Contacts of the helix formed by residues 1629 - 1656 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1710A PHE* 4.2 5.4 - - + -
1714A ASN* 3.7 19.1 - - - +
1625D ALA 3.4 21.5 - - - +
1626D LEU 3.4 11.9 - - - +
1627D ILE 3.0 0.6 + - - -
1628D SER* 1.3 77.4 - - - +
1630D ILE* 1.4 64.0 - - - +
1632D GLY* 3.2 14.2 + - - -
1633D MET* 3.7 15.3 + - + +
1719D ILE* 3.8 40.6 - - + +
1722D ASP* 4.9 16.2 - - - +
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Residues in contact with ILE1630 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1710A PHE* 3.8 26.9 - - + -
1626D LEU 4.0 1.8 - - - +
1627D ILE* 3.5 44.6 - - + +
1629D VAL* 1.4 73.9 - - - +
1631D PRO* 1.4 65.0 - - + +
1633D MET* 2.9 23.5 + - + +
1634D LEU* 3.0 31.3 + - + +
1637D ILE* 4.7 10.1 - - + -
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Residues in contact with PRO1631 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1627D ILE 3.4 10.3 - - - +
1628D SER* 3.3 22.2 - - - +
1630D ILE* 1.4 89.3 - - + +
1632D GLY* 1.3 59.9 + - - +
1634D LEU* 3.4 30.3 - - + +
1635D SER* 4.6 3.5 + - - -
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Residues in contact with GLY1632 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1628D SER 5.0 0.6 + - - -
1629D VAL 3.2 9.8 + - - -
1631D PRO* 1.3 77.3 - - - +
1633D MET* 1.3 60.4 + - - +
1634D LEU 3.7 0.2 + - - -
1635D SER* 3.9 14.7 + - - -
1636D VAL* 4.3 5.9 - - - +
1722D ASP* 5.1 10.5 - - - -
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Residues in contact with MET1633 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1710A PHE* 3.8 35.9 - - + -
1629D VAL* 3.7 11.2 + - + +
1630D ILE* 2.9 16.7 + - + +
1632D GLY* 1.3 72.8 - - - +
1634D LEU* 1.4 56.5 + - - +
1635D SER 3.1 3.6 - - - -
1636D VAL* 2.9 29.1 + - - +
1637D ILE* 3.0 35.5 + - + +
1715D LEU* 3.8 34.1 - - + +
1718D ALA* 6.0 2.5 - - + -
1719D ILE* 3.8 28.5 - - + -
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Residues in contact with LEU1634 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1618C GLN* 5.9 0.4 - - - -
1803C PX4 5.9 0.2 - - - +
1630D ILE* 3.0 31.5 + - + +
1631D PRO* 3.4 26.2 - - + +
1632D GLY 3.4 0.6 - - - -
1633D MET* 1.4 73.1 - - - +
1635D SER* 1.3 60.3 + - - +
1637D ILE* 3.9 15.3 - - + +
1638D ALA* 3.2 24.9 + - - +
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Residues in contact with SER1635 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1618C GLN* 5.0 16.0 + - - +
1619C MET* 5.1 2.1 - - - +
1622C ILE* 3.6 37.4 - - - +
1631D PRO 4.6 3.0 + - - -
1632D GLY 3.9 11.5 + - - -
1633D MET 3.0 0.6 + - - -
1634D LEU* 1.3 79.0 - - - +
1636D VAL* 1.4 63.9 + - - +
1638D ALA* 3.4 4.6 + - - +
1639D LEU* 3.3 20.6 + - - +
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Residues in contact with VAL1636 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1622C ILE* 4.3 13.4 - - + +
1626C LEU* 4.5 17.9 - - + -
1632D GLY 4.3 6.3 - - - +
1633D MET* 2.9 18.6 + - - +
1635D SER* 1.4 72.1 - - - +
1637D ILE* 1.4 58.7 + - - +
1639D LEU* 3.5 4.4 + - + +
1640D MET* 3.0 29.2 + - - +
1711D VAL* 3.8 33.2 - - + +
1714D ASN 5.2 0.7 - - - -
1715D LEU* 3.8 26.0 - - + +
1718D ALA* 5.4 8.3 - - + -
