Contacts of the helix formed by residues 1663 - 1669 (chain B) in PDB entry 2OPG
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 GLY1663 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1637B THR* 3.5 10.5 - - - -
1638B GLY 3.7 5.8 - - - -
1639B LEU 3.9 7.6 - - - -
1640B GLY* 4.3 9.4 - - - -
1660B TYR* 3.8 5.4 + - - +
1661B GLU 3.3 2.8 + - - -
1662B GLU* 1.3 77.7 - - - +
1664B ALA* 1.3 66.0 + - - -
1665B ALA 3.3 2.6 + - - -
1666B CYS* 3.5 4.8 + - - +
1667B LYS* 3.2 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1664 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1632B ILE* 4.3 9.0 - - + +
1633B SER 3.2 27.6 - - - +
1634B LYS* 3.5 12.1 - - - +
1635B GLY* 5.4 0.7 - - - -
1637B THR* 3.8 2.7 + - - +
1638B GLY 2.9 21.9 + - - +
1639B LEU* 3.5 3.5 + - - -
1663B GLY* 1.3 73.6 - - - -
1665B ALA* 1.3 63.4 + - - +
1667B LYS* 3.4 10.3 + - - +
1668B ASP* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1665 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1632B ILE* 4.1 10.9 - - + +
1639B LEU 3.0 18.7 + - - +
1641B LEU* 3.5 26.5 - - + -
1659B VAL* 3.9 9.4 - - + +
1664B ALA* 1.3 79.2 - - - +
1666B CYS* 1.3 57.7 + - - +
1668B ASP* 3.4 4.5 + - - +
1669B GLY* 2.9 26.9 + - - -
1670B ARG 4.3 1.0 + - - -
1671B LEU* 3.8 23.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1666 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1659B VAL* 3.6 13.4 - - + +
1660B TYR 3.3 22.0 + - - +
1661B GLU* 3.8 39.3 - - - +
1663B GLY 3.5 8.1 + - - +
1664B ALA 3.4 0.2 - - - -
1665B ALA* 1.3 78.5 - - - +
1667B LYS* 1.3 65.3 + - - +
1669B GLY* 3.2 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1667 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1637B THR* 3.3 22.8 + - - +
1661B GLU 5.4 2.9 - - - +
1662B GLU 3.2 26.9 + - - -
1663B GLY 3.2 12.6 + - - +
1664B ALA* 3.7 10.9 - - - +
1665B ALA 3.3 0.2 - - - -
1666B CYS* 1.3 79.6 - - + +
1668B ASP* 1.3 61.9 + - - +
1669B GLY* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1668 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1630B ILE* 3.9 6.1 - - - +
1631B GLU 4.2 0.9 - - - +
1632B ILE* 3.7 20.7 - - + +
1664B ALA 3.0 17.1 + - - +
1665B ALA* 3.7 3.8 - - - +
1667B LYS* 1.3 80.4 - - - +
1669B GLY* 1.3 57.5 + - - +
1670B ARG* 2.8 62.2 + - - +
1671B LEU* 4.5 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1669 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1665B ALA 2.9 11.2 + - - -
1666B CYS* 3.2 13.5 + - - -
1667B LYS 4.6 0.2 - - - -
1668B ASP* 1.3 75.5 - - - +
1670B ARG* 1.3 61.5 + - - +
1671B LEU 3.6 5.9 - - - +
1672B TRP* 4.2 10.7 + - - -
----------------------------------------------------------
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