Contacts of the helix formed by residues 1815 - 1838 (chain A) in PDB entry 5XJY
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 LEU1815 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1662A ILE* 6.1 0.2 - - - -
1777A ILE* 4.0 10.4 - - - +
1778A GLY* 5.9 1.3 - - - -
1780A ASN* 4.1 12.3 - - - +
1781A GLY* 3.7 35.6 - - - +
1784A ALA* 4.2 7.6 - - + -
1805A SER* 5.3 3.1 - - - +
1809A ILE* 3.7 25.1 - - + -
1812A HIS* 3.6 32.8 + - + +
1813A PHE 3.7 0.4 - - - +
1814A CYS* 1.3 76.1 - - - +
1816A GLY* 1.3 64.6 + - - +
1817A ARG 3.3 0.2 - - - -
1818A GLY* 3.2 5.1 + - - +
1819A LEU* 3.1 41.1 + - + +
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Residues in contact with GLY1816 (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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1809A ILE* 5.2 7.2 - - - -
1812A HIS 4.8 4.6 + - - -
1813A PHE 4.5 4.6 - - - -
1814A CYS* 3.3 4.0 - - - +
1815A LEU* 1.3 83.8 - - - +
1817A ARG* 1.3 58.1 + - - +
1819A LEU* 4.8 0.7 - - - -
1820A ILE* 2.7 52.2 + - - +
1854A PHE* 4.8 7.4 - - - -
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Residues in contact with ARG1817 (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 VAL* 2.8 56.3 + - - +
1662A ILE* 3.3 17.8 - - + +
1665A MET* 3.5 10.7 - - - +
1738A LEU* 6.1 2.0 - - - +
1741A LEU* 3.6 32.0 - - + +
1742A LEU* 3.6 23.6 - - - +
1745A TYR* 3.3 55.7 - - + -
1813A PHE 5.3 1.2 + - - -
1814A CYS 4.3 1.6 + - - -
1815A LEU 3.3 0.4 - - - -
1816A GLY* 1.3 76.5 - - - +
1818A GLY* 1.3 52.5 + - - +
1821A ASP* 2.6 49.8 + - + +
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Residues in contact with GLY1818 (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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1658A SER* 3.3 26.8 + - - -
1662A ILE* 4.3 16.4 - - - +
1815A LEU* 3.2 8.1 + - - -
1817A ARG* 1.3 79.7 - - - +
1819A LEU* 1.3 61.5 + - - +
1821A ASP* 3.1 6.2 + - - +
1822A MET* 3.0 24.1 + - - +
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Residues in contact with LEU1819 (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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1655A VAL* 5.6 5.2 - - + -
1658A SER* 5.1 3.8 - - - +
1781A GLY* 3.2 39.9 - - - +
1782A SER* 4.3 3.1 - - - +
1784A ALA* 3.8 9.2 - - + +
1785A THR* 3.2 40.0 + - + +
1805A SER* 5.9 2.9 - - - -
1815A LEU* 3.1 36.2 + - + +
1816A GLY* 5.5 0.4 - - - -
1818A GLY* 1.3 80.3 - - - +
1820A ILE* 1.3 60.7 + - + +
1822A MET* 3.1 11.5 + - + +
1823A VAL* 3.0 31.4 + - + +
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Residues in contact with ILE1820 (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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1741A LEU* 4.7 9.6 - - + +
1809A ILE* 6.1 3.4 - - + +
1816A GLY* 2.7 29.9 + - - +
1819A LEU* 1.3 75.7 - - + +
1821A ASP* 1.3 59.2 + - - +
1823A VAL* 3.2 10.7 + - + +
1824A LYS* 3.0 25.3 + - - +
1850A GLY* 3.3 38.3 - - - +
1851A ARG* 3.7 12.1 - - + +
1853A LEU* 3.8 11.0 - - + -
1854A PHE* 3.4 33.2 - - + +
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Residues in contact with ASP1821 (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 VAL 5.7 0.2 - - - -
1658A SER* 4.9 5.1 - - - +
1727A LYS* 2.4 42.6 + - - -
1737A VAL 5.3 1.6 - - - +
1738A LEU* 4.5 8.0 - - - +
1741A LEU* 4.3 15.2 - - + +
1817A ARG* 2.6 35.0 + - + +
1818A GLY* 3.1 6.3 + - - +
1820A ILE* 1.3 78.6 - - - +
1822A MET* 1.3 72.5 + - + +
1824A LYS* 3.1 12.1 + - - +
1825A ASN* 3.1 23.2 + - - +
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Residues in contact with MET1822 (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 THR* 4.0 11.7 - - + +