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Residues in contact with ILE1637 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1706A PHE* 6.2 3.4 - - + -
1630D ILE* 4.7 7.4 - - + -
1633D MET* 3.0 52.0 + - + +
1634D LEU* 3.9 20.6 - - + +
1635D SER 3.3 0.2 - - - -
1636D VAL* 1.4 72.4 - - - +
1638D ALA* 1.4 55.0 + - - +
1640D MET* 3.0 9.2 + - - +
1641D THR* 2.7 46.0 + - - +
1715D LEU* 4.1 14.8 - - + -
1801D PX4 5.3 9.9 - - + -
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Residues in contact with ALA1638 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1618C GLN* 5.6 0.2 - - - +
1619C MET* 4.2 11.7 - - - +
1803C PX4 4.1 32.1 - - + +
1634D LEU 3.2 16.9 + - - +
1635D SER* 3.6 6.7 - - - +
1637D ILE* 1.4 76.8 - - - +
1639D LEU* 1.4 55.6 + - - +
1641D THR* 3.5 9.4 - - - -
1642D LEU* 3.2 28.2 + - - +
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Residues in contact with LEU1639 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1613C VAL* 3.8 15.7 - - + -
1619C MET* 3.9 16.9 - - + -
1622C ILE* 3.8 26.0 - - + +
1623C VAL* 3.6 35.2 - - + +
1626C LEU* 4.7 14.4 - - + -
1635D SER 3.3 8.7 + - - +
1636D VAL* 3.6 8.7 - - + +
1637D ILE 3.2 0.6 - - - -
1638D ALA* 1.4 74.1 - - - +
1640D MET* 1.4 59.2 + - - +
1642D LEU* 3.4 2.3 + - - +
1643D PHE* 3.0 66.1 + - + -
1711D VAL* 5.2 5.4 - - + -
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Residues in contact with MET1640 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1636D VAL 3.0 14.1 + - - +
1637D ILE* 3.0 12.9 + - - +
1639D LEU* 1.4 72.3 - - - +
1641D THR* 1.3 62.4 + - - +
1643D PHE* 3.6 9.2 + - - +
1644D PHE* 3.2 32.5 + - + -
1677D MET* 3.7 31.2 - - + -
1708D VAL* 3.3 44.2 - - + +
1711D VAL* 3.8 28.2 - - + +
1712D MET* 3.8 17.3 - - + -
1715D LEU* 6.5 0.4 - - + -
1801D PX4 3.8 19.5 - - + -
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Residues in contact with THR1641 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1803C PX4 6.3 1.8 - - + -
1637D ILE* 2.7 39.0 + - - +
1638D ALA* 3.5 10.3 - - - -
1640D MET* 1.3 71.3 - - - +
1642D LEU* 1.3 59.5 + - - +
1644D PHE* 3.1 10.5 - - - +
1645D TYR* 3.1 51.9 + - + +
1670D PHE* 5.6 2.5 - - + -
1801D PX4 4.6 13.3 - - + +
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Residues in contact with LEU1642 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1518C MET* 4.3 10.8 - - + -
1612C LEU* 3.6 38.6 - - + +
1613C VAL* 3.7 25.6 - - + -
1619C MET* 3.8 16.4 - - + -
1803C PX4 3.9 33.7 - - + -
1638D ALA 3.2 13.2 + - - +
1639D LEU 3.4 4.7 + - - +
1641D THR* 1.3 77.1 - - - +
1643D PHE* 1.4 63.7 + - - +
1645D TYR* 3.1 20.6 + - + +
1646D ILE* 3.1 36.6 + - + +
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Residues in contact with PHE1643 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1610C LEU* 5.6 7.9 - - + -
1613C VAL* 4.7 13.7 - - + -
1623C VAL* 5.4 8.5 - - + -
1626C LEU* 6.3 0.2 - - + -
1639D LEU* 3.0 58.8 + - + +
1640D MET* 3.8 12.8 - - - +
1642D LEU* 1.4 73.9 - - - +
1644D PHE* 1.4 56.5 + - - +
1646D ILE* 3.3 15.5 + - + +
1647D PHE* 2.9 58.9 + + + -
1704D PHE* 5.8 0.2 - - - -
1707D VAL* 4.1 23.6 - - + -
1708D VAL* 5.6 3.6 - - + -
1711D VAL* 4.9 10.5 - - + -
