Contacts of the helix formed by residues 1712 - 1733 (chain A) in PDB entry 4J5L
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 SER1712 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1709A ASP 4.5 7.5 + - - -
1710A MET 3.3 2.2 + - - -
1711A CYS* 1.3 77.1 - - - +
1713A TRP* 1.3 65.0 + - - +
1714A SER* 3.8 7.1 + - - -
1715A LYS* 3.4 21.7 + - - +
1716A GLY 3.1 17.7 + - - -
1754A LEU* 3.6 8.9 - - - +
1786A TYR* 4.2 7.2 - - - -
1787A THR* 3.6 23.8 - - - -
1788A PRO 5.9 0.7 - - - -
1789A VAL* 6.1 2.0 - - - -
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Residues in contact with TRP1713 (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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1638A VAL 4.4 3.1 - - - -
1639A SER* 3.6 43.3 - - - -
1712A SER* 1.3 74.0 - - - +
1714A SER* 1.3 74.4 + - - +
1716A GLY* 3.3 2.6 + - - -
1717A MET* 3.1 42.0 + - + -
1754A LEU 3.6 10.5 - - - +
1755A GLN* 3.4 57.8 + - - +
1758A LYS* 5.5 0.2 - - - -
1786A TYR* 4.0 17.0 + - - +
1787A THR 4.7 1.0 + - - -
1789A VAL* 5.8 8.3 - - + -
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Residues in contact with SER1714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1633A GLU* 5.6 2.7 - - - -
1639A SER* 5.5 3.6 - - - -
1712A SER* 3.3 7.9 + - - -
1713A TRP* 1.3 92.4 - - - +
1715A LYS* 1.3 57.1 + - - +
1717A MET* 3.0 7.5 + - - +
1718A GLN* 2.9 42.0 + - - +
1789A VAL* 5.6 5.9 - - - +
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Residues in contact with LYS1715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1629A MET 5.2 0.2 - - - +
1630A LEU* 3.1 35.8 + - + +
1631A GLU* 5.3 2.4 + - - +
1633A GLU* 5.1 5.5 - - - +
1709A ASP 4.8 4.5 - - - -
1710A MET* 3.1 54.1 - - + +
1712A SER* 3.4 14.6 + - - +
1713A TRP 3.4 0.2 - - - -
1714A SER* 1.3 77.6 - - - +
1716A GLY* 1.3 58.1 + - - +
1718A GLN* 3.2 32.0 + - + +
1719A ILE* 2.9 47.4 + - + +
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Residues in contact with GLY1716 (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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1712A SER 3.1 11.0 + - - -
1713A TRP 3.3 4.7 + - - -
1715A LYS* 1.3 77.4 - - - +
1717A MET* 1.3 60.0 + - - +
1719A ILE* 3.5 0.8 + - - -
1720A ARG* 3.1 26.3 + - - +
1751A ALA* 3.6 28.0 - - - +
1754A LEU* 3.9 15.6 - - - +
1755A GLN* 4.2 6.1 - - - -
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Residues in contact with MET1717 (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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1635A ILE* 4.7 6.5 - - + -
1638A VAL* 4.3 33.9 - - + -
1713A TRP* 3.1 30.6 + - + +
1714A SER* 3.0 10.4 + - - +
1716A GLY* 1.3 76.8 - - - +
1718A GLN* 1.3 60.9 + - + +
1720A ARG* 3.4 27.6 + - + +
1721A TYR* 3.1 32.9 + - + +
1755A GLN* 3.3 29.7 - - - +
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Residues in contact with GLN1718 (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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1629A MET 5.1 2.6 - - - +
1630A LEU 4.2 1.6 - - - +
1632A HIS 3.8 6.2 - - - +
1633A GLU* 3.2 48.6 + - - +
1634A THR* 3.8 13.2 + - - +
1635A ILE* 4.0 19.1 + - + +
1636A GLN* 5.4 0.2 - - - +
1714A SER* 2.9 28.1 + - - +
1715A LYS* 3.2 39.8 + - + +
1717A MET* 1.3 73.7 - - + +
1719A ILE* 1.3 60.4 + - + +
1721A TYR* 3.2 4.4 + - - +
1722A ASN* 2.9 40.1 + - - +
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Residues in contact with ILE1719 (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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1629A MET* 4.5 4.9 - - + +
