Contacts of the helix formed by residues 1565 - 1591 (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 ASP1565 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1561D SER 4.0 2.9 + - - +
1562D PHE* 3.4 16.1 + - - +
1563D PHE 4.1 0.7 - - - +
1564D LYS* 1.4 83.5 - - + +
1566D PRO* 1.4 64.2 - - - +
1567D TRP* 3.1 33.4 - - - +
1568D SER* 3.1 30.8 + - - +
1569D LEU* 3.1 24.6 + - - +
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Residues in contact with PRO1566 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1564D LYS* 3.7 10.1 - - + +
1565D ASP* 1.4 90.4 - - - +
1567D TRP* 1.4 69.6 + - + +
1569D LEU* 3.3 17.4 - - + +
1570D PHE* 3.0 27.2 + - - +
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Residues in contact with TRP1567 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1554D ARG* 4.8 0.7 - - - -
1565D ASP* 3.1 24.0 + - - +
1566D PRO* 1.4 86.9 - - + +
1568D SER* 1.4 58.1 + - - +
1570D PHE* 3.2 7.9 + + + +
1571D ASP* 3.0 35.5 + - - +
1614D THR* 3.8 39.5 - - + -
1620D ARG* 3.6 44.9 - - + -
1623D VAL* 5.5 6.5 - - + -
1624D SER* 4.0 21.3 - - - -
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Residues in contact with SER1568 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1554D ARG* 2.8 29.2 + - - +
1558D HIS* 5.9 2.3 + - - -
1562D PHE* 3.3 50.1 - - - -
1565D ASP* 3.1 25.2 + - - +
1567D TRP* 1.4 70.7 - - - +
1569D LEU* 1.3 63.2 + - - +
1571D ASP* 3.6 2.3 + - - +
1572D PHE* 3.2 16.8 + - - +
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Residues in contact with LEU1569 (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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1562D PHE* 4.7 4.6 + - - -
1563D PHE* 3.8 34.5 - - + +
1565D ASP 3.1 17.0 + - - +
1566D PRO* 3.3 17.0 - - + +
1568D SER* 1.3 76.2 - - - +
1570D PHE* 1.4 56.0 + - - +
1572D PHE* 3.2 14.9 + - + +
1573D VAL* 3.1 38.1 + - + +
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Residues in contact with PHE1570 (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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1566D PRO 3.0 14.4 + - - +
1567D TRP* 3.2 9.4 + - + +
1569D LEU* 1.4 71.5 - - - +
1571D ASP* 1.4 70.0 + - - +
1572D PHE 3.0 3.8 - - - -
1573D VAL* 2.8 32.2 + - + +
1574D VAL* 2.9 31.2 + - + +
1610D LEU* 4.1 32.3 - - + -
1611D ARG* 3.6 18.8 - - + -
1614D THR* 3.3 38.6 - - + -
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Residues in contact with ASP1571 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1550D GLU* 5.4 0.5 - - - +
1551D ILE* 4.1 7.4 - - + +
1554D ARG* 3.0 42.2 + - - +
1567D TRP* 3.0 20.6 + - - +
1568D SER 3.8 1.6 - - - +
1570D PHE* 1.4 87.4 - - - +
1572D PHE* 1.4 58.5 + - - +
1574D VAL* 3.5 20.6 - - - +
1575D VAL* 3.6 10.4 + - - +
1611D ARG* 3.0 32.1 + - - +
1614D THR* 3.7 10.1 + - - -
1615D ALA* 5.0 5.9 - - - +
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Residues in contact with PHE1572 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1551D ILE* 4.1 17.0 - - + +
1555D ILE* 3.8 31.2 - - + -
1562D PHE* 3.9 12.3 - + + -
1563D PHE* 4.6 18.4 - + - -
1568D SER 3.2 13.7 + - - +
1569D LEU* 3.2 17.9 - - + +
1570D PHE 3.0 0.4 - - - -
1571D ASP* 1.4 74.3 - - - +
1573D VAL* 1.4 69.1 + - + +
1574D VAL 3.2 1.3 - - - -
1575D VAL* 3.3 7.8 - - + +
1576D ILE* 3.2 43.0 + - + +
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Residues in contact with VAL1573 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1569D LEU* 3.1 27.8 - - + +
1570D PHE* 2.8 17.4 + - + +
1572D PHE* 1.4 77.2 - - + +
1574D VAL* 1.4 56.9 + - - +
1576D ILE* 3.3 18.3 - - + +
1577D ILE* 3.0 43.8 + - + +