1654A ASP* 3.2 55.0 - - - +
1655A VAL* 3.5 26.0 - - + -
1657A VAL 4.9 0.2 - - - -
1658A SER* 3.6 21.3 - - - +
1727A LYS* 4.2 2.0 - - - +
1785A THR* 5.5 3.4 - - - +
1818A GLY 3.0 12.8 + - - +
1819A LEU* 3.1 14.6 + - + +
1821A ASP* 1.3 101.8 - - - +
1823A VAL* 1.3 60.5 + - - +
1825A ASN* 4.4 2.0 - - + +
1826A GLN* 2.9 34.9 + - - +
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Residues in contact with VAL1823 (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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1785A THR* 6.2 3.6 - - + -
1819A LEU* 3.0 15.9 + - + +
1820A ILE* 3.2 14.8 + - + +
1822A MET* 1.3 76.3 - - + +
1824A LYS* 1.3 57.2 + - - +
1826A GLN* 3.9 11.1 - - - +
1827A ALA* 2.9 32.8 + - + +
1849A VAL* 4.8 5.2 - - + -
1850A GLY* 3.6 29.6 - - - +
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Residues in contact with LYS1824 (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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1727A LYS* 3.8 28.7 - - - +
1728A SER* 4.5 1.8 - - - -
1733A THR 2.5 30.0 + - - -
1734A ASN* 3.0 38.4 + - - +
1737A VAL* 3.7 25.1 - - + +
1738A LEU* 5.1 2.9 - - - +
1741A LEU* 6.4 0.7 - - + -
1820A ILE 3.0 12.9 + - - +
1821A ASP* 3.1 15.4 + - - +
1823A VAL* 1.3 76.6 - - - +
1825A ASN* 1.3 64.8 + - - +
1827A ALA* 3.2 5.5 + - - +
1828A MET* 3.0 34.3 + - + +
1845A SER* 4.9 8.8 - - - +
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Residues in contact with ASN1825 (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 THR* 4.9 3.3 + - - -
1654A ASP* 2.8 43.7 + - + +
1727A LYS* 3.9 25.6 - - + +
1821A ASP 3.1 12.5 + - - +
1822A MET* 4.6 3.6 - - + +
1823A VAL 3.5 0.2 - - - -
1824A LYS* 1.3 79.2 - - + +
1826A GLN* 1.3 60.8 + - - +
1828A MET* 3.6 23.8 - - - +
1829A ALA* 2.9 30.5 + - - +
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Residues in contact with GLN1826 (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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1647A ALA* 5.4 2.8 - - + +
1648A LEU* 4.5 25.8 - - + +
1651A THR* 3.6 36.2 + - + +
1822A MET* 2.9 21.0 + - - +
1823A VAL* 3.9 12.4 - - - +
1825A ASN* 1.3 77.9 - - - +
1827A ALA* 1.3 57.5 + - - +
1829A ALA* 3.9 1.4 - - - +
1830A ASP* 2.9 36.8 + - + +
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Residues in contact with ALA1827 (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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1823A VAL* 2.9 22.2 + - + +
1824A LYS* 3.6 5.4 - - - +
1826A GLN* 1.3 78.5 - - - +
1828A MET* 1.3 57.6 + - - +
1830A ASP* 4.0 3.5 - - - +
1831A ALA* 3.0 33.3 + - - +
1844A LEU* 5.1 19.3 - - + +
1845A SER* 5.6 3.1 - - - +
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Residues in contact with MET1828 (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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1727A LYS* 4.2 9.0 - - - +
1729A TYR* 3.6 30.3 - - + -
1733A THR* 4.9 9.6 - - - +
1734A ASN* 3.4 28.5 - - - +
1824A LYS* 3.0 24.2 + - - +
1825A ASN* 3.6 19.5 - - - +
1827A ALA* 1.3 74.4 - - - +
1829A ALA* 1.3 61.6 + - - +
1831A ALA* 4.9 2.5 - - - -
1832A LEU* 2.8 51.8 + - + +
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Residues in contact with ALA1829 (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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1647A ALA* 5.2 10.8 - - + +
1650A THR* 5.7 9.9 - - + -
1651A THR* 5.0 6.1 - - - +
1825A ASN* 2.9 24.2 + - - +
1826A GLN* 3.9 4.9 - - - +
1828A MET* 1.3 80.4 - - - +
1830A ASP* 1.3 62.7 + - - +
1832A LEU* 3.2 9.0 + - - +
1833A GLU* 3.0 27.5 + - - +
