Contacts of the helix formed by residues 1697 - 1730 (chain A) in PDB entry 5NUG
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 LYS1697 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1554A SER* 4.3 24.5 + - - +
1555A ALA* 4.9 4.8 + - - +
1622A GLU* 4.8 9.3 + - - -
1625A SER* 5.8 0.7 - - - -
1696A PRO* 1.3 76.4 - - - +
1698A ILE* 1.3 72.6 + - + +
1699A ASN* 3.3 28.0 - - - +
1700A GLU* 3.0 30.6 + - + +
1701A TRP* 3.2 12.0 + - - -
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Residues in contact with ILE1698 (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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1554A SER* 4.9 10.1 - - - +
1622A GLU* 4.0 20.2 - - - +
1629A PHE* 5.7 1.3 - - + -
1640A ILE* 3.6 6.1 - - + +
1641A ILE* 3.4 45.1 - - + +
1644A SER* 3.4 37.2 - - - +
1696A PRO 3.7 2.2 + - - -
1697A LYS* 1.3 75.9 - - + +
1699A ASN* 1.3 71.5 + - + +
1701A TRP* 3.1 28.6 + - + +
1702A LEU* 3.5 19.5 - - + +
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Residues in contact with ASN1699 (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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1622A GLU* 3.7 16.9 + - - +
1625A SER* 3.6 31.0 + - - +
1626A PHE* 3.9 29.2 - - + +
1629A PHE* 5.1 4.5 - - + -
1697A LYS* 3.6 30.0 - - - +
1698A ILE* 1.3 80.6 - - + +
1700A GLU* 1.3 78.2 + - - +
1702A LEU* 4.0 5.4 + - - +
1703A THR* 2.5 32.9 + - - -
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Residues in contact with GLU1700 (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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1696A PRO* 4.8 6.3 - - + -
1697A LYS* 3.0 29.9 + - + +
1699A ASN* 1.3 92.2 - - - +
1701A TRP* 1.3 61.0 + - - +
1703A THR* 3.2 11.3 + - - +
1704A LEU* 2.9 37.3 + - + +
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Residues in contact with TRP1701 (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* 4.6 15.1 - - - -
1647A VAL* 5.4 5.8 - - + -
1650A LEU* 4.3 23.8 - - + -
1654A PHE* 5.2 0.2 - + - -
1664A ILE* 4.9 14.1 - - + -
1673A VAL* 4.2 13.2 - - + -
1690A VAL* 4.9 2.9 - - + +
1691A SER 5.1 0.4 - - - +
1692A ILE* 3.3 42.9 - - + +
1696A PRO* 4.5 21.7 - - + +
1697A LYS 3.2 9.6 + - - +
1698A ILE* 3.1 42.8 + - - +
1700A GLU* 1.3 78.8 - - - +
1702A LEU* 1.3 90.4 + - + +
1704A LEU* 3.2 14.8 + - + +
1705A VAL* 2.9 46.9 + - + +
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Residues in contact with LEU1702 (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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1626A PHE* 3.9 34.6 - - + -
1629A PHE* 4.4 15.5 - - + -
1640A ILE* 5.0 7.0 - - + -
1650A LEU* 5.9 2.0 - - + -
1654A PHE* 4.0 28.5 - - + -
1657A MET* 5.5 2.7 - - + -
1658A PHE* 5.6 2.9 - - + -
1698A ILE* 3.5 26.0 + - + +
1699A ASN* 4.2 2.5 - - - +
1700A GLU 3.3 0.2 - - - -
1701A TRP* 1.3 112.9 - - + +
1703A THR* 1.3 58.3 + - - +
1705A VAL* 3.2 11.0 + - + +
1706A GLU* 2.9 28.4 + - - +
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Residues in contact with THR1703 (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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1625A SER 5.0 4.2 + - - -
1626A PHE* 3.7 17.2 - - + -
