Contacts of the strand formed by residues 1736 - 1744 (chain A) in PDB entry 4PY4
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 LYS1736 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1643A PHE* 3.8 16.4 - - + -
1723A ALA 2.7 29.3 + - - -
1724A ASN 3.9 1.4 + - - -
1725A ASP* 3.0 22.1 + - - +
1728A SER* 2.9 38.4 + - - +
1729A ARG 4.6 0.7 - - - -
1730A PRO* 3.7 14.6 - - + -
1734A GLY 4.2 4.7 - - - +
1735A ARG* 1.3 76.3 - - - +
1737A HIS* 1.3 66.2 + - - +
1798A THR* 3.4 5.9 - - - +
1799A PHE* 2.6 71.9 + - + +
1800A ARG* 4.8 3.8 - - - -
1801A LYS* 4.8 10.1 - - + +
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Residues in contact with HIS1737 (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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1683A GLY* 3.3 2.8 - - - -
1684A THR* 2.9 40.0 + - + +
1686A ALA* 3.6 34.9 - - + +
1689A VAL* 4.3 18.4 - - + +
1728A SER* 3.4 6.7 - - - -
1729A ARG 4.8 2.5 - - - -
1731A ASP* 3.8 13.0 + - - -
1735A ARG* 3.8 14.4 + - + -
1736A LYS* 1.3 81.6 + - - +
1738A VAL* 1.3 62.1 + - - +
1739A TYR 4.3 0.2 - - - -
1796A LEU* 3.9 17.9 - - + +
1797A ILE 3.6 2.7 - - - -
1798A THR* 3.8 30.5 + - + +
1690B PRO* 6.3 4.0 - - + -
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Residues in contact with VAL1738 (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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1636A PHE* 4.7 10.3 - - + -
1681A PHE* 3.6 30.7 - - + -
1682A HIS 3.5 7.2 - - - +
1683A GLY* 3.8 3.8 - - - -
1719A ALA* 5.1 1.6 - - + +
1722A SER* 3.7 29.4 - - - +
1723A ALA* 4.3 2.0 - - + -
1728A SER* 4.0 1.8 - - - -
1737A HIS* 1.3 77.0 - - - +
1739A TYR* 1.3 74.3 + - - +
1796A LEU* 4.0 3.1 - - - -
1797A ILE* 2.9 34.7 + - + +
1799A PHE* 3.6 29.1 - - + -
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Residues in contact with TYR1739 (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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1651A ILE* 4.0 4.5 - - + -
1680A LEU 3.7 0.3 - - - +
1681A PHE* 3.2 7.6 - - - -
1682A HIS* 2.8 39.9 + + - +
1684A THR* 3.9 25.1 - - + -
1689A VAL* 3.2 26.0 + - + +
1692A VAL* 3.5 20.7 - - + +
1693A ASN* 2.8 27.8 + - - -
1697A PHE* 4.6 5.4 - + + -
1738A VAL* 1.3 78.3 - - - +
1740A TYR* 1.3 59.4 + - - +
1741A VAL* 3.4 19.2 + - + -
1793A PRO* 3.6 29.8 - - + -
1795A TYR 3.1 20.2 - - - +
1796A LEU* 4.0 27.6 - - + -
1797A ILE* 5.2 0.2 - - - -
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Residues in contact with TYR1740 (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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1631A THR* 5.2 2.9 - - + -
1632A VAL* 3.9 26.5 - - + -
1635A LYS* 3.2 29.3 - - + +
1679A GLN* 3.3 58.9 + - + +
1680A LEU 3.9 6.3 - - - -
1681A PHE* 3.5 33.2 - + - -
1738A VAL 4.0 1.0 + - - -
1739A TYR* 1.3 70.9 - - - +
1741A VAL* 1.3 58.9 + - - +
1794A GLU* 3.6 8.7 + - - +
1795A TYR* 2.8 62.1 + + + +
1797A ILE* 4.4 6.2 - - + +
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Residues in contact with VAL1741 (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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1679A GLN* 3.2 5.8 - - - -
1680A LEU 2.6 43.0 + - - +
1682A HIS* 4.3 4.3 - - + -
1697A PHE* 4.0 18.6 - - + -
1715A PHE* 3.8 13.7 - - + -
1739A TYR* 3.4 33.7 - - + +
1740A TYR* 1.3 73.4 - - - +
1742A ARG* 1.3 65.3 + - - +
1743A VAL* 3.5 20.4 + - + +
1791A ALA* 3.7 18.6 - - + -
1792A TYR 3.4 14.8 - - - +
1793A PRO* 4.2 3.8 - - + -
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Residues in contact with ARG1742 (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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1657A TRP* 4.5 20.6 - - - -
1660A TYR* 3.4 20.2 - - + +
1677A GLU* 3.1 33.0 + - - +
1678A LYS 3.6 4.7 - - - -
1679A GLN* 3.5 38.0 + - + +
1740A TYR 4.2 0.8 + - - -
1741A VAL* 1.3 69.4 - - - +
1743A VAL* 1.3 60.0 + - - +
1791A ALA* 3.1 3.8 - - - -
1792A TYR* 2.8 43.8 + - + +
1794A GLU* 2.9 41.4 + - + +
1795A TYR* 5.4 2.4 + - - -
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Residues in contact with VAL1743 (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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1660A TYR* 4.0 3.6 + - - -
1677A GLU* 3.3 3.3 - - - -
1678A LYS 2.8 32.7 + - - +
1680A LEU* 3.7 29.2 - - + -
1715A PHE* 3.9 27.6 - - + -
1741A VAL* 3.7 25.8 - - + +
1742A ARG* 1.3 77.3 - - - +
1744A LEU* 1.3 68.8 + - - +
1745A THR* 3.3 13.0 + - + +
1772A THR* 4.9 2.0 - - + -
1783A PHE* 5.6 0.7 - - + -
1785A ALA* 4.5 11.7 - - + -
1790A GLN 3.5 9.0 - - - +
1791A ALA* 4.2 5.8 - - + +
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Residues in contact with LEU1744 (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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1660A TYR* 3.4 34.5 - - + +
1663A LYS* 3.7 31.6 - - + -
1664A LYS* 3.8 39.7 - - + +
1667A MET* 3.7 20.9 - - + +
1676A ASN* 3.3 12.3 - - + +
1677A GLU* 3.9 14.4 - - + -
1743A VAL* 1.3 70.2 - - - +
1745A THR* 1.3 60.8 + - - +
1746A GLY 3.3 2.8 + - - -
1790A GLN* 2.7 47.5 + - + +
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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