Contacts of the helix formed by residues 1684 - 1689 (chain A) in PDB entry 2VK7
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 ASN1684 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1245A GLY 2.8 25.7 + - - -
1246A ALA* 3.7 0.2 - - - -
1247A VAL* 2.9 34.6 + - + +
1665A ASN* 3.2 28.9 - - - +
1683A MET* 1.3 76.6 - - - +
1685A LEU* 1.3 67.2 + - - +
1686A LYS* 3.8 14.6 - - - +
1687A TYR* 2.9 25.3 + - - +
1688A LEU* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1685 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1595A TYR* 3.5 48.5 - - + +
1597A GLN* 6.0 0.4 - - + -
1598A LYS 5.6 1.3 - - - +
1599A VAL* 4.2 11.2 - - + -
1606A ILE* 4.9 4.0 - - + -
1622A ILE* 4.2 17.3 - - + -
1664A GLY 4.8 2.2 + - - +
1665A ASN* 4.6 2.6 + - - +
1666A ILE* 4.6 7.2 - - + -
1684A ASN* 1.3 72.4 - - - +
1686A LYS* 1.3 62.5 + - + +
1688A LEU* 3.1 14.4 + - + +
1689A GLU* 2.8 56.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1686 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1243A VAL* 4.2 8.5 - - + +
1244A GLU 4.4 5.2 + - - +
1245A GLY* 3.8 29.7 - - - +
1246A ALA* 4.3 7.0 - - + +
1684A ASN* 3.2 14.7 + - + +
1685A LEU* 1.3 78.7 - - + +
1687A TYR* 1.3 61.9 + - - +
1689A GLU* 3.5 6.6 + - - +
1690A SER* 3.2 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1687 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1246A ALA* 3.9 15.8 - - + +
1247A VAL 3.3 24.7 - - - +
1248A LYS* 3.4 40.1 + - + +
1646A LYS* 3.1 36.3 - - + +
1647A LEU 3.3 21.7 + - - -
1648A VAL* 3.8 2.2 - - + +
1683A MET* 3.8 38.4 - - + -
1684A ASN* 2.9 13.5 + - - +
1686A LYS* 1.3 76.4 - - - +
1688A LEU* 1.3 66.8 + - + +
1690A SER* 2.7 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1688 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1606A ILE* 4.8 1.8 - - + -
1620A VAL* 3.7 38.4 - - + +
1622A ILE* 3.9 21.3 - - + -
1644A TYR* 3.7 15.2 - - - +
1645A ASN 4.3 4.9 + - - +
1646A LYS* 4.0 25.8 - - + +
1666A ILE* 4.0 29.2 - - + -
1683A MET* 3.9 23.6 - - + -
1684A ASN 3.1 14.0 + - - +
1685A LEU* 3.1 15.9 + - + +
1687A TYR* 1.3 84.6 - - + +
1689A GLU* 1.3 60.4 + - - +
1690A SER 3.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1689 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1599A VAL* 3.7 19.0 - - - +
1600A ASP* 5.2 2.2 - - - +
1622A ILE* 3.9 6.1 - - + +
1644A TYR* 3.7 53.2 + - + -
1685A LEU* 2.8 41.9 + - - +
1686A LYS* 3.8 5.1 - - - +
1687A TYR 3.1 0.2 - - - -
1688A LEU* 1.3 78.2 - - - +
1690A SER* 1.3 61.6 + - - +
1691A GLY 3.3 2.9 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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