1627A PRO* 5.5 4.2 - - + +
1699A ASN 2.5 23.9 + - - -
1700A GLU* 3.2 15.2 + - - +
1702A LEU* 1.3 78.0 - - - +
1704A LEU* 1.3 56.9 + - - +
1706A GLU* 3.2 14.8 + - - +
1707A LYS* 2.9 35.2 + - + +
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Residues in contact with LEU1704 (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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1690A VAL* 4.6 13.0 - - + -
1691A SER* 6.0 1.6 - - - +
1696A PRO* 5.1 11.9 - - + -
1700A GLU* 2.9 25.0 + - + +
1701A TRP* 3.4 15.7 - - + +
1703A THR* 1.3 75.5 - - - +
1705A VAL* 1.3 58.0 + - - +
1707A LYS* 3.2 19.8 + - + +
1708A GLU* 2.9 29.5 + - - +
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Residues in contact with VAL1705 (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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1654A PHE* 6.5 0.9 - - + -
1658A PHE* 6.3 2.7 - - + -
1664A ILE* 5.8 5.8 - - + -
1673A VAL* 4.8 5.8 - - + -
1676A ILE* 5.3 4.9 - - + -
1686A PHE* 3.8 22.6 - - + -
1690A VAL* 3.5 37.2 - - + +
1701A TRP* 2.9 33.4 + - + +
1702A LEU* 3.2 14.8 - - + +
1704A LEU* 1.3 76.9 - - - +
1706A GLU* 1.3 58.7 + - - +
1708A GLU* 3.2 6.1 + - - +
1709A MET* 2.9 29.9 + - + +
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Residues in contact with GLU1706 (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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1626A PHE* 3.7 21.5 - - - -
1627A PRO* 6.0 1.0 - - - +
1628A ARG* 3.1 34.9 + - - +
1658A PHE* 4.1 15.7 - - + -
1702A LEU 2.9 11.7 + - - +
1703A THR* 3.3 14.5 - - - +
1705A VAL* 1.3 78.1 - - - +
1707A LYS* 1.3 64.5 + - - +
1709A MET* 3.2 27.2 + - + +
1710A ARG* 2.8 47.3 + - - +
1951A VAL* 5.4 1.7 - - - +
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Residues in contact with LYS1707 (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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1703A THR* 2.9 20.0 + - + +
1704A LEU* 3.2 22.9 + - + +
1706A GLU* 1.3 78.6 - - - +
1708A GLU* 1.3 62.3 + - - +
1710A ARG* 3.6 19.7 + - - +
1711A VAL* 3.4 30.1 + - + +
1854A LEU* 5.5 1.7 - - + +
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Residues in contact with GLU1708 (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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1686A PHE* 3.6 20.0 - - + -
1687A LYS* 3.8 8.0 + - - +
1688A THR* 2.8 53.3 + - - +
1690A VAL* 5.2 5.2 - - + -
1704A LEU 2.9 13.2 + - - +
1705A VAL* 3.4 11.7 - - - +
1707A LYS* 1.3 78.5 - - - +
1709A MET* 1.3 53.3 + - - +
1711A VAL* 3.2 18.9 + - - +
1712A THR* 2.7 45.6 + - - -
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Residues in contact with MET1709 (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 PHE* 4.4 16.2 - - + -
1661A VAL* 4.1 8.5 - - - -
1676A ILE* 3.8 37.7 - - + -
1684A VAL* 6.2 0.9 - - + -
1686A PHE* 3.8 13.0 - - + -
1705A VAL* 2.9 14.8 + - - +
1706A GLU* 3.2 18.3 + - + +
1708A GLU* 1.3 76.0 - - - +
1710A ARG* 1.3 58.2 + - + +
1712A THR* 3.2 10.1 + - - -
1713A LEU* 2.9 43.0 + - + +
1870A PHE 4.6 6.1 - - - +
1871A GLU* 3.4 26.0 - - - +
1872A TYR* 4.0 19.3 - - + +
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Residues in contact with ARG1710 (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 ARG* 3.8 11.7 - - - +
