Contacts of the helix formed by residues 1565 - 1591 (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 ASP1565 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1561A SER 3.8 9.1 + - - +
1562A PHE* 2.9 13.7 + - - +
1563A PHE 3.7 1.3 - - - +
1564A LYS* 1.4 77.0 - - - +
1566A PRO* 1.4 64.9 - - - +
1567A TRP* 3.2 36.6 - - - +
1568A SER* 2.7 34.8 + - - +
1569A LEU* 3.0 27.4 + - - +
1620A ARG* 5.3 0.5 + - - -
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Residues in contact with PRO1566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1564A LYS 3.7 7.6 - - - +
1565A ASP* 1.4 91.7 - - - +
1567A TRP* 1.4 77.1 + - + +
1569A LEU* 3.5 8.1 - - + +
1570A PHE* 2.9 33.0 + - - +
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Residues in contact with TRP1567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1554A ARG* 5.5 0.7 + - - -
1565A ASP* 3.2 32.9 - - - +
1566A PRO* 1.4 89.9 - - + +
1568A SER* 1.4 58.9 + - - +
1570A PHE* 4.2 7.4 - - - +
1571A ASP* 3.5 20.1 + - - +
1614A THR* 3.5 27.1 + - - +
1620A ARG* 3.4 58.9 + - + +
1623A VAL* 6.4 0.4 - - - +
1624A SER* 4.4 14.1 + - - -
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Residues in contact with SER1568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1551A ILE* 3.9 10.4 - - - +
1554A ARG* 5.3 9.5 + - - +
1562A PHE* 3.4 37.9 - - - -
1565A ASP* 2.7 25.2 + - - +
1566A PRO 3.2 0.4 - - - -
1567A TRP* 1.4 75.5 - - - +
1569A LEU* 1.4 65.0 + - - +
1571A ASP* 3.4 18.4 - - - +
1572A PHE 3.4 4.3 + - - -
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Residues in contact with LEU1569 (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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1562A PHE* 4.1 12.3 + - + +
1563A PHE* 3.4 43.3 - - + +
1565A ASP 3.0 16.6 + - - +
1566A PRO* 3.5 9.9 - - + +
1568A SER* 1.4 75.2 - - - +
1570A PHE* 1.4 62.8 + - - +
1572A PHE* 3.1 10.9 + - + +
1573A VAL* 3.1 37.8 + - + +
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Residues in contact with PHE1570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1566A PRO 2.9 18.5 + - - +
1567A TRP* 4.2 5.4 - - - +
1569A LEU* 1.4 74.3 - - - +
1571A ASP* 1.4 61.7 + - - +
1573A VAL* 3.0 18.5 + - + +
1574A VAL* 2.9 53.1 + - + +
1607A GLY* 6.2 0.2 - - - -
1610A LEU* 3.7 30.1 - - + -
1611A ARG* 4.5 5.2 - - + -
1614A THR* 4.0 31.2 - - + -
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Residues in contact with ASP1571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1510A ILE* 5.8 0.2 - - - +
1550A GLU* 3.6 4.5 - - - +
1551A ILE* 3.4 17.5 - - + +
1554A ARG* 3.0 26.4 + - - +
1567A TRP 3.5 14.5 + - - +
1568A SER 3.4 13.0 + - - +
1569A LEU 3.3 0.2 - - - -
1570A PHE* 1.4 79.6 - - - +
1572A PHE* 1.4 60.5 + - - +
1574A VAL* 3.5 7.5 - - - +
1575A VAL* 3.3 21.1 + - - +
1611A ARG* 2.9 55.1 + - + +
1614A THR* 6.4 0.2 - - + -
1615A ALA* 6.1 0.2 - - - +
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Residues in contact with PHE1572 (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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1551A ILE* 3.7 38.1 - - + +
1555A ILE* 3.7 22.2 - - + -
1562A PHE* 4.2 17.9 - + + -
1563A PHE* 5.8 8.3 - + - -
1568A SER 3.4 4.1 + - - +
1569A LEU* 3.1 12.0 + - + +
1571A ASP* 1.4 74.9 - - - +
1573A VAL* 1.4 65.9 + - + +
1575A VAL* 3.2 7.6 + - + +
1576A ILE* 3.0 52.4 + - + +
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Residues in contact with VAL1573 (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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1569A LEU* 3.2 33.2 - - + +
1570A PHE* 3.0 21.0 + - + +