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Residues in contact with PHE1644 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1640D MET* 3.2 25.5 + - + +
1641D THR* 3.1 14.6 - - - +
1643D PHE* 1.4 74.8 - - - +
1645D TYR* 1.4 48.3 + - - +
1647D PHE* 3.4 7.5 + - - +
1648D ALA* 2.7 36.2 + - - +
1670D PHE* 3.7 31.6 - + + -
1673D LEU* 3.6 29.4 - - + +
1674D PHE* 3.6 25.8 - - - -
1677D MET* 3.4 35.7 - - + -
1704D PHE* 4.2 4.7 - + - -
1708D VAL* 4.2 13.7 - - + -
1801D PX4 3.6 33.4 - - + -
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Residues in contact with TYR1645 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1518C MET* 4.0 22.0 - - + -
1522C MET* 3.5 39.9 - - + -
1803C PX4 5.5 12.3 - - + -
1641D THR* 3.1 50.7 + - + +
1642D LEU* 3.1 13.0 + - + +
1644D PHE* 1.4 73.6 - - - +
1646D ILE* 1.4 53.1 + - - +
1648D ALA* 3.1 2.6 + - - +
1649D ILE* 2.8 42.3 + - + +
1666D LEU* 4.7 4.7 - - + -
1670D PHE* 3.6 29.6 - + - -
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Residues in contact with ILE1646 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1518C MET* 4.1 4.9 - - + -
1606C ILE* 4.8 14.9 - - + +
1609C ILE* 3.8 30.9 - - + +
1610C LEU* 4.5 30.3 - - + -
1613C VAL* 5.0 2.9 - - + -
1642D LEU* 3.1 41.8 + - + +
1643D PHE* 3.3 17.0 + - + +
1645D TYR* 1.4 73.1 - - - +
1647D PHE* 1.3 61.5 + - + +
1649D ILE* 3.4 2.6 + - - +
1650D MET* 3.1 50.5 + - + +
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Residues in contact with PHE1647 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1643D PHE* 2.9 43.7 + + + +
1644D PHE 3.8 4.0 - - - +
1646D ILE* 1.3 77.4 - - + +
1648D ALA* 1.4 55.6 + - - +
1650D MET* 3.6 12.1 - - + +
1651D ALA* 3.0 26.2 + - - +
1673D LEU* 3.7 7.7 - - + +
1700D PHE* 3.3 36.1 - + + -
1703D PRO* 4.7 2.7 - - + -
1704D PHE* 3.5 59.0 - + + -
1707D VAL* 4.0 32.5 - - + -
1708D VAL* 5.4 0.7 - - + -
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Residues in contact with ALA1648 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1644D PHE 2.7 21.8 + - - +
1645D TYR 3.1 4.9 + - - +
1647D PHE* 1.4 69.2 - - - +
1649D ILE* 1.4 63.3 + - - +
1650D MET 3.2 1.1 - - - -
1651D ALA 3.4 0.7 + - - -
1652D THR* 3.3 28.6 + - - +
1666D LEU* 3.9 13.5 - - + +
1669D SER* 3.7 4.7 - - - -
1670D PHE* 3.5 31.4 - - + -
1673D LEU* 3.4 16.6 - - + +
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Residues in contact with ILE1649 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1518C MET* 3.7 33.9 - - + +
1521C MET* 3.9 18.2 - - + +
1522C MET* 4.1 15.0 - - + -
1605C ARG* 3.4 32.3 + - - +
1606C ILE* 6.0 3.4 - - + -
1609C ILE* 3.8 18.6 - - + -
1645D TYR* 2.8 27.6 + - + +
1646D ILE 3.9 3.8 - - - +
1648D ALA* 1.4 72.3 - - - +
1650D MET* 1.3 58.9 + - + +
1652D THR* 2.8 22.6 + - - +
1653D GLN* 3.4 11.1 + - - +
1666D LEU* 3.7 19.1 - - + -
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Residues in contact with MET1650 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1603C LEU* 3.6 23.8 - - + -
1606C ILE* 3.7 32.3 - - + -
1646D ILE* 3.1 40.2 + - - +
1647D PHE* 3.6 13.9 - - + +
1648D ALA 3.2 0.2 - - - -
1649D ILE* 1.3 74.4 - - - +
1651D ALA* 1.3 54.2 + - - +