1706A GLU* 2.8 46.7 + - - +
1707A LYS* 3.8 17.8 - - - +
1709A MET* 1.3 81.8 - - + +
1711A VAL* 1.3 58.7 + - - +
1713A LEU* 3.2 5.0 + - - +
1714A ALA* 2.9 28.6 + - - +
1854A LEU* 3.5 32.0 - - + +
1869A GLY 3.7 15.5 + - - -
1870A PHE* 3.2 37.5 + - + +
1871A GLU* 5.2 3.8 + - - +
1951A VAL* 4.6 11.5 + - - +
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Residues in contact with VAL1711 (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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1687A LYS* 6.4 0.2 - - + -
1707A LYS* 3.4 20.2 - - + +
1708A GLU* 3.2 22.4 + - - +
1710A ARG* 1.3 77.1 - - - +
1712A THR* 1.3 56.8 + - - +
1714A ALA* 3.2 8.7 + - - +
1715A LYS* 2.9 58.8 + - + +
1853A VAL* 4.2 13.9 - - + -
1854A LEU* 4.8 14.4 - - + -
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Residues in contact with THR1712 (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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1684A VAL* 3.6 19.5 - - + -
1685A MET 3.2 26.9 - - - +
1686A PHE* 3.7 15.1 - - + -
1687A LYS* 4.1 22.1 + - + -
1708A GLU* 2.7 32.6 + - - -
1709A MET* 3.2 9.2 - - - -
1711A VAL* 1.3 75.1 - - - +
1713A LEU* 1.3 60.2 + - - +
1715A LYS* 3.2 3.9 + - - +
1716A LEU* 2.9 37.5 + - + +
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Residues in contact with LEU1713 (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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1676A ILE* 5.6 0.2 - - + -
1684A VAL* 4.4 16.2 - - + -
1709A MET* 2.9 33.6 + - + +
1710A ARG* 3.2 5.6 + - - +
1712A THR* 1.3 77.7 - - - +
1714A ALA* 1.3 55.8 + - - +
1716A LEU* 3.2 8.6 + - + +
1717A LEU* 2.9 32.1 + - - +
1748A GLN* 4.8 4.3 - - - +
1749A LEU* 3.7 31.2 - - + +
1870A PHE* 3.2 43.7 - - + +
1871A GLU 4.6 0.4 - - - -
1872A TYR* 4.3 30.7 - - + +
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Residues in contact with ALA1714 (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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1710A ARG 2.9 13.4 + - - +
1711A VAL* 3.4 10.3 - - - +
1713A LEU* 1.3 76.7 - - - +
1715A LYS* 1.3 62.4 + - - +
1717A LEU* 3.2 19.8 + - - +
1718A ALA* 3.3 8.7 + - - +
1846A PHE* 4.8 4.1 - - + -
1853A VAL* 3.5 40.8 - - + +
1854A LEU* 4.7 1.6 - - - +
1870A PHE* 3.7 21.7 - - + -
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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
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1687A LYS* 4.0 35.2 - - + +
1711A VAL* 2.9 40.0 + - + +
1712A THR 3.2 7.8 + - - +
1714A ALA* 1.3 74.6 - - - +
1716A LEU* 1.3 63.5 + - - +
1718A ALA* 3.2 17.0 + - - +
1719A GLU* 3.6 21.4 + - - +
1853A VAL* 4.4 20.0 - - + +
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Residues in contact with LEU1716 (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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1684A VAL* 3.5 32.3 - - + -
1685A MET 5.3 0.4 - - - +
1687A LYS* 4.1 21.3 - - - +
1712A THR* 2.9 24.9 + - + +
1713A LEU* 3.4 7.2 - - - +
1715A LYS* 1.3 78.3 - - - +
1717A LEU* 1.3 62.0 + - - +
1718A ALA 3.4 0.2 + - - -
1719A GLU* 3.6 5.3 + - - +
1720A SER* 3.2 18.4 + - - -
