Contacts of the helix formed by residues 1629 - 1655 (chain A) in PDB entry 5EK0
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 VAL1629 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1625A ALA 3.3 18.8 - - - +
1626A LEU 2.9 9.9 + - - +
1628A SER* 1.4 76.6 - - - +
1630A ILE* 1.4 62.8 + - - +
1631A PRO* 3.3 4.3 - - - -
1632A GLY 3.5 7.8 + - - -
1633A MET* 3.6 7.0 + - - +
1719A ILE* 3.8 39.3 - - + -
1722A ASP* 3.2 27.5 - - - +
1710B PHE* 3.6 17.0 - - + -
1714B ASN* 3.6 15.3 - - - +
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Residues in contact with ILE1630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1626A LEU 3.7 9.4 - - - +
1627A ILE* 3.2 38.4 - - + +
1629A VAL* 1.4 71.4 - - - +
1631A PRO* 1.4 61.9 - - + +
1632A GLY 3.4 0.2 - - - -
1633A MET* 3.5 25.3 - - + +
1634A LEU* 3.0 27.5 + - + +
1637A ILE* 4.5 11.2 - - + +
1710B PHE* 4.4 13.5 - - + -
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Residues in contact with PRO1631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1627A ILE 3.5 12.6 - - - +
1628A SER* 3.4 20.9 - - - +
1629A VAL 3.3 7.4 - - - +
1630A ILE* 1.4 89.4 - - + +
1632A GLY* 1.3 56.8 + - - +
1634A LEU* 3.1 29.5 - - + +
1635A SER 4.9 0.2 + - - -
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Residues in contact with GLY1632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1628A SER 5.3 0.6 + - - -
1629A VAL 3.5 6.6 + - - -
1630A ILE 3.4 0.2 - - - -
1631A PRO* 1.3 78.7 - - - +
1633A MET* 1.3 62.0 + - - +
1634A LEU 3.2 1.4 + - - -
1635A SER* 3.8 11.4 + - - -
1636A VAL* 5.0 3.5 + - - +
1722A ASP* 4.8 7.8 + - - -
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Residues in contact with MET1633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1629A VAL 3.6 9.6 + - - +
1630A ILE* 3.5 24.2 - - + +
1632A GLY* 1.3 74.4 - - - +
1634A LEU* 1.4 58.9 + - - +
1636A VAL* 3.1 23.1 + - - +
1637A ILE* 3.2 28.9 + - + +
1715A LEU* 3.8 35.9 - - + -
1718A ALA* 5.8 5.6 - - + -
1719A ILE* 3.6 24.9 - - + -
1722A ASP* 5.0 1.2 + - - -
1710B PHE* 3.5 39.0 - - + -
1713B ILE* 5.9 2.7 - - + -
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Residues in contact with LEU1634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1630A ILE* 3.0 15.8 + - + +
1631A PRO* 3.1 24.2 - - + +
1632A GLY 3.2 0.4 - - - -
1633A MET* 1.4 73.1 - - - +
1635A SER* 1.3 60.0 - - - +
1636A VAL 3.4 0.2 - - - -
1637A ILE* 3.7 13.1 + - + +
1638A ALA* 3.0 31.5 + - + +
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Residues in contact with SER1635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1632A GLY 3.8 9.1 + - - -
1633A MET 3.2 1.2 + - - -
1634A LEU* 1.3 78.1 - - - +
1636A VAL* 1.3 65.1 + - - +
1638A ALA* 3.6 6.2 + - - +
1639A LEU* 3.1 17.0 + - - +
1622D ILE* 3.4 38.8 - - - +
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Residues in contact with VAL1636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1632A GLY 5.1 2.9 - - - +
1633A MET* 3.1 15.2 + - - +
1635A SER* 1.3 72.8 - - - +
1637A ILE* 1.4 53.7 + - - +
1639A LEU* 3.1 6.4 + - + +
