7 6.5 - - - +
100B ASN 3.2 0.4 - - - -
101B ASP* 1.3 76.4 - - - +
103B SER* 1.3 64.3 + - - +
105B LEU* 3.0 15.8 + - - -
107B LEU* 3.1 35.8 + - + +
109B THR* 3.7 21.1 - - + +
111B PHE* 3.9 19.1 - - + -
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Residues in contact with SER 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ALA* 5.5 0.9 - - - -
99B LYS* 3.3 15.2 + - - +
100B ASN* 3.4 13.6 + - - -
102B CYS* 1.3 78.9 - - - +
104B ALA* 1.3 56.6 + - - +
106B ASP* 3.0 25.1 + - - +
107B LEU 4.4 7.5 + - - +
109B THR* 5.5 2.6 + - - -
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ASN* 4.9 6.1 - - + +
104A ALA* 3.7 34.0 - - + +
100B ASN* 3.1 14.9 + - - +
101B ASP* 3.8 8.7 - - - +
102B CYS 3.2 0.2 - - - -
103B SER* 1.3 78.2 - - - +
105B LEU* 1.3 63.3 + - + +
106B ASP* 3.2 5.9 + - - +
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LYS* 3.8 42.8 - - + +
74B GLN* 3.2 23.3 + - + +
75B TRP* 4.0 29.9 + - + -
101B ASP* 3.5 22.0 + - - +
102B CYS* 3.0 10.2 + - - +
104B ALA* 1.3 79.7 - - + +
106B ASP* 1.3 71.6 + - - +
107B LEU* 3.2 4.0 - - + +
340B LEU* 4.2 18.4 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il