Contacts of the helix formed by residues 1565 - 1591 (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 ASP1565 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1561B SER* 3.2 18.1 + - - +
1562B PHE 3.3 12.5 - - - +
1563B PHE 3.4 0.4 - - - -
1564B LYS* 1.3 76.2 - - - +
1566B PRO* 1.4 74.8 - - - +
1567B TRP* 3.4 17.4 + - - +
1568B SER* 2.7 41.1 + - - +
1569B LEU* 3.3 16.0 + - - +
1620B ARG* 5.1 1.0 + - - -
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Residues in contact with PRO1566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1564B LYS 3.6 8.2 - - - +
1565B ASP* 1.4 93.7 - - - +
1567B TRP* 1.4 75.6 + - + +
1569B LEU* 3.2 32.1 - - + +
1570B PHE* 3.2 11.4 + - - +
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Residues in contact with TRP1567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1554B ARG* 4.7 0.7 - - - +
1565B ASP* 3.4 17.2 + - - +
1566B PRO* 1.4 86.8 - - + +
1568B SER* 1.4 63.9 + - - +
1570B PHE* 3.3 18.4 + + + +
1571B ASP* 2.9 22.7 + - - +
1614B THR* 3.5 27.6 - - + -
1620B ARG* 3.4 60.8 - - + +
1623B VAL* 4.9 9.4 - - + -
1624B SER* 3.4 25.8 - - - -
1627B ILE* 6.1 4.0 - - + -
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Residues in contact with SER1568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1551B ILE* 4.1 7.4 - - - +
1554B ARG* 3.4 24.6 + - - +
1555B ILE* 4.7 7.0 - - - +
1561B SER 5.0 0.2 + - - -
1562B PHE* 3.7 26.5 - - - -
1565B ASP* 2.7 32.8 + - - +
1566B PRO 3.4 0.4 - - - -
1567B TRP* 1.4 75.6 - - - +
1569B LEU* 1.4 59.3 + - - +
1571B ASP* 3.8 4.5 + - - +
1572B PHE* 3.5 18.4 + - - +
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Residues in contact with LEU1569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1562B PHE* 4.2 10.7 + - + +
1563B PHE* 3.5 27.4 - - + +
1565B ASP 3.3 16.9 + - - +
1566B PRO* 3.2 25.8 - - + +
1568B SER* 1.4 77.1 - - - +
1570B PHE* 1.4 54.9 + - + +
1571B ASP 3.4 0.2 - - - -
1572B PHE* 3.1 10.6 + - + +
1573B VAL* 2.8 46.3 + - + +
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Residues in contact with PHE1570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1566B PRO 3.2 13.2 + - - +
1567B TRP* 3.3 13.7 + + + +
1569B LEU* 1.4 79.3 - - + +
1571B ASP* 1.3 79.9 + - - +
1573B VAL* 3.3 7.1 + - + +
1574B VAL* 2.9 52.8 + - + +
1610B LEU* 3.7 34.8 - - + -
1611B ARG* 4.0 13.9 - - + -
1613B VAL* 5.6 0.4 - - + -
1614B THR* 3.2 36.6 - - + -
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Residues in contact with ASP1571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1551B ILE* 4.1 5.5 - - + +
1554B ARG* 3.0 36.9 + - - +
1567B TRP 2.9 18.6 + - - +
1568B SER 4.0 3.8 - - - +
1569B LEU 3.4 0.2 - - - -
1570B PHE* 1.3 90.2 - - - +
1572B PHE* 1.4 55.9 + - - +
1574B VAL* 4.0 6.9 - - - +
1575B VAL* 3.1 29.8 + - - +
1611B ARG* 3.3 37.8 + - - +
1614B THR* 4.3 8.6 - - - +
1615B ALA* 5.3 2.6 + - - -
1620B ARG* 4.8 4.7 + - - -
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Residues in contact with PHE1572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1551B ILE* 4.1 28.3 - - + -
1555B ILE* 4.6 7.2 - - + -
1562B PHE* 4.5 28.5 - + + -
1568B SER 3.5 12.5 + - - +
1569B LEU* 3.1 15.9 + - + +
1570B PHE 3.1 0.6 - - - -
1571B ASP* 1.4 76.4 - - - +
1573B VAL* 1.4 66.4 + - + +
1574B VAL 3.2 1.6 - - - -
1575B VAL* 3.1 7.5 + - + +
1576B ILE* 2.9 60.5 + - + +
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Residues in contact with VAL1573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1569B LEU* 2.8 32.8 + - + +
1570B PHE* 3.9 7.6 - - + +
1572B PHE* 1.4 75.5 - - + +
1574B VAL* 1.4 56.4 + - + +
1576B ILE* 3.2 21.0 - - + +
1577B ILE* 3.0 46.3 + - + +
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Residues in contact with VAL1574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1570B PHE* 2.9 43.8 + - + +
1571B ASP* 4.0 6.5 - - - +
1573B VAL* 1.4 75.6 - - + +
1575B VAL* 1.4 58.3 + - + +
1577B ILE* 3.2 11.4 + - + +
1578B SER* 2.8 33.9 + - - -
1607B GLY* 3.6 41.5 - - - +
1608B ARG* 3.9 12.1 - - + +
1610B LEU* 5.8 0.2 - - + -
1611B ARG* 4.3 13.7 - - + +
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Residues in contact with VAL1575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1547B PHE* 3.8 30.5 - - + +