1640A MET* 2.8 31.9 + - - +
1711A VAL* 3.8 24.2 - - + +
1714A ASN* 5.0 4.3 - - + +
1715A LEU* 3.8 39.0 - - + +
1718A ALA* 4.9 12.1 - - + -
1622D ILE* 4.3 18.6 - - + -
1626D LEU* 5.6 6.3 - - + -
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Residues in contact with ILE1637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1630A ILE* 4.5 11.9 - - + +
1633A MET* 3.4 45.8 - - + +
1634A LEU* 3.8 13.2 - - + +
1636A VAL* 1.4 74.0 - - - +
1638A ALA* 1.4 49.2 + - - +
1640A MET* 3.1 9.6 + - - +
1641A THR* 2.7 46.6 + - - +
1715A LEU* 3.8 17.3 - - + -
1802A PX4 4.4 17.3 - - + -
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Residues in contact with ALA1638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1634A LEU* 3.0 24.1 + - + +
1635A SER* 3.6 9.2 - - - +
1637A ILE* 1.4 74.6 - - - +
1639A LEU* 1.4 56.5 + - - +
1641A THR* 3.5 7.7 + - - -
1642A LEU* 3.1 28.2 + - - +
1803A PX4 5.9 2.6 - - + +
1619D MET* 4.1 13.3 - - - +
1622D ILE* 5.7 0.2 - - + -
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Residues in contact with LEU1639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1635A SER 3.1 12.2 + - - +
1636A VAL* 3.1 10.5 + - + +
1638A ALA* 1.4 73.5 - - - +
1640A MET* 1.3 58.2 + - - +
1642A LEU* 3.1 3.1 + - - +
1643A PHE* 2.9 54.1 + - + -
1711A VAL* 4.3 10.8 - - + -
1613D VAL* 3.8 8.3 - - + -
1619D MET* 3.7 34.2 - - + +
1622D ILE* 4.5 14.8 - - + -
1623D VAL* 3.7 27.8 - - + -
1626D LEU* 3.8 29.4 - - + -
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Residues in contact with MET1640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1636A VAL* 2.8 17.1 + - + +
1637A ILE* 3.1 13.2 + - - +
1639A LEU* 1.3 71.1 - - - +
1641A THR* 1.3 57.0 + - - +
1643A PHE* 3.4 12.8 + - + -
1644A PHE* 3.1 37.0 + - + -
1677A MET* 3.7 16.6 - - + -
1707A VAL 5.4 0.2 - - - -
1708A VAL* 3.5 38.8 - - + +
1711A VAL* 3.6 31.8 - - + +
1712A MET* 4.6 8.7 - - + -
1715A LEU* 6.0 2.2 - - + -
1802A PX4 3.8 26.2 - - + -
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Residues in contact with THR1641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1637A ILE* 2.7 34.0 + - - +
1638A ALA* 3.5 8.7 - - - -
1640A MET* 1.3 70.7 - - - +
1642A LEU* 1.4 60.0 + - - +
1644A PHE* 3.1 10.6 + - - +
1645A TYR* 3.0 53.7 + - + -
1670A PHE* 5.4 3.6 - - + -
1802A PX4 4.2 14.6 - - + +
1803A PX4 6.5 0.9 - - + -
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Residues in contact with LEU1642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1638A ALA 3.1 9.4 + - - +
1639A LEU 3.1 9.0 + - - +
1641A THR* 1.4 73.7 - - - +
1643A PHE* 1.3 61.6 - - + +
1645A TYR* 3.0 24.2 + - + +
1646A ILE* 3.1 36.9 + - + +
1803A PX4 3.8 38.4 - - + -
1518D MET* 4.9 7.2 - - + -
1612D LEU* 3.8 33.2 - - + -
1613D VAL* 3.7 28.7 - - + +
1619D MET* 3.8 17.7 - - + -
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Residues in contact with PHE1643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1639A LEU* 2.9 58.3 + - + +
1640A MET* 3.6 22.2 - - + +
1642A LEU* 1.3 75.8 - - + +
1644A PHE* 1.3 58.4 + - - +
