Contacts of the helix formed by residues 92 - 105 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A GLY 3.1 4.7 + - - +
91A ALA* 1.3 76.6 - - - +
93A ILE* 1.3 64.8 + - - +
94A GLN* 3.3 19.3 - - - +
95A GLY* 3.0 12.5 + - - -
96A LYS* 3.1 19.4 + - - +
119A MET* 3.2 30.5 - - - +
120A THR* 2.8 46.6 + - - +
60B TYR* 4.1 13.5 - - - +
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Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ASP* 1.3 72.8 - - + +
94A GLN* 1.3 80.2 + - - +
96A LYS* 3.3 3.3 + - - -
97A TYR* 2.8 28.8 + - - +
17B LEU* 3.8 30.5 - - + -
60B TYR* 3.7 34.5 - - + -
93B ILE* 4.2 17.0 - - + +
94B GLN* 4.0 21.3 - - + +
97B TYR* 3.9 35.4 - - + -
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Residues in contact with GLN 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 3.7 31.7 - - + +
92A ASP* 3.3 26.7 - - - +
93A ILE* 1.3 87.1 - - - +
95A GLY* 1.3 61.9 - - - +
97A TYR* 3.3 9.1 + - - +
98A ILE* 3.0 29.7 + - - +
119A MET* 5.4 0.7 - - - +
120A THR* 4.1 16.8 - - + +
93B ILE* 4.1 21.2 - - + +
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Residues in contact with GLY 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ILE* 3.3 34.0 - - - +
90A GLY 4.1 1.3 - - - -
92A ASP* 3.0 14.5 + - - -
94A GLN* 1.3 76.3 - - - +
96A LYS* 1.3 57.9 + - - +
98A ILE* 3.3 3.3 + - - +
99A LYS* 2.9 23.6 + - - +
120A THR* 3.3 17.7 + - - -
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Residues in contact with LYS 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ILE* 4.4 1.3 - - - +
92A ASP 3.1 13.6 + - - +
93A ILE* 3.8 10.1 - - - +
95A GLY* 1.3 74.4 - - - +
97A TYR* 1.3 58.8 + - - +
99A LYS* 3.3 12.0 + - + +
100A ASN* 2.9 44.7 + - - +
59B ASN* 2.8 29.4 + - - +
60B TYR* 3.2 22.9 + - + +
61B ILE* 3.5 14.8 - - - +
97B TYR* 3.3 27.4 - - + +
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Residues in contact with TYR 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 3.7 24.5 - - + -
61A ILE* 3.5 6.2 - - - +
62A ALA* 3.0 42.6 + - + +
93A ILE 2.8 18.0 + - - +
94A GLN* 3.6 7.2 - - - +
96A LYS* 1.3 77.6 - - - +
98A ILE* 1.3 65.2 + - + +
100A ASN* 3.3 3.6 + - - +
101A ASP* 3.0 26.0 + - - +
93B ILE* 4.4 12.1 - - + -
96B LYS* 3.2 35.9 + - + -
97B TYR* 3.7 25.0 - + + -
100B ASN* 3.8 38.6 - - + -
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Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PRO* 4.2 13.5 - - + -
16A LEU 3.7 34.3 - - - +
17A LEU* 4.0 5.6 - - + +
62A ALA* 4.2 15.0 - - + -
67A LEU* 3.9 27.4 - - + -
89A ILE* 4.8 1.8 - - + -
94A GLN 3.0 19.6 + - - +
95A GLY* 3.3 7.2 + - - +
97A TYR* 1.3 85.9 - - + +
99A LYS* 1.3 62.3 + - - +
101A ASP* 3.3 8.6 + - - +
102A CYS* 3.2 21.5 + - - -
111A PHE* 4.3 9.0 - - + -
120A THR* 3.8 20.6 - - + -
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Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE* 4.3 12.5 - - + +
95A GLY 2.9 16.0 + - - +
96A LYS* 3.7 12.0 - - + +
98A ILE* 1.3 78.0 - - - +
100A ASN* 1.3 67.7 + - - +
102A CYS* 3.2 5.6 + - - +
103A SER* 3.1 25.8 + - - +
109A THR* 4.5 6.5 + - - +
111A PHE* 3.8 40.6 - - + -
113A ILE* 4.5 14.1 - - - +
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Residues in contact with ASN 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LYS* 2.9 26.3 + - - +
97A TYR* 3.8 4.7 - - - +
99A LYS* 1.3 78.8 - - - +
101A ASP* 1.3 59.6 + - - +
103A SER* 3.4 8.8 + - - -
104A ALA* 3.0 28.4 + - - +
97B TYR* 3.0 43.0 + - + -
100B ASN* 3.9 13.4 - - - +
101B ASP* 4.3 13.0 + - - +
104B ALA* 4.9 2.9 - - - +
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Residues in contact with ASP 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ALA* 3.9 12.1 - - + +
71A LYS* 3.0 33.4 + - - +
97A TYR* 3.0 19.4 + - + +
98A ILE* 3.4 13.2 - - - +
99A LYS 3.2 0.2 - - - -
100A ASN* 1.3 76.2 - - - +
102A CYS* 1.3 63.5 + - - +
104A ALA* 3.4 7.2 + - - +
105A LEU* 3.4 26.6 + - - +
100B ASN* 3.1 27.5 + - - +
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Residues in contact with CYS 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 3.8 34.3 - - - -
71A LYS* 5.5 3.6 - - - -
98A ILE 3.2 15.3 + - - -
99A LYS 3.2 7.8 + - - +
101A ASP* 1.3 78.0 - - - +
103A SER* 1.3 64.7 + - - +
105A LEU* 3.0 15.9 + - - -
107A LEU* 3.1 31.8 + - + +
109A THR* 3.6 31.4 - - + +
111A PHE* 4.0 11.7 - - - -
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Residues in contact with SER 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LYS* 3.1 17.2 + - - +
100A ASN* 3.8 10.8 + - - -
101A ASP 3.4 0.2 - - - -
102A CYS* 1.3 78.2 - - - +
104A ALA* 1.3 62.7 + - - +
106A ASP* 3.1 19.2 + - - +
107A LEU 4.5 7.4 + - - +
109A THR* 5.2 3.8 + - - -
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Residues in contact with ALA 104 (chain A).
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 3.0 18.3 + - - +
101A ASP* 3.5 10.8 - - - +
102A CYS 3.2 0.2 - - - -
103A SER* 1.3 77.0 - - - +
105A LEU* 1.3 61.9 + - + +
106A ASP* 3.3 5.5 + - - +
100B ASN* 5.2 4.7 - - - +
103B SER* 5.5 0.9 - - - -
104B ALA* 3.7 33.7 - - + +
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LYS* 3.7 42.2 - - + +
74A GLN* 3.2 19.5 + - + +
75A TRP* 3.9 32.3 - - + -
101A ASP* 3.4 20.1 + - - +
102A CYS* 3.0 11.1 + - - +
104A ALA* 1.3 83.2 - - + +
106A ASP* 1.3 69.9 + - - +
107A LEU* 4.4 5.6 - - + +
340A LEU* 4.3 16.2 - - + +
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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