Contacts of the helix formed by residues 1689 - 1699 (chain A) 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 THR1689 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1646A GLY* 4.1 0.2 - - - -
1647A SER* 3.4 13.0 + - - +
1648A ASP* 3.4 26.2 - - + +
1654A ILE* 4.3 0.2 - - - -
1687A LYS 5.2 0.4 - - - +
1688A ALA* 1.3 76.5 - - - +
1690A HIS* 1.3 66.7 + - - +
1691A ASP* 3.7 5.9 + - - +
1692A GLU* 3.0 45.1 + - - +
1693A ALA* 3.0 20.8 + - - +
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Residues in contact with HIS1690 (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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1643A ILE* 3.4 34.5 - - + +
1644A VAL* 4.0 4.8 + - - -
1645A GLY 2.8 30.6 + - - +
1646A GLY* 3.8 1.6 - - - -
1648A ASP* 3.0 17.0 + - - +
1649A THR* 5.1 1.6 - - + -
1654A ILE* 4.1 5.8 - - - +
1689A THR* 1.3 72.7 - - - +
1691A ASP* 1.3 66.6 + - - +
1693A ALA* 3.1 2.4 + - - +
1694A ILE* 3.0 33.8 + - + +
1716B LYS* 3.6 51.5 - - + +
1718B THR* 2.7 30.2 + - - -
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Residues in contact with ASP1691 (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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1648A ASP* 5.2 0.4 + - - -
1689A THR* 3.3 6.1 + - - +
1690A HIS* 1.3 80.8 - - - +
1692A GLU* 1.3 65.1 + - + +
1694A ILE* 3.9 6.7 - - - +
1695A ASN* 3.0 34.3 + - - +
1716B LYS* 2.8 37.2 + - - +
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Residues in contact with GLU1692 (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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1685A LEU* 5.8 0.2 - - + -
1687A LYS 4.4 2.3 - - - +
1688A ALA* 3.5 13.6 - - + -
1689A THR* 3.0 46.5 + - - +
1691A ASP* 1.3 77.7 - - + +
1693A ALA* 1.3 62.0 + - - +
1695A ASN* 3.3 5.8 + - - +
1696A VAL* 3.1 29.1 + - + +
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Residues in contact with ALA1693 (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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1654A ILE* 3.4 44.0 - - + -
1685A LEU* 4.0 22.0 - - + -
1688A ALA* 4.2 2.8 - - + +
1689A THR 3.0 6.3 + - - +
1690A HIS 3.5 4.0 - - - +
1692A GLU* 1.3 76.3 - - - +
1694A ILE* 1.3 61.7 + - + +
1696A VAL* 3.3 2.1 + - - +
1697A LEU* 2.8 36.9 + - + +
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Residues in contact with ILE1694 (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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1643A ILE* 4.3 11.4 - - + -
1690A HIS* 3.0 38.5 + - + +
1691A ASP* 3.9 7.9 - - - +
1693A ALA* 1.3 76.7 - - + +
1695A ASN* 1.3 64.7 + - - +
1697A LEU* 3.7 3.7 - - + +
1698A ARG* 2.8 42.4 + - - +
1718B THR* 3.6 37.9 - - + +
1720B LEU* 3.7 28.5 - - + -
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Residues in contact with ASN1695 (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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1691A ASP* 3.0 28.3 + - - +
1692A GLU* 3.7 6.1 - - - +
1693A ALA 3.2 0.2 - - - -
1694A ILE* 1.3 81.6 - - - +
1696A VAL* 1.3 64.0 + - + +
1698A ARG* 3.3 8.6 + - - +
1699A GLN* 3.0 49.6 + - - +
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Residues in contact with VAL1696 (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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1680A VAL* 3.0 35.9 - - + -
1683A ILE* 4.0 35.2 - - + +
1685A LEU* 4.0 17.9 - - + -
1692A GLU* 3.1 15.7 + - + +
1693A ALA 3.3 7.2 + - - +
1695A ASN* 1.3 76.3 - - + +
1697A LEU* 1.3 60.3 + - - +
1699A GLN* 3.2 19.0 + - - +
1700A THR* 3.4 12.5 + - + +
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Residues in contact with LEU1697 (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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1634A LYS* 4.6 1.7 + - - -
1639A LEU* 4.3 25.0 - - + +
1643A ILE* 4.5 5.2 - - + -
1654A ILE* 4.8 2.0 - - + -
1677A ILE* 4.2 22.4 - - + -
1680A VAL* 4.1 27.1 - - + -
1685A LEU* 4.5 12.8 - - + -
1693A ALA* 2.8 32.1 + - + +
1694A ILE* 3.9 2.2 - - + +
1696A VAL* 1.3 73.4 - - - +
1698A ARG* 1.3 58.6 + - - +
1700A THR* 2.8 27.8 + - + -
1706A LEU* 4.4 8.1 - - + -
1720B LEU* 3.6 37.9 - - + +
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Residues in contact with ARG1698 (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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1634A LYS* 4.7 3.6 + - - -
1694A ILE* 2.8 32.4 + - + +
1695A ASN* 3.5 11.2 - - - +
1696A VAL 3.3 0.2 - - - -
1697A LEU* 1.3 79.4 - - - +
1699A GLN* 1.3 62.4 + - + +
1700A THR* 3.3 7.3 + - - +
1720B LEU* 4.3 10.9 - - + +
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Residues in contact with GLN1699 (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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1695A ASN* 3.0 43.7 + - - +
1696A VAL* 3.2 11.2 + - - +
1697A LEU 3.2 0.8 - - - -
1698A ARG* 1.3 80.4 - - + +
1700A THR* 1.3 62.6 + - - +
1701A PRO* 4.4 1.6 - - - +
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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