Contacts of the strand formed by residues 1676 - 1680 (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 GLN1676 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A NA 3.0 20.6 - - - -
1653A ALA* 3.5 24.1 - - + +
1654A ILE 3.2 13.5 - - - +
1655A ILE* 3.7 10.3 - - + +
1674A GLY 3.5 1.0 + - - +
1675A ASP* 1.3 73.1 - - - +
1677A ILE* 1.3 65.8 + - - +
1678A LEU* 3.4 23.4 + - + +
1686A ARG* 4.3 10.7 + - - +
1708A LEU* 3.1 8.9 - - - +
1709A TYR* 2.9 51.2 + - + +
1650B LEU* 6.0 0.8 - - + +
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Residues in contact with ILE1677 (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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1A NA 2.8 25.6 - - - -
1639A LEU* 6.1 0.7 - - + -
1641A LEU* 5.2 3.8 - - + -
1643A ILE* 3.8 28.0 - - + -
1654A ILE* 2.9 24.6 + - + +
1656A ILE* 4.4 15.0 - - + -
1676A GLN* 1.3 71.7 - - - +
1678A LEU* 1.3 57.4 + - - +
1679A GLU 3.8 19.5 - - - +
1680A VAL* 4.8 1.3 - - + -
1685A LEU* 3.9 24.1 - - + +
1697A LEU* 4.2 18.4 - - + -
1706A LEU* 4.1 19.3 - - + -
1707A THR 3.8 4.3 - - - +
1708A LEU* 4.0 14.8 - - + -
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Residues in contact with LEU1678 (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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1627A GLU* 4.3 13.7 - - + +
1676A GLN* 3.6 31.6 - - - +
1677A ILE* 1.3 73.4 - - - +
1679A GLU* 1.3 63.7 + - + +
1684A ASP* 3.4 2.8 - - - +
1685A LEU* 2.8 23.6 + - - -
1686A ARG* 3.4 46.5 + - + +
1707A THR* 2.8 28.4 + - + +
1708A LEU 4.2 4.9 - - - +
1709A TYR* 4.0 29.8 - - + +
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Residues in contact with GLU1679 (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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1677A ILE* 3.6 8.3 - - - +
1678A LEU* 1.3 78.8 - - + +
1680A VAL* 1.3 61.3 + - - +
1681A ASN 4.3 0.2 - - - -
1682A GLY* 4.6 14.3 + - - +
1683A ILE 3.1 16.8 - - - +
1684A ASP* 4.4 4.0 - - - -
1685A LEU* 4.2 1.3 - - - +
1686A ARG* 2.9 45.3 + - - +
1705A ARG 4.5 0.2 - - - -
1706A LEU* 3.6 4.0 - - - -
1707A THR* 2.9 46.2 + - - +
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Residues in contact with VAL1680 (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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1677A ILE* 4.8 2.0 - - + -
1679A GLU* 1.3 75.3 - - - +
1681A ASN* 1.3 88.3 + - - +
1682A GLY 3.2 1.1 - - - -
1683A ILE* 2.9 29.8 + - + +
1685A LEU* 4.1 11.2 - - + -
1696A VAL* 3.0 35.0 - - + -
1697A LEU* 4.1 8.5 - - + -
1700A THR* 3.7 14.6 - - + -
1704A VAL* 3.5 21.5 - - + -
1705A ARG 3.5 2.5 - - - +
1706A LEU* 3.8 11.4 - - + -
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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