Contacts of the helix formed by residues 1633 - 1655 (chain B) 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 MET1633 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1629B VAL* 3.6 10.8 - - - +
1630B ILE* 3.3 25.1 - - + +
1631B PRO 2.8 0.8 + - - -
1632B GLY* 1.3 76.2 - - - +
1634B LEU* 1.4 60.0 + - - +
1635B SER 3.3 3.6 - - - -
1636B VAL* 3.1 18.4 + - + +
1637B ILE* 3.0 45.5 + - + +
1715B LEU* 3.9 28.5 - - + +
1718B ALA* 4.9 2.7 - - + -
1719B ILE* 3.7 33.9 - - + -
1710C PHE* 3.6 28.9 - - + -
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Residues in contact with LEU1634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1804A PX4 5.5 12.3 - - + -
1630B ILE* 3.3 39.4 + - + +
1631B PRO* 3.0 20.0 + - + +
1633B MET* 1.4 74.6 - - - +
1635B SER* 1.3 59.5 + - - +
1637B ILE* 3.6 14.1 - - + +
1638B ALA* 3.0 29.7 + - + +
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Residues in contact with SER1635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1618A GLN* 3.7 29.7 + - - +
1619A MET* 5.8 0.2 - - - -
1622A ILE* 3.2 39.6 - - - +
1804A PX4 4.3 8.3 - - - +
1631B PRO 4.7 0.4 + - - -
1633B MET 3.3 0.8 - - - -
1634B LEU* 1.3 75.4 - - - +
1636B VAL* 1.4 55.6 + - - +
1638B ALA* 3.3 7.5 + - - +
1639B LEU 2.8 29.5 + - - -
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Residues in contact with VAL1636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1622A ILE* 4.7 11.9 - - + -
1626A LEU* 5.6 5.2 - - + -
1633B MET* 3.1 19.0 + - + +
1635B SER* 1.4 77.5 - - - +
1637B ILE* 1.4 58.2 + - - +
1639B LEU* 3.6 8.9 + - + +
1640B MET* 3.1 27.5 + - - +
1711B VAL* 3.7 34.4 - - + +
1714B ASN* 5.0 4.0 - - + +
1715B LEU* 3.8 29.7 - - + +
1718B ALA* 5.1 8.3 - - + -
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Residues in contact with ILE1637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1630B ILE* 3.8 8.3 - - + +
1633B MET* 3.0 44.2 + - + +
1634B LEU* 3.6 26.2 - - + +
1635B SER 3.3 0.2 - - - -
1636B VAL* 1.4 73.5 - - - +
1638B ALA* 1.4 57.0 + - - +
1640B MET* 3.4 8.1 + - - +
1641B THR* 2.9 35.8 + - - +
1715B LEU* 3.8 16.2 - - + -
1802B PX4 4.6 9.5 - - + +
1706C PHE* 6.1 4.0 - - + -
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Residues in contact with ALA1638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1619A MET* 3.7 25.3 - - + +
1804A PX4 4.6 20.1 - - + +
1634B LEU* 3.0 20.0 + - + +
1635B SER* 3.4 9.0 - - - +
1637B ILE* 1.4 74.3 - - - +
1639B LEU* 1.4 63.1 + - - +
1641B THR* 3.4 8.5 + - - -
1642B LEU* 3.2 17.3 + - - +
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Residues in contact with LEU1639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1613A VAL* 4.2 8.7 - - + -
1619A MET* 3.9 13.9 - - - +
1622A ILE* 3.6 18.2 - - + -
1623A VAL* 3.6 20.0 - - + -
1626A LEU* 3.5 31.9 - - + -
1635B SER 2.8 20.8 + - - +
1636B VAL* 3.8 5.6 - - - +
1638B ALA* 1.4 68.9 - - - +
1640B MET* 1.3 58.7 + - - +
1642B LEU* 3.3 2.8 + - - +
1643B PHE* 2.9 70.0 + - + -
1711B VAL* 4.2 18.2 - - + -
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Residues in contact with MET1640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1636B VAL 3.1 18.2 + - - +
1637B ILE* 3.4 8.5 - - - +
1638B ALA 3.3 0.2 - - - -
1639B LEU* 1.3 77.5 - - - +
1641B THR* 1.4 56.0 + - - +
1643B PHE* 3.2 9.6 + - - +
1644B PHE* 2.8 31.5 + - + +
1677B MET* 4.1 2.2 - - - -
1708B VAL* 3.3 48.5 - - + +
1711B VAL* 3.7 26.9 - - + -
1712B MET* 3.6 33.7 - - + +
1715B LEU* 6.2 1.3 - - + -
1802B PX4 3.7 24.2 - - + -