1653D GLN* 3.2 8.4 + - - +
1654D LEU* 2.8 44.1 + - + +
1700D PHE* 3.5 32.3 - - + -
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Residues in contact with ALA1651 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1647D PHE 3.0 18.8 + - - +
1648D ALA* 3.4 4.2 + - - +
1650D MET* 1.3 74.5 - - - +
1652D THR* 1.4 53.4 + - - +
1655D PHE* 2.8 49.7 + - + -
1656D GLY 3.1 4.7 + - - -
1663D PHE* 3.5 31.3 - - + +
1669D SER* 3.7 9.9 - - - +
1673D LEU* 4.7 3.8 - - + -
1700D PHE* 4.2 4.9 - - + -
----------------------------------------------------------
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Residues in contact with THR1652 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1521C MET 5.5 0.7 + - - -
1524C GLU* 4.5 21.6 + - - +
1525C LYS* 5.8 2.6 - - - +
1605C ARG* 5.0 1.0 + - - -
1648D ALA 3.3 10.7 + - - +
1649D ILE* 2.8 25.8 + - - +
1651D ALA* 1.4 74.3 - - - +
1653D GLN* 1.3 62.7 + - - +
1656D GLY* 2.8 24.9 + - - -
1657D GLU* 4.0 4.5 + - - +
1663D PHE 3.4 13.5 - - - +
1664D GLY 4.7 3.4 - - - -
1665D THR 3.2 24.9 - - - +
1666D LEU* 3.7 9.6 - - + +
1669D SER* 3.1 17.9 - - - +
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Residues in contact with GLN1653 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1524C GLU* 4.5 7.2 - - - +
1599C ARG* 2.8 36.7 + - - +
1602C ARG* 3.6 26.9 - - - +
1603C LEU* 3.5 35.9 - - - +
1605C ARG* 2.9 48.1 + - - +
1606C ILE* 4.7 2.6 - - - +
1649D ILE 3.4 6.6 - - - +
1650D MET* 3.2 7.8 + - - +
1652D THR* 1.3 81.0 + - - +
1654D LEU* 1.3 60.3 + - - +
1657D GLU* 3.1 22.0 - - - +
----------------------------------------------------------
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Residues in contact with LEU1654 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1599C ARG* 3.3 29.4 + - - +
1600C VAL* 4.6 16.2 - - + -
1603C LEU* 3.7 33.7 - - + -
1650D MET* 2.8 27.7 + - + +
1653D GLN* 1.3 77.5 - - - +
1655D PHE* 1.3 76.8 + - + +
1656D GLY 3.7 0.4 - - - -
1657D GLU* 3.3 6.0 - - - +
1694D TYR* 3.4 8.3 + - - -
1700D PHE* 3.7 32.5 - - + -
1802D PX4 3.7 27.4 - - + +
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Residues in contact with PHE1655 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1651D ALA* 2.8 43.0 + - + -
1654D LEU* 1.3 81.8 - - + +
1656D GLY* 1.3 61.8 + - - +
1657D GLU 3.3 2.5 - - - -
1659D PHE* 3.1 29.7 + - + +
1663D PHE* 3.7 21.1 - + + +
1690D LEU* 3.6 23.3 - - + -
1694D TYR* 3.5 28.3 - + + -
1697D ALA* 4.6 5.6 - - + -
1700D PHE* 3.6 33.2 - + + -
1701D PHE* 3.5 28.0 - + - -
1802D PX4 3.6 23.1 - - + -
----------------------------------------------------------
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Residues in contact with GLY1656 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1525C LYS 6.5 0.2 - - - -
1526C GLU* 3.2 22.0 - - - +
1651D ALA 3.1 2.6 + - - -
1652D THR* 2.8 25.5 + - - -
1654D LEU 3.7 0.2 - - - -
1655D PHE* 1.3 74.0 - - - +
1657D GLU* 1.3 61.3 - - - +
1660D PRO* 3.5 7.1 - - - +
1663D PHE 3.2 26.0 - - - -
1664D GLY* 3.4 11.2 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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).
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