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Residues in contact with VAL1574 (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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1547D PHE* 6.3 2.0 - - + -
1570D PHE* 2.9 44.8 + - + +
1571D ASP* 3.5 11.2 - - - +
1573D VAL* 1.4 76.0 - - - +
1575D VAL* 1.3 59.2 + - + +
1577D ILE* 3.3 10.0 - - + +
1578D SER* 3.1 28.1 + - - -
1607D GLY* 3.4 36.8 - - - +
1608D ARG* 3.8 12.9 + - + +
1611D ARG* 3.7 22.9 - - + +
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Residues in contact with VAL1575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1544D ILE* 4.3 3.8 - - - +
1547D PHE* 3.8 14.6 - - + +
1548D THR* 3.3 44.4 - - + +
1551D ILE* 3.7 24.5 - - + -
1571D ASP 3.6 6.1 + - - +
1572D PHE* 3.3 17.8 + - + +
1573D VAL 3.4 0.2 - - - -
1574D VAL* 1.3 78.8 - - + +
1576D ILE* 1.3 68.2 + - + +
1578D SER* 3.4 6.3 + - - +
1579D ILE* 2.9 41.6 + - + +
1608D ARG* 6.0 0.7 - - - -
1611D ARG* 6.3 0.7 - - - +
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Residues in contact with ILE1576 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1572D PHE* 3.2 38.3 + - + +
1573D VAL* 3.3 28.7 - - + +
1575D VAL* 1.3 82.5 - - + +
1577D ILE* 1.4 60.4 + - + +
1579D ILE* 3.4 7.5 + - + +
1580D VAL* 2.8 47.9 + - + +
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Residues in contact with ILE1577 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1573D VAL* 3.0 28.7 + - + +
1574D VAL* 3.3 17.9 - - - +
1576D ILE* 1.4 79.0 - - + +
1578D SER* 1.3 62.3 + - - +
1580D VAL* 4.3 4.6 - - + +
1581D GLY* 2.9 27.4 + - - -
1604D ALA* 3.9 27.8 - - + +
1607D GLY* 5.0 6.5 - - - -
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Residues in contact with SER1578 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1544D ILE* 3.4 13.7 - - - +
1574D VAL 3.1 20.5 + - - -
1575D VAL* 3.4 9.6 - - - -
1576D ILE 3.3 0.2 - - - -
1577D ILE* 1.3 74.8 - - - +
1579D ILE* 1.4 57.9 + - - +
1582D MET* 2.9 31.5 + - - +
1604D ALA 4.5 3.4 - - - -
1608D ARG* 3.3 42.6 + - - -
1806D 5P2 3.3 14.1 - - - -
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Residues in contact with ILE1579 (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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1544D ILE* 3.9 20.2 - - + -
1548D THR* 3.3 32.8 - - + +
1575D VAL* 2.9 31.5 + - + +
1576D ILE* 4.0 7.2 - - + +
1578D SER* 1.4 72.1 - - - +
1580D VAL* 1.4 65.7 + - + +
1582D MET* 3.3 14.0 - - + +
1583D PHE* 3.2 44.2 - - + -
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Residues in contact with VAL1580 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1576D ILE* 2.8 32.2 + - + +
1577D ILE* 4.3 5.2 - - + +
1579D ILE* 1.4 73.3 - - + +
1581D GLY* 1.3 58.3 + - - +
1583D PHE* 3.5 4.7 + - - +
1584D LEU* 2.9 47.7 + - + +
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Residues in contact with GLY1581 (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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1577D ILE 2.9 19.7 + - - -
1580D VAL* 1.3 75.4 - - - +
1582D MET* 1.4 55.6 + - - +
1584D LEU* 3.6 7.4 - - - +
1585D ALA* 2.8 37.2 + - - +
1601D ILE* 4.3 7.1 - - - +
1604D ALA* 4.4 7.0 - - - -
1806D 5P2 3.4 14.8 - - - -
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Residues in contact with MET1582 (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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1541D VAL* 4.0 18.6 - - + -
1544D ILE* 3.5 46.4 - - + -
1545D ILE* 5.5 6.5 - - + -
1578D SER 2.9 17.5 + - - +
1579D ILE* 3.3 9.4 - - + +
1581D GLY* 1.4 74.2 - - - +
1583D PHE* 1.3 74.9 + - + +