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Residues in contact with THR1641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1637B ILE* 2.9 19.9 + - - +
1638B ALA* 3.4 7.7 + - - -
1640B MET* 1.4 74.7 - - - +
1642B LEU* 1.4 57.7 + - - +
1644B PHE* 3.2 8.8 + - - +
1645B TYR* 3.0 53.3 + - + +
1670B PHE* 5.0 5.4 - - + -
1802B PX4 4.2 20.9 - - + +
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Residues in contact with LEU1642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1518A MET* 4.0 30.3 - - + -
1612A LEU* 3.9 35.7 - - + +
1613A VAL* 3.6 33.9 - - + +
1619A MET* 3.9 23.3 - - + -
1804A PX4 5.2 8.7 - - + -
1638B ALA 3.2 10.4 + - - +
1639B LEU* 3.6 9.0 - - - +
1640B MET 3.3 0.2 - - - -
1641B THR* 1.4 75.4 - - - +
1643B PHE* 1.3 61.7 + - - +
1645B TYR* 3.2 8.6 + - + +
1646B ILE* 3.2 35.2 + - + +
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Residues in contact with PHE1643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1613A VAL* 3.5 25.6 - - + -
1623A VAL* 4.4 9.2 - - + -
1626A LEU* 6.0 0.9 - - + -
1639B LEU* 2.9 51.4 + - + +
1640B MET* 3.4 13.7 - - - +
1642B LEU* 1.3 74.6 - - - +
1644B PHE* 1.3 63.2 + - + +
1646B ILE* 3.7 9.5 + - + +
1647B PHE* 3.2 37.3 + + + -
1707B VAL* 3.6 32.1 - - + -
1708B VAL* 5.9 2.2 - - + -
1711B VAL* 3.9 26.0 - - + -
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Residues in contact with PHE1644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1640B MET* 2.8 19.8 + - + +
1641B THR* 3.2 13.4 + - - +
1643B PHE* 1.3 75.0 - - - +
1645B TYR* 1.4 53.8 + - - +
1647B PHE* 3.5 6.0 + - - +
1648B ALA* 2.8 36.2 + - - +
1670B PHE* 3.7 36.6 - + + -
1673B LEU* 3.5 29.2 - - + +
1674B PHE* 3.6 29.8 - + + -
1677B MET* 3.5 28.9 - - - -
1704B PHE* 4.1 5.4 - + - -
1708B VAL* 3.7 17.9 - - + -
1802B PX4 3.7 24.0 - - + -
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Residues in contact with TYR1645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1518A MET* 4.1 26.2 - - + -
1522A MET* 3.6 45.1 - - + +
1804A PX4 5.5 11.5 - - + +
1641B THR* 3.0 42.8 + - + +
1642B LEU* 3.2 11.8 + - + +
1644B PHE* 1.4 70.0 - - - +
1646B ILE* 1.4 54.9 + - - +
1648B ALA* 2.8 6.9 + - - +
1649B ILE* 2.8 38.8 + - + +
1666B LEU* 4.2 3.4 - - + -
1670B PHE* 3.5 32.1 - + - -
1802B PX4 4.1 13.9 - - + +
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Residues in contact with ILE1646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1518A MET* 5.2 1.1 - - - -
1606A ILE* 3.4 31.7 - - + +
1609A ILE* 3.8 38.8 - - + +
1610A LEU* 3.8 25.4 - - + -
1613A VAL* 4.5 11.9 - - + -
1642B LEU* 3.2 35.8 + - + +
1643B PHE* 4.0 11.9 - - + +
1645B TYR* 1.4 74.0 - - + +
1647B PHE* 1.4 61.8 + - + +
1649B ILE* 3.5 3.7 + - - +
1650B MET* 3.2 36.2 + - + +
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Residues in contact with PHE1647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1643B PHE* 3.2 30.6 + + + +
1644B PHE 3.8 3.6 - - - +
1645B TYR 3.2 0.6 - - - -
1646B ILE* 1.4 75.0 - - + +
1648B ALA* 1.4 60.2 + - - +
1649B ILE 3.4 0.2 - - - -
1650B MET* 3.5 18.7 + - + -
1651B ALA 3.1 20.6 + - - -
1673B LEU* 3.4 20.6 - - + +
1700B PHE* 3.5 36.4 - + - -
1703B PRO* 4.9 3.4 - - + -
1704B PHE* 3.5 48.7 - + + -
1707B VAL* 3.7 34.3 - - + -
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Residues in contact with ALA1648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1644B PHE* 2.8 21.4 + - + +
1645B TYR 2.8 4.2 + - - +
1647B PHE* 1.4 69.0 - - - +
1649B ILE* 1.4 62.1 + - - +
1650B MET 3.2 1.6 - - - -
1652B THR* 2.9 32.4 + - - -
1666B LEU* 3.9 9.6 - - + +
1669B SER* 3.6 10.9 - - - -