1630A LEU* 3.7 25.1 - - + -
1700A THR* 4.8 2.0 - - + -
1704A LEU* 3.8 40.2 - - + -
1715A LYS* 2.9 27.0 + - + +
1716A GLY* 3.9 6.7 - - - +
1718A GLN* 1.3 75.4 - - - +
1720A ARG* 1.3 59.1 + - - +
1722A ASN* 3.2 8.7 + - + +
1723A VAL* 2.9 32.8 + - + +
1747A LEU* 3.8 37.0 - - + -
1751A ALA* 3.8 12.6 - - + -
1754A LEU* 4.6 1.8 - - + -
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Residues in contact with ARG1720 (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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1716A GLY 3.1 15.0 + - - +
1717A MET* 3.4 33.8 - - + +
1719A ILE* 1.3 81.6 - - - +
1721A TYR* 1.3 60.6 + - - +
1723A VAL* 3.8 7.1 + - - +
1724A SER* 3.4 19.8 + - - -
1748A ILE* 5.6 8.1 - - + +
1751A ALA* 4.4 6.3 - - + -
1752A GLN* 4.1 33.6 - - - +
1755A GLN* 3.1 25.2 + - - -
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Residues in contact with TYR1721 (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 THR* 4.1 14.8 - - + -
1635A ILE* 4.1 40.0 - - + +
1661A LEU* 5.0 3.1 - - + -
1717A MET* 3.1 24.4 + - + +
1718A GLN 3.5 3.4 - - - +
1719A ILE 3.1 0.2 - - - -
1720A ARG* 1.3 77.3 - - - +
1722A ASN* 1.3 77.3 + - - +
1724A SER* 2.4 30.7 + - - -
1725A GLN* 3.2 40.3 + - + +
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Residues in contact with ASN1722 (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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1628A GLY 4.1 3.2 + - - -
1629A MET* 3.1 51.5 + - - +
1632A HIS 5.4 0.6 + - - -
1634A THR* 3.2 32.9 + - - +
1661A LEU* 3.4 24.3 - - + +
1718A GLN* 2.9 23.8 + - - +
1719A ILE* 3.5 6.5 - - - +
1721A TYR* 1.3 76.4 - - - +
1723A VAL* 1.3 63.5 + - - +
1725A GLN* 3.1 6.8 + - - +
1726A LEU* 3.1 24.9 + - - +
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Residues in contact with VAL1723 (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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1629A MET* 5.7 1.8 - - - -
1719A ILE* 2.9 25.3 + - + +
1720A ARG* 4.0 7.2 - - - +
1722A ASN* 1.3 76.3 - - + +
1724A SER* 1.3 57.7 + - - +
1726A LEU* 2.9 13.1 + - + +
1727A GLU* 2.9 44.5 + - + +
1744A LEU* 3.8 24.7 - - + -
1747A LEU* 4.0 26.5 - - + -
1748A ILE* 3.9 28.0 - - + -
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Residues in contact with SER1724 (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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1720A ARG 3.4 11.8 + - - -
1721A TYR* 2.4 31.8 + - - -
1723A VAL* 1.3 79.4 - - - +
1725A GLN* 1.3 72.4 + - - +
1727A GLU* 3.6 14.6 + - - +
1728A GLU* 3.0 30.6 + - - +
1731A ARG* 5.3 0.7 + - - -
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Residues in contact with GLN1725 (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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1661A LEU* 4.0 23.6 - - + -
1665A LEU* 4.0 16.4 - - + +
1721A TYR* 3.5 40.4 + - + +
1722A ASN 3.1 7.8 + - - +
1723A VAL 3.1 0.4 - - - -
1724A SER* 1.3 101.9 + - - +
1726A LEU* 1.3 63.3 + - - +
1728A GLU* 3.5 18.9 + - - +
1729A TRP* 3.1 21.1 + - - +
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Residues in contact with LEU1726 (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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1629A MET* 3.6 32.3 - - + -
1661A LEU* 4.7 4.0 - - + -
1664A ILE* 4.8 2.9 - - + -
1665A LEU* 4.2 12.6 - - + -
1668A LEU* 4.1 25.8 - - + -
1693A PHE* 3.5 25.6 - - + -
1696A ILE* 4.0 21.8 - - + -
1722A ASN 3.1 16.2 + - - +
1723A VAL* 2.9 14.2 + - + +
1725A GLN* 1.3 76.8 - - - +