1646A ILE* 4.1 9.7 - - + +
1647A PHE* 2.9 52.8 + + + -
1704A PHE* 5.7 0.2 - - - -
1707A VAL* 3.6 30.7 - - + -
1711A VAL* 5.1 5.8 - - + -
1610D LEU* 6.0 6.7 - - + -
1613D VAL* 4.2 18.2 - - + -
1623D VAL* 4.7 7.4 - - + -
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Residues in contact with PHE1644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1640A MET* 3.1 38.8 + - + +
1641A THR 3.1 13.3 + - - +
1643A PHE* 1.3 77.9 - - - +
1645A TYR* 1.4 50.9 + - - +
1647A PHE* 3.8 2.9 - - - +
1648A ALA* 2.8 36.0 + - - +
1670A PHE* 3.7 37.5 - + + -
1673A LEU* 3.4 30.7 - - + -
1674A PHE* 3.4 31.4 - - + -
1677A MET* 3.8 21.3 - - + -
1704A PHE* 3.6 15.3 - + - -
1708A VAL* 4.1 1.1 - - + -
1802A PX4 3.8 18.8 - - + -
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Residues in contact with TYR1645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1641A THR* 3.0 44.1 + - + -
1642A LEU* 3.0 12.8 + - + +
1644A PHE* 1.4 74.1 - - - +
1646A ILE* 1.4 59.4 + - - +
1648A ALA* 3.5 1.2 + - - +
1649A ILE* 3.0 35.0 + - - +
1666A LEU* 4.8 1.6 - - + -
1670A PHE* 3.5 30.1 - + - -
1802A PX4 4.7 9.8 + - + +
1803A PX4 4.7 24.0 - - + +
1518D MET* 3.8 23.1 - - + -
1522D MET* 3.8 41.2 - - + +
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Residues in contact with ILE1646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1642A LEU* 3.1 46.1 + - + +
1643A PHE* 4.3 9.9 - - + +
1645A TYR* 1.4 72.2 - - - +
1647A PHE* 1.3 66.5 + - + +
1649A ILE* 3.3 19.8 - - - +
1650A MET* 3.3 28.5 + - + +
1518D MET* 3.7 16.8 - - + -
1606D ILE* 3.8 21.1 - - + -
1609D ILE* 3.8 23.6 - - + +
1610D LEU* 4.8 18.8 - - + +
1613D VAL* 5.6 2.5 - - + -
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Residues in contact with PHE1647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1643A PHE* 2.9 55.8 + + + +
1644A PHE 4.1 1.1 - - - +
1646A ILE* 1.3 78.6 - - + +
1648A ALA* 1.4 56.9 + - - +
1650A MET* 3.4 20.5 + - + -
1651A ALA 3.0 22.7 + - - -
1673A LEU* 3.4 8.8 - - + +
1700A PHE* 3.4 29.3 - + + -
1703A PRO* 5.1 3.8 - - + -
1704A PHE* 3.4 57.0 - + + -
1707A VAL* 4.1 21.1 - - + -
1708A VAL* 5.4 0.7 - - + -
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Residues in contact with ALA1648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1644A PHE 2.8 21.1 + - - +
1645A TYR 3.8 1.6 - - - +
1647A PHE* 1.4 75.2 - - - +
1649A ILE* 1.4 58.7 + - - +
1650A MET 3.2 0.2 - - - -
1652A THR* 2.7 33.4 + - - -
1666A LEU* 3.4 11.1 - - + +
1669A SER* 3.4 10.9 - - - -
1670A PHE* 3.5 33.0 - - + +
1673A LEU* 3.7 10.7 - - + +
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Residues in contact with ILE1649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1645A TYR* 3.0 21.2 + - + +
1646A ILE* 3.3 17.0 - - - +
1648A ALA* 1.4 75.3 - - - +
1650A MET* 1.3 56.5 + - - +
1652A THR* 4.2 4.2 - - - -
1653A GLN* 3.3 24.3 + - - +
1666A LEU* 3.6 18.2 - - + -
1518D MET* 4.8 8.1 - - + +
1521D MET* 3.7 33.0 - - + +
1522D MET* 3.7 31.4 - - + +
1605D ARG* 3.8 12.5 + - - +
1606D ILE* 3.6 32.8 - - + -
1609D ILE* 4.4 7.4 - - + -