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Residues in contact with ASP1830 (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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1644A SER* 5.0 9.0 + - - -
1647A ALA* 4.5 14.7 - - + +
1826A GLN* 2.9 23.6 + - + +
1827A ALA* 4.0 4.0 - - - +
1829A ALA* 1.3 76.5 - - - +
1831A ALA* 1.3 58.8 + - - +
1833A GLU* 2.8 34.6 - - - +
1834A ARG* 2.9 40.5 + - - +
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Residues in contact with ALA1831 (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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1827A ALA 3.0 17.7 + - - +
1828A MET* 4.6 2.2 - - - +
1830A ASP* 1.3 78.2 + - - +
1832A LEU* 1.3 65.3 + - - +
1834A ARG* 4.4 14.4 - - - +
1835A PHE* 3.0 31.8 + - + +
1841A VAL 6.0 1.6 - - - +
1842A SER 5.9 1.1 - - - +
1843A PRO* 5.4 14.4 - - + -
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Residues in contact with LEU1832 (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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1729A TYR* 6.1 1.6 - - + -
1828A MET* 2.8 42.8 + - + +
1829A ALA* 3.2 8.9 + - - +
1831A ALA* 1.3 77.1 - - - +
1833A GLU* 1.3 58.6 + - - +
1836A GLY* 2.9 24.6 + - - -
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Residues in contact with GLU1833 (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 LEU* 3.3 56.9 - - + +
1644A SER* 4.9 1.9 + - - -
1647A ALA* 4.6 4.8 - - + +
1829A ALA 3.0 17.5 + - - +
1830A ASP* 2.8 30.6 - - - +
1832A LEU* 1.3 76.5 - - - +
1834A ARG* 1.3 82.4 + - - +
1836A GLY* 2.7 22.9 + - - -
1837A GLU* 3.0 13.5 + - - +
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Residues in contact with ARG1834 (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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1640A LYS* 4.3 19.7 - - + +
1830A ASP* 2.9 37.5 + - - +
1831A ALA* 4.7 13.1 - - - +
1833A GLU* 1.3 88.9 - - - +
1835A PHE* 1.3 63.0 + - - +
1837A GLU* 3.7 3.9 + - - +
1838A ASN* 3.0 34.4 + - + +
1839A ARG* 3.8 18.7 + - - +
1840A PHE 4.8 0.6 - - - -
1841A VAL* 3.3 36.1 - - - +
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Residues in contact with PHE1835 (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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1831A ALA* 3.0 19.6 + - + +
1834A ARG* 1.3 79.3 - - - +
1836A GLY* 1.3 61.8 + - - +
1837A GLU 3.1 2.2 + - - -
1838A ASN 3.3 15.9 + - - +
1839A ARG* 3.3 22.9 + - - +
1840A PHE* 3.6 26.7 - - + -
1841A VAL 5.6 1.1 - - - +
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Residues in contact with GLY1836 (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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1832A LEU 2.9 18.4 + - - -
1833A GLU* 2.7 13.9 + - - -
1835A PHE* 1.3 78.4 - - - +
1837A GLU* 1.3 57.6 + - - +
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Residues in contact with GLU1837 (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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524A MET* 6.1 1.0 - - - +
1638A LEU 5.4 3.9 - - - +
1640A LYS* 2.7 36.3 + - - -
1643A LEU* 4.1 23.9 - - + +
1833A GLU 3.0 15.2 + - - +
1834A ARG* 4.5 1.5 - - - +
1835A PHE 4.2 0.9 - - - -
1836A GLY* 1.3 80.8 - - - +
1838A ASN* 1.3 60.5 + - + +
1C NAG 4.4 20.4 - - - +
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Residues in contact with ASN1838 (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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1640A LYS* 3.3 27.8 - - - +
1834A ARG* 3.0 14.1 + - + +
1835A PHE* 3.3 19.5 + - - +
1837A GLU* 1.3 84.9 - - - +
1839A ARG* 1.3 70.8 + - - +
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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