1727A GLU* 1.3 62.7 + - - +
1729A TRP* 3.2 8.5 + - - +
1730A LEU 3.2 16.1 + - - -
1744A LEU* 4.0 20.4 - - + -
1747A LEU* 6.3 0.4 - - + -
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Residues in contact with GLU1727 (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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1723A VAL* 2.9 41.1 + - + +
1724A SER* 3.8 10.8 + - - +
1726A LEU* 1.3 73.5 - - - +
1728A GLU* 1.3 64.3 + - - +
1730A LEU* 3.2 21.7 + - + +
1731A ARG* 3.2 36.5 + - - +
1736A MET* 4.0 3.9 - - - +
1741A LYS* 3.4 37.9 - - + +
1744A LEU* 4.9 5.4 - - + -
1748A ILE* 4.3 8.5 - - - +
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Residues in contact with GLU1728 (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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1724A SER* 3.0 20.9 + - - +
1725A GLN* 3.6 22.9 + - - +
1727A GLU* 1.3 76.7 - - - +
1729A TRP* 1.3 57.8 + - - +
1731A ARG* 3.3 29.4 + - - +
1732A ASP* 3.0 28.7 + - - +
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Residues in contact with TRP1729 (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 LEU* 4.0 26.0 + - + -
1668A LEU* 3.4 39.3 - - + -
1669A ASN* 3.0 33.8 + - - +
1672A HIS* 3.9 18.8 - - + -
1689A VAL* 4.1 11.4 - - + -
1692A MET* 5.0 4.9 - - + -
1693A PHE* 4.1 19.3 - + - -
1725A GLN 3.1 13.4 + - - +
1726A LEU* 3.3 10.1 - - - +
1728A GLU* 1.3 77.4 - - - +
1730A LEU* 1.3 86.2 + - + +
1732A ASP* 3.3 9.8 + - - +
1733A LYS* 3.1 43.9 + - + +
1735A LEU* 4.0 18.4 - - + -
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Residues in contact with LEU1730 (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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1689A VAL* 3.8 25.4 - - + -
1693A PHE* 3.6 41.7 - - + -
1726A LEU 3.2 3.3 + - - +
1727A GLU* 3.2 13.5 + - - +
1729A TRP* 1.3 87.8 - - + +
1731A ARG* 1.3 55.1 + - - +
1733A LYS* 3.2 2.3 + - - -
1734A ASN 2.9 8.1 + - - -
1735A LEU* 2.7 48.9 + - + +
1736A MET* 3.6 22.2 - - - -
1740A ALA* 4.1 3.8 - - + -
1741A LYS* 4.0 25.1 - - + +
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Residues in contact with ARG1731 (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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1724A SER 5.3 0.8 + - - -
1727A GLU* 3.2 32.1 + - - +
1728A GLU* 3.5 31.6 + - - +
1730A LEU* 1.3 77.3 - - - +
1732A ASP* 1.3 59.1 + - - +
1733A LYS 3.1 0.2 - - - -
1734A ASN* 3.0 19.0 + - - +
1736A MET* 3.6 36.1 - - + +
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Residues in contact with ASP1732 (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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1728A GLU 3.0 17.5 + - - +
1729A TRP* 3.3 12.1 + - + +
1731A ARG* 1.3 76.1 - - - +
1733A LYS* 1.3 76.4 + - + +
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Residues in contact with LYS1733 (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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1669A ASN* 3.2 28.8 + - - +
1672A HIS* 3.8 33.4 + - + +
1673A SER* 6.3 0.6 - - - -
1729A TRP* 3.1 43.3 + - + +
1730A LEU 3.2 0.6 + - - +
1731A ARG 3.1 0.6 - - - -
1732A ASP* 1.3 94.0 + - - +
1734A ASN* 1.3 71.4 + - - +
1735A LEU* 3.4 26.2 - - + +
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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
------------------------------------------------------------
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) + - + + + + + -
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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