1586D ASP* 3.3 25.8 + - - +
1806D 5P2 3.3 75.8 + - + +
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Residues in contact with PHE1583 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1579D ILE* 3.2 35.9 + - + -
1580D VAL* 4.2 4.0 - - - +
1581D GLY 3.3 0.2 - - - -
1582D MET* 1.3 87.7 - - + +
1584D LEU* 1.3 60.6 + - - +
1585D ALA 3.3 0.7 - - - -
1586D ASP* 3.7 6.8 - - + +
1587D LEU* 2.9 34.4 + - + +
1805D PX4 5.6 2.2 - - + -
1806D 5P2 3.2 41.3 - + + -
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Residues in contact with LEU1584 (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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1580D VAL* 2.9 34.3 + - + +
1581D GLY* 3.2 8.0 + - - +
1583D PHE* 1.3 77.7 - - - +
1585D ALA* 1.4 59.6 + - - +
1587D LEU* 3.7 5.8 + - - +
1588D ILE* 3.4 31.5 + - + +
1601D ILE* 3.8 33.7 - - + -
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Residues in contact with ALA1585 (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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1581D GLY 2.8 20.7 + - - +
1582D MET 4.1 0.2 - - - +
1584D LEU* 1.4 70.7 - - - +
1586D ASP* 1.4 57.1 + - - +
1588D ILE* 3.3 6.3 + - - +
1589D GLU 3.0 23.4 + - - -
1598D PHE* 3.4 24.5 - - + -
1601D ILE* 4.1 16.1 - - + +
1602D ARG* 4.3 13.5 - - + +
1806D 5P2 3.3 23.3 - - - +
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Residues in contact with ASP1586 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1582D MET 3.3 16.6 + - - +
1583D PHE* 3.3 9.7 + - + +
1585D ALA* 1.4 73.4 - - - +
1587D LEU* 1.4 63.9 + - - +
1589D GLU* 3.3 2.2 + - - +
1590D THR* 3.1 35.9 + - - +
1805D PX4 4.6 10.8 - - - +
1806D 5P2 3.1 73.8 + - + +
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Residues in contact with LEU1587 (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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1583D PHE* 2.9 17.7 + - + +
1584D LEU* 3.8 7.2 - - - +
1585D ALA 3.4 0.2 - - - -
1586D ASP* 1.4 73.9 - - - +
1588D ILE* 1.4 64.3 + - + +
1590D THR* 3.0 17.8 + - - -
1591D TYR* 3.1 38.3 + - + +
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Residues in contact with ILE1588 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1584D LEU* 3.4 23.1 + - + +
1585D ALA* 3.3 8.0 + - - +
1586D ASP 3.3 0.6 - - - -
1587D LEU* 1.4 79.4 - - + +
1589D GLU* 1.4 61.3 + - - +
1591D TYR* 2.9 27.3 - - - +
1595D PRO* 4.6 15.0 - - + -
1597D LEU* 3.9 36.1 - - + +
1598D PHE* 4.4 23.6 - - + +
1601D ILE* 4.1 16.8 - - + -
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Residues in contact with GLU1589 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1530D GLN* 5.5 2.3 - - - +
1533D THR* 5.9 1.0 - - - +
1537D TYR* 4.5 7.1 + - - -
1585D ALA 3.0 15.9 + - - +
1586D ASP* 3.3 8.9 + - - +
1588D ILE* 1.4 76.7 - - - +
1590D THR* 1.3 62.0 + - - +
1591D TYR 4.6 2.1 - - - +
1598D PHE* 3.4 42.0 - - + +
1806D 5P2 3.8 34.7 - - + +
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Residues in contact with THR1590 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1586D ASP* 3.1 27.8 + - - +
1587D LEU* 3.0 20.1 + - - -
1589D GLU* 1.3 76.5 - - - +
1591D TYR* 1.3 70.5 + - - +
1805D PX4 5.8 5.2 - - + -
1806D 5P2 4.4 14.6 - - - -
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Residues in contact with TYR1591 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1587D LEU* 3.1 45.6 + - + +
1588D ILE* 2.9 20.3 - - - +
1589D GLU 4.6 1.8 - - - -
1590D THR* 1.3 92.9 + - - +
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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