1572A PHE* 1.4 76.6 - - + +
1574A VAL* 1.4 63.9 + - + +
1576A ILE* 3.3 14.4 - - + +
1577A ILE* 3.1 41.1 + - + +
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Residues in contact with VAL1574 (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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1547A PHE* 6.2 1.1 - - + -
1570A PHE* 2.9 44.7 + - + +
1571A ASP 3.5 9.4 - - - +
1573A VAL* 1.4 75.3 - - - +
1575A VAL* 1.4 53.0 + - - +
1577A ILE* 3.2 10.6 + - + +
1578A SER* 2.8 40.9 + - - +
1607A GLY* 3.4 40.6 - - - +
1608A ARG* 3.9 9.9 - - + +
1611A ARG* 4.1 23.6 - - + +
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Residues in contact with VAL1575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1544A ILE* 5.3 0.9 - - + +
1547A PHE* 3.7 19.7 - - + +
1548A THR* 3.6 33.4 - - + +
1551A ILE* 3.8 20.2 - - + -
1571A ASP 3.3 15.5 + - - +
1572A PHE* 3.2 11.6 + - + +
1574A VAL* 1.4 74.9 - - + +
1576A ILE* 1.4 63.0 + - + +
1578A SER* 3.3 6.4 + - - -
1579A ILE* 3.2 33.5 + - + +
1611A ARG* 3.4 19.1 - - - +
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Residues in contact with ILE1576 (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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1572A PHE* 3.0 38.4 + - + +
1573A VAL* 3.3 25.1 - - + +
1575A VAL* 1.4 78.4 - - + +
1577A ILE* 1.4 60.0 + - + +
1579A ILE* 4.1 13.3 - - + +
1580A VAL* 3.3 40.9 + - + +
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Residues in contact with ILE1577 (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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1573A VAL* 3.1 39.7 + - + +
1574A VAL* 3.5 8.7 - - + +
1576A ILE* 1.4 78.4 - - + +
1578A SER* 1.3 58.2 + - - +
1579A ILE 3.1 4.0 - - - -
1580A VAL* 4.8 2.9 - - - -
1581A GLY* 2.8 31.5 + - - -
1604A ALA* 3.9 31.2 - - + +
1607A GLY* 5.3 4.9 - - - -
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Residues in contact with SER1578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1544A ILE* 3.4 20.6 - - - +
1574A VAL* 2.8 24.6 + - - +
1575A VAL* 3.8 6.5 - - - -
1577A ILE* 1.3 71.4 - - - +
1579A ILE* 1.4 56.0 + - - +
1582A MET* 3.2 22.5 + - - +
1604A ALA 4.3 5.2 + - - -
1607A GLY 4.7 0.3 - - - -
1608A ARG* 3.1 47.3 + - - +
1808A 5P2 3.9 10.3 - - - -
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Residues in contact with ILE1579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1544A ILE* 3.7 17.7 - - + -
1545A ILE* 6.4 1.3 - - + -
1548A THR* 3.5 31.9 - - + +
1575A VAL* 3.2 27.2 + - + +
1576A ILE* 4.2 13.0 - - + +
1577A ILE 3.1 0.6 - - - -
1578A SER* 1.4 76.1 - - - +
1580A VAL* 1.4 70.3 + - + +
1582A MET* 3.2 13.8 + - + +
1583A PHE* 3.1 47.0 + - + -
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Residues in contact with VAL1580 (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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1576A ILE* 3.3 26.2 + - + +
1577A ILE* 4.2 3.4 - - - +
1579A ILE* 1.4 77.1 - - + +
1581A GLY* 1.3 55.0 + - - +
1583A PHE* 3.0 10.1 + - - +
1584A LEU* 2.8 50.1 + - + +
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Residues in contact with GLY1581 (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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1577A ILE 2.8 20.4 + - - -
1580A VAL* 1.3 75.2 - - - +
1582A MET* 1.4 53.3 + - - -
1584A LEU* 4.5 5.4 - - - -
1585A ALA* 2.9 37.8 + - - +
1601A ILE* 4.4 6.8 - - - +
1604A ALA* 4.1 9.2 - - - -
1808A 5P2 3.1 17.9 - - - -
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Residues in contact with MET1582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1541A VAL* 3.8 26.9 - - + -