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Residues in contact with MET1650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1646A ILE* 3.3 37.0 + - + +
1647A PHE* 3.5 37.9 - - + +
1648A ALA 3.2 0.2 - - - -
1649A ILE* 1.3 75.9 - - - +
1651A ALA* 1.3 59.4 + - - +
1652A THR 3.4 0.2 - - - -
1653A GLN* 3.5 5.9 + - - +
1654A LEU* 3.2 38.5 + - + +
1700A PHE* 3.6 18.8 - - + -
1603D LEU* 5.2 14.4 - - + -
1606D ILE* 3.6 35.9 - - + -
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Residues in contact with ALA1651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1647A PHE 3.0 17.0 + - - +
1648A ALA 3.6 0.2 + - - -
1649A ILE 3.6 0.2 - - - -
1650A MET* 1.3 72.8 - - - +
1652A THR* 1.4 62.5 + - - +
1655A PHE* 3.3 38.0 + - + -
1663A PHE* 3.6 24.8 - - + +
1669A SER* 3.5 20.2 - - - +
1673A LEU* 4.0 9.9 - - + -
1700A PHE* 4.0 10.3 - - + -
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Residues in contact with THR1652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1648A ALA 2.7 15.7 + - - -
1649A ILE* 4.2 5.4 - - - -
1651A ALA* 1.4 75.3 - - - +
1653A GLN* 1.3 62.2 + - - +
1656A GLY* 3.4 19.1 - - - -
1657A GLU* 5.2 0.3 - - - +
1663A PHE 3.5 9.2 - - - +
1664A GLY 3.4 25.1 - - - +
1665A THR* 3.3 18.2 + - - +
1666A LEU* 3.5 9.2 - - + +
1669A SER* 2.7 19.9 + - - -
1524D GLU* 4.1 18.7 - - + +
1525D LYS* 4.6 5.1 - - - -
1526D GLU* 5.8 1.0 + - - -
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Residues in contact with GLN1653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1649A ILE 3.3 16.4 + - - +
1650A MET* 3.6 7.0 - - - +
1651A ALA 3.3 0.2 - - - -
1652A THR* 1.3 80.4 - - - +
1654A LEU* 1.3 66.3 + - - +
1657A GLU* 3.6 10.4 - - - +
1524D GLU* 4.2 17.9 - - - +
1599D ARG* 2.9 38.3 + - - +
1602D ARG* 3.5 21.8 - - - +
1603D LEU* 3.5 11.2 - - - +
1605D ARG* 2.8 41.7 + - - +
1606D ILE* 3.5 15.9 - - - +
----------------------------------------------------------
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Residues in contact with LEU1654 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1650A MET* 3.2 22.5 + - + +
1652A THR 3.5 0.2 - - - -
1653A GLN* 1.3 78.2 - - - +
1655A PHE* 1.3 85.7 + - + +
1656A GLY 3.2 7.1 + - - -
1657A GLU* 3.2 17.0 - - - +
1694A TYR* 3.8 4.7 + - - -
1700A PHE* 4.4 15.9 - - + -
1801A PX4 3.7 15.9 - - + +
1599D ARG* 3.2 56.4 + - - +
1600D VAL* 4.4 4.7 - - - +
1603D LEU* 4.2 24.2 - - + -
----------------------------------------------------------
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Residues in contact with PHE1655 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1651A ALA* 3.3 26.4 + - - -
1654A LEU* 1.3 81.0 - - + +
1656A GLY* 1.3 56.7 + - - +
1657A GLU 3.8 0.4 - - - -
1659A PHE* 3.2 32.9 - - + +
1663A PHE* 3.4 21.6 - + + +
1690A LEU* 3.7 14.4 - - + -
1694A TYR* 3.7 36.8 - + + -
1697A ALA* 3.8 15.9 - - + -
1700A PHE* 3.7 39.9 - + + -
1701A PHE* 3.7 22.0 - + - -
1801A PX4 3.5 23.1 - - + -
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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