1744A LYS 6.0 0.4 - - - +
1745A TYR* 3.4 34.8 - - + -
1746A GLN* 4.1 9.0 - - - +
1749A LEU* 3.4 25.8 - - + -
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Residues in contact with LEU1717 (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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1713A LEU 2.9 14.7 + - - +
1714A ALA* 3.2 9.2 - - - +
1716A LEU* 1.3 76.9 - - - +
1718A ALA* 1.3 57.0 + - - +
1720A SER* 3.2 5.6 + - - -
1721A VAL* 2.8 35.8 + - + +
1749A LEU* 3.3 45.0 - - + +
1752A LEU* 3.6 35.2 - - + -
1753A SER* 4.0 5.1 + - - +
1756A ILE* 5.4 0.4 - - + -
1846A PHE* 4.4 13.9 - - + -
1857A LEU* 4.3 3.4 - - + -
1870A PHE* 3.4 37.0 - - + -
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Residues in contact with ALA1718 (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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1714A ALA 3.3 6.4 + - - +
1715A LYS* 3.2 13.3 + - - +
1717A LEU* 1.3 77.4 - - - +
1719A GLU* 1.3 53.9 + - + +
1721A VAL* 3.2 4.2 + - - +
1722A THR* 2.7 38.7 + - - +
1846A PHE* 3.9 25.0 - - + -
1848A PRO* 6.4 1.3 - - + -
1853A VAL* 6.1 2.9 - - + -
1856A GLN* 5.2 2.7 - - - +
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Residues in contact with GLU1719 (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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1687A LYS* 4.3 16.5 + - - -
1715A LYS* 3.8 17.4 - - - +
1716A LEU* 3.6 5.0 + - - +
1717A LEU 3.3 0.2 - - - -
1718A ALA* 1.3 78.1 - - + +
1720A SER* 1.3 57.5 + - - +
1722A THR* 3.2 10.5 + - - -
1723A GLU* 2.9 32.2 + - + +
1744A LYS* 4.5 7.6 + - - -
1745A TYR* 3.0 31.8 + - + +
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Residues in contact with SER1720 (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 LEU 3.2 11.2 + - - -
1717A LEU* 3.2 7.5 + - - -
1719A GLU* 1.3 80.5 - - - +
1721A VAL* 1.3 56.9 + - - +
1723A GLU* 3.2 4.3 + - - +
1724A VAL* 2.9 32.6 + - - +
1741A TRP* 2.8 35.9 + - - +
1745A TYR* 4.0 17.1 - - - -
1749A LEU* 5.1 2.0 - - - -
1750A VAL* 4.5 2.9 - - - -
1753A SER* 2.7 25.0 + - - -
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Residues in contact with VAL1721 (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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1717A LEU* 2.8 21.9 + - + +
1718A ALA* 3.4 10.3 - - - +
1720A SER* 1.3 75.8 - - - +
1722A THR* 1.3 57.7 + - - +
1724A VAL* 3.2 8.7 + - - +
1725A GLU* 2.9 47.5 + - + +
1753A SER* 4.2 13.5 - - - +
1756A ILE* 3.6 41.5 - - + -
1757A ALA* 5.0 4.4 - - + +
1760A GLU* 5.3 2.2 - - - +
1846A PHE* 4.2 20.4 - - + -
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Residues in contact with THR1722 (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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1718A ALA* 2.7 22.2 + - - +
1719A GLU* 3.3 10.1 - - - -
1721A VAL* 1.3 76.0 - - - +
1723A GLU* 1.3 64.9 + - - +
1725A GLU* 3.2 32.1 + - - +
1726A ILE* 3.5 12.1 + - + +
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Residues in contact with GLU1723 (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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1719A GLU* 2.9 15.7 + - + +
1720A SER 3.2 8.7 + - - +