1544A ILE* 3.7 42.8 - - + -
1545A ILE* 5.7 5.6 - - + -
1578A SER 3.2 18.4 + - - +
1579A ILE* 3.2 23.0 + - + +
1581A GLY* 1.4 74.0 - - - +
1583A PHE* 1.3 85.4 + - + +
1586A ASP* 3.4 10.6 + - - +
1808A 5P2 3.2 64.8 + - + +
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Residues in contact with PHE1583 (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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1579A ILE* 3.1 38.5 + - + -
1580A VAL* 3.0 7.8 + - - +
1582A MET* 1.3 92.8 - - + +
1584A LEU* 1.4 53.9 + - - +
1585A ALA 3.3 0.2 - - - -
1586A ASP* 3.1 7.5 + - + +
1587A LEU* 2.8 35.8 + - - +
1808A 5P2 3.1 33.9 - + - -
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Residues in contact with LEU1584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1580A VAL* 2.8 35.2 + - + +
1581A GLY* 4.1 2.2 - - - +
1583A PHE* 1.4 71.1 - - - +
1585A ALA* 1.4 61.5 + - - +
1587A LEU* 3.4 20.4 - - + +
1588A ILE* 3.3 36.4 + - + +
1601A ILE* 3.7 37.5 - - + -
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Residues in contact with ALA1585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1581A GLY 2.9 20.9 + - - +
1584A LEU* 1.4 71.8 - - - +
1586A ASP* 1.4 58.2 + - - +
1588A ILE* 3.2 5.2 + - - +
1589A GLU 3.1 21.8 + - - -
1598A PHE* 3.2 26.1 - - + -
1601A ILE* 3.9 14.3 - - + +
1602A ARG* 4.6 9.9 - - + +
1808A 5P2 3.4 30.1 - - - +
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Residues in contact with ASP1586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1582A MET 3.4 18.2 + - - +
1583A PHE* 3.1 7.5 + - + +
1585A ALA* 1.4 74.2 - - - +
1587A LEU* 1.4 60.0 + - - +
1589A GLU* 3.2 3.6 + - - +
1590A THR* 2.9 42.4 + - - -
1807A PX4 3.8 20.2 - - - +
1808A 5P2 3.1 68.6 + - + +
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Residues in contact with LEU1587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1583A PHE 2.8 13.2 + - - +
1584A LEU* 3.4 27.6 - - + +
1586A ASP* 1.4 76.6 + - - +
1588A ILE* 1.4 60.5 + - + +
1590A THR* 3.3 5.2 + - - -
1591A TYR* 3.1 58.6 + - + +
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Residues in contact with ILE1588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1584A LEU* 3.3 26.7 - - + +
1585A ALA* 3.2 9.0 + - - +
1587A LEU* 1.4 78.5 - - + +
1589A GLU* 1.3 57.5 + - - +
1591A TYR 2.9 21.5 - - - +
1592A PHE* 3.7 7.6 - - - -
1593A VAL 3.4 12.0 - - - +
1594A SER* 3.3 28.7 - - - +
1595A PRO* 5.5 0.2 - - + -
1597A LEU* 4.0 24.0 - - + -
1598A PHE* 3.9 21.1 - - + +
1601A ILE* 4.2 21.3 - - + -
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Residues in contact with GLU1589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1537A TYR* 5.1 3.0 + - + -
1585A ALA 3.1 12.3 + - - +
1586A ASP* 3.4 13.2 - - - +
1587A LEU 3.2 0.2 - - - -
1588A ILE* 1.3 76.6 - - - +
1590A THR* 1.4 62.7 + - - +
1592A PHE* 3.3 45.4 - - - -
1598A PHE* 3.4 32.7 - - + -
1808A 5P2 3.8 31.4 - - + +
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Residues in contact with THR1590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1586A ASP* 2.9 27.9 + - - -
1587A LEU* 3.3 5.8 + - - -
1589A GLU* 1.4 74.0 - - - +
1591A TYR* 1.3 82.7 + - + +
1592A PHE* 3.3 24.9 - - - -
1807A PX4 5.2 2.9 - - - -
1808A 5P2 3.9 14.7 - - + +
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Residues in contact with TYR1591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1587A LEU* 3.1 42.0 + - + +
1588A ILE* 2.9 17.8 - - - +
1590A THR* 1.3 89.6 - - + +
1592A PHE* 1.4 49.9 + - - +
1593A VAL* 2.7 31.2 + - + +
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il