1670B PHE* 3.6 31.0 - - + -
1673B LEU* 3.5 13.6 - - + +
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Residues in contact with ILE1649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1518A MET* 3.8 32.1 - - + +
1521A MET* 3.8 18.8 - - + +
1522A MET* 4.0 10.3 - - + -
1524A GLU* 4.0 1.9 - - - +
1605A ARG* 3.4 26.3 + - - +
1606A ILE* 3.7 15.9 - - + -
1609A ILE* 4.0 17.0 - - + -
1645B TYR* 2.8 28.5 + - + +
1646B ILE 3.7 5.2 - - - +
1648B ALA* 1.4 74.2 - - - +
1650B MET* 1.3 60.4 + - - +
1652B THR* 4.4 2.5 - - - -
1653B GLN* 3.6 19.4 + - - +
1666B LEU* 3.7 20.2 - - + -
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Residues in contact with MET1650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1603A LEU* 3.7 29.4 - - + -
1606A ILE* 3.5 29.8 - - + -
1610A LEU* 5.9 0.7 - - + -
1646B ILE* 3.2 41.6 + - + +
1647B PHE* 3.5 32.3 - - + +
1648B ALA 3.2 0.2 - - - -
1649B ILE* 1.3 76.5 - - - +
1651B ALA* 1.3 58.8 + - - +
1652B THR 3.4 0.2 - - - -
1653B GLN* 3.3 5.5 + - - +
1654B LEU* 3.1 33.7 + - - +
1700B PHE* 3.6 19.7 - - + -
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Residues in contact with ALA1651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1647B PHE 3.1 17.5 + - - +
1648B ALA 3.6 0.2 + - - -
1650B MET* 1.3 71.4 - - - +
1652B THR* 1.3 65.2 + - - +
1655B PHE* 3.1 39.8 + - + +
1656B GLY 3.3 5.2 + - - -
1663B PHE* 3.6 30.7 - - + +
1669B SER* 3.9 11.7 - - - +
1673B LEU* 4.3 6.5 - - + -
1700B PHE* 4.1 8.0 - - + -
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Residues in contact with THR1652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1524A GLU* 3.9 24.7 - - - +
1525A LYS* 4.0 7.6 - - - -
1526A GLU 4.8 0.4 + - - +
1648B ALA 2.9 15.6 + - - -
1649B ILE* 4.4 4.7 - - - -
1651B ALA* 1.3 75.6 - - - +
1653B GLN* 1.3 62.7 + - - +
1656B GLY* 3.2 20.1 - - - -
1657B GLU* 4.5 0.5 + - - +
1663B PHE 3.2 18.6 - - - +
1664B GLY 3.6 18.8 - - - +
1665B THR 3.3 11.8 + - - -
1666B LEU* 3.8 6.0 - - + +
1669B SER* 2.7 21.2 + - - -
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Residues in contact with GLN1653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1524A GLU* 3.8 11.8 + - - +
1599A ARG* 2.8 37.9 + - + +
1602A ARG* 3.2 24.4 + - - +
1603A LEU* 3.2 42.1 - - - +
1605A ARG* 3.3 32.5 + - - +
1606A ILE* 4.5 2.8 - - - +
1649B ILE 3.6 13.2 + - - +
1650B MET 3.3 8.5 + - - +
1651B ALA 3.3 0.2 - - - -
1652B THR* 1.3 82.5 - - - +
1654B LEU* 1.3 63.2 + - - +
1656B GLY 4.5 0.3 + - - -
1657B GLU* 4.7 10.2 - - - +
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Residues in contact with LEU1654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1599A ARG* 3.5 52.6 - - + +
1600A VAL* 4.4 10.8 - - + -
1603A LEU* 3.8 27.8 - - + -
1650B MET 3.1 19.2 + - - +
1653B GLN* 1.3 78.2 - - - +
1655B PHE* 1.3 83.8 + - + +
1657B GLU* 4.3 6.1 + - - +
1694B TYR* 3.5 10.7 + - - -
1700B PHE* 4.2 25.4 - - + -
1801B PX4 4.1 21.1 - - + +
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Residues in contact with PHE1655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1651B ALA* 3.1 24.6 + - + +
1654B LEU* 1.3 84.2 - - + +
1656B GLY* 1.3 55.1 + - - +
1657B GLU 3.1 3.8 + - - -
1658B ARG 3.5 2.1 + - - -
1659B PHE* 2.8 37.0 + - + +
1663B PHE* 3.6 20.0 - + + -
1690B LEU* 3.7 12.6 - - + -
1694B TYR* 3.6 30.6 + + + -
1697B ALA* 4.0 19.5 - - + -
1700B PHE* 3.8 30.5 - + + -
1701B PHE* 3.5 34.5 - + - -
1801B PX4 3.8 19.3 - - - -
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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