1722A THR* 1.3 77.3 - - - +
1724A VAL* 1.3 62.3 + - - +
1726A ILE* 3.1 27.9 - - + +
1727A PHE* 3.1 24.0 - - + -
1737A THR 5.4 0.2 - - - +
1741A TRP* 3.3 38.1 - - + +
1744A LYS* 3.4 21.4 + - - +
1745A TYR* 3.4 20.1 + - - -
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Residues in contact with VAL1724 (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 SER 2.9 19.0 + - - +
1721A VAL* 3.5 7.9 - - - +
1723A GLU* 1.3 77.1 - - - +
1725A GLU* 1.3 55.5 + - - +
1727A PHE* 2.9 11.6 + - + +
1728A GLY* 2.7 38.6 + - - +
1738A TYR* 5.9 2.2 - - + -
1741A TRP* 3.5 34.8 - - + -
1753A SER* 4.1 16.2 - - - +
1754A ALA* 4.8 4.9 - - - +
1757A ALA* 3.4 27.6 - - + -
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Residues in contact with GLU1725 (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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1721A VAL* 2.9 34.8 + - + +
1722A THR* 3.2 21.5 + - - +
1724A VAL* 1.3 78.0 - - - +
1726A ILE* 1.3 62.4 + - + +
1728A GLY 4.8 0.2 - - - +
1729A LYS* 3.4 25.7 + - - +
1757A ALA* 5.1 8.7 - - + -
1760A GLU* 4.1 15.2 - - - +
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Residues in contact with ILE1726 (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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1722A THR* 3.5 10.3 + - + +
1723A GLU* 3.1 23.3 + - + +
1725A GLU* 1.3 76.7 - - + +
1727A PHE* 1.3 81.3 + - + +
1729A LYS* 4.8 1.5 - - - +
1730A ALA* 4.1 15.6 + - - +
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Residues in contact with PHE1727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1723A GLU* 3.1 42.4 - - + -
1724A VAL* 2.9 12.3 + - + +
1726A ILE* 1.3 94.1 - - + +
1728A GLY* 1.3 63.4 + - - +
1729A LYS 3.3 1.2 + - - -
1730A ALA* 3.4 21.4 + - - +
1732A SER 4.3 5.2 - - - +
1733A ILE* 3.8 29.8 - - + +
1737A THR* 3.6 42.0 - - + -
1738A TYR* 4.0 21.5 - + + -
1741A TRP* 4.0 25.6 - + + -
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Residues in contact with GLY1728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1724A VAL* 2.7 24.2 + - - +
1725A GLU* 5.5 0.4 - - - -
1727A PHE* 1.3 74.2 - - - +
1729A LYS* 1.3 57.3 + - - +
1730A ALA 3.5 1.1 - - - -
1733A ILE* 5.9 0.9 - - - -
1757A ALA* 6.3 0.7 - - - -
1761A ASN* 4.0 16.4 + - - -
1784A ASN* 3.2 33.7 - - - +
1788A THR* 6.0 5.6 - - - -
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Residues in contact with LYS1729 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1725A GLU* 3.4 18.8 + - - +
1726A ILE* 4.8 2.7 - - - +
1727A PHE 3.3 1.0 - - - -
1728A GLY* 1.3 74.4 - - - +
1730A ALA* 1.3 64.5 + - - +
1731A THR* 5.3 2.1 - - - +
1761A ASN* 4.8 20.5 + - - +
1764A THR* 4.6 20.8 + - - +
1780A SER* 5.6 1.2 + - - -
1784A ASN* 4.3 5.5 - - - +
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Residues in contact with ALA1730 (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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1726A ILE 4.1 10.8 + - - +
1727A PHE 3.4 17.5 + - - +
1728A GLY* 3.6 1.7 - - - +
1729A LYS* 1.3 82.4 - - - +
1731A THR* 1.3 64.9 + - - +
1732A SER 3.7 14.8 - - - +
1733A ILE* 5.9 0.2 - - - +
1784A ASN* 3.3 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