Contacts of the helix formed by residues 1663 - 1669 (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 GLY1663 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1637A THR* 4.3 15.5 - - - -
1640A GLY* 4.4 10.1 - - - -
1660A TYR* 3.1 15.8 + - - -
1661A GLU 3.1 2.8 + - - -
1662A GLU* 1.3 78.9 - - - +
1664A ALA* 1.3 66.2 + - - -
1665A ALA 3.3 2.5 - - - -
1666A CYS 3.3 3.4 + - - -
1667A LYS* 3.1 26.2 + - - +
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Residues in contact with ALA1664 (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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1632A ILE* 3.8 12.1 - - + +
1633A SER 3.3 25.6 - - - +
1635A GLY* 3.9 9.0 - - - +
1637A THR* 5.0 1.0 + - - -
1638A GLY 3.7 19.6 + - - +
1639A LEU 3.8 5.9 + - - +
1663A GLY* 1.3 72.4 - - - -
1665A ALA* 1.3 63.2 + - - +
1667A LYS* 3.4 7.6 + - - +
1668A ASP* 3.0 24.3 + - - +
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Residues in contact with ALA1665 (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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1632A ILE* 4.4 12.7 - - + +
1639A LEU* 2.9 20.3 + - + +
1640A GLY* 4.2 5.1 - - - +
1641A LEU* 4.4 7.4 - - + -
1659A VAL* 3.7 18.7 - - + +
1663A GLY 3.3 0.2 - - - -
1664A ALA* 1.3 76.1 - - - +
1666A CYS* 1.3 62.1 + - - +
1668A ASP* 3.5 3.5 + - - +
1669A GLY* 3.2 17.7 + - - -
1670A ARG 4.5 2.4 + - - -
1671A LEU* 3.8 32.2 + - + +
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Residues in contact with CYS1666 (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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1659A VAL* 3.4 15.6 - - + +
1660A TYR 3.2 22.6 + - - +
1661A GLU* 4.0 13.0 - - - -
1662A GLU* 3.9 16.6 - - - +
1663A GLY 3.3 7.2 + - - +
1665A ALA* 1.3 79.6 - - - +
1667A LYS* 1.3 65.1 + - - +
1669A GLY* 3.0 16.4 + - - -
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Residues in contact with LYS1667 (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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1662A GLU* 3.5 40.2 - - - +
1663A GLY 3.1 17.1 + - - +
1664A ALA* 3.9 6.5 - - - +
1665A ALA 3.3 0.2 - - - -
1666A CYS* 1.3 79.0 - - - +
1668A ASP* 1.3 63.9 + - - +
1669A GLY* 3.4 0.7 + - - -
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Residues in contact with ASP1668 (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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1630A ILE* 4.0 1.7 - - - +
1631A GLU 4.4 2.3 - - - +
1632A ILE* 3.4 34.7 - - + +
1664A ALA 3.0 12.5 + - - +
1665A ALA 3.8 2.2 - - - +
1667A LYS* 1.3 77.6 - - - +
1669A GLY* 1.3 55.1 + - - +
1670A ARG* 2.9 61.5 + - - +
1671A LEU 4.5 0.7 + - - -
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Residues in contact with GLY1669 (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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1665A ALA 3.2 7.3 + - - -
1666A CYS* 3.0 17.7 + - - -
1667A LYS 4.3 0.7 - - - -
1668A ASP* 1.3 75.6 - - - +
1670A ARG* 1.3 61.6 + - - +
1671A LEU 3.7 5.6 - - - +
1672A TRP* 4.4 10.6 + - - -
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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