1548B THR* 4.0 24.5 - - + +
1551B ILE* 3.8 26.9 - - + -
1571B ASP 3.1 20.6 + - - +
1572B PHE* 3.1 11.5 + - + +
1574B VAL* 1.4 79.8 - - + +
1576B ILE* 1.4 62.1 + - + +
1578B SER* 3.3 6.8 + - - -
1579B ILE* 3.0 34.2 + - + +
1611B ARG* 4.9 5.6 - - - +
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Residues in contact with ILE1576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1572B PHE* 2.9 49.4 + - + +
1573B VAL* 3.2 30.7 - - + +
1575B VAL* 1.4 78.8 - - + +
1577B ILE* 1.4 57.0 + - + +
1579B ILE* 4.0 6.8 - - + +
1580B VAL* 3.1 36.8 + - + +
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Residues in contact with ILE1577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1573B VAL* 3.0 39.1 + - + +
1574B VAL* 3.2 10.5 + - + +
1576B ILE* 1.4 77.5 - - + +
1578B SER* 1.3 56.5 - - - +
1580B VAL* 3.9 3.7 - - - +
1581B GLY* 2.8 33.4 + - - -
1604B ALA* 3.9 32.7 - - + +
1607B GLY* 5.6 4.5 - - - -
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Residues in contact with SER1578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1544B ILE* 3.5 14.5 - - - +
1574B VAL* 2.8 21.1 + - - -
1575B VAL* 3.3 7.2 + - - -
1577B ILE* 1.3 73.3 - - - +
1579B ILE* 1.3 57.5 + - - +
1582B MET* 3.1 29.8 + - - +
1604B ALA 4.8 3.1 - - - -
1608B ARG* 2.8 47.0 + - - +
1806B 5P2 3.7 10.4 + - - -
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Residues in contact with ILE1579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1544B ILE* 3.6 23.3 - - + -
1545B ILE* 6.2 1.3 - - + -
1548B THR* 3.8 23.8 - - + +
1575B VAL* 3.0 25.2 + - + +
1576B ILE* 4.0 7.2 - - - +
1578B SER* 1.3 73.6 - - - +
1580B VAL* 1.4 68.8 + - + +
1582B MET* 3.5 10.2 - - + +
1583B PHE* 3.1 44.5 - - + -
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Residues in contact with VAL1580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1576B ILE* 3.1 25.4 + - + +
1577B ILE* 3.9 4.5 - - - +
1579B ILE* 1.4 77.4 - - + +
1581B GLY* 1.3 57.1 + - - +
1583B PHE* 3.6 2.8 + - - +
1584B LEU* 3.0 49.4 + - + +
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Residues in contact with GLY1581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1577B ILE 2.8 20.6 + - - -
1580B VAL* 1.3 72.1 - - - +
1582B MET* 1.3 57.4 + - - +
1584B LEU* 3.0 8.0 + - - -
1585B ALA* 2.8 36.1 + - - +
1601B ILE* 5.3 4.3 - - - -
1604B ALA* 4.4 7.4 - - - -
1806B 5P2 3.3 19.7 - - - -
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Residues in contact with MET1582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1541B VAL* 3.8 16.6 - - + +
1544B ILE* 3.6 42.0 - - + -
1545B ILE* 5.7 3.6 - - + -
1578B SER 3.1 18.1 + - - +
1579B ILE* 3.5 9.9 - - + +
1581B GLY* 1.3 74.1 - - - +
1583B PHE* 1.3 76.2 + - + +
1586B ASP* 3.3 13.3 + - - +
1806B 5P2 3.3 92.4 + - + +
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Residues in contact with PHE1583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1579B ILE* 3.1 43.1 - - + -
1580B VAL* 3.6 3.7 + - - +
1581B GLY 3.3 0.2 - - - -
1582B MET* 1.3 95.0 - - + +
1584B LEU* 1.4 55.8 - - - +
1585B ALA 3.4 0.7 - - - -
1586B ASP* 3.6 10.6 - - - +
1587B LEU* 2.8 35.8 + - - +
1805B PX4 5.0 14.4 - - + -
1806B 5P2 3.1 41.3 - + - -
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Residues in contact with LEU1584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1580B VAL* 3.0 35.9 + - + +
1581B GLY* 3.7 5.2 - - - +
1583B PHE* 1.4 74.8 - - - +
1585B ALA* 1.4 61.4 + - - +
1587B LEU* 3.4 17.7 - - + +
1588B ILE* 3.2 33.3 + - + +
1601B ILE* 3.8 32.3 - - + -
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Residues in contact with ALA1585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1581B GLY 2.8 19.2 + - - +
1582B MET 4.4 0.4 - - - +
1584B LEU* 1.4 69.6 - - - +
1586B ASP* 1.4 59.5 + - - +
1588B ILE* 3.4 2.0 + - - -
1589B GLU 3.0 22.7 + - - -
1598B PHE* 3.3 19.5 - - + -
1601B ILE* 3.8 26.1 - - + +
1602B ARG* 4.7 4.7 - - + -
1806B 5P2 3.5 31.6 - - - +
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Residues in contact with ASP1586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1582B MET 3.3 19.3 + - - +
1583B PHE* 3.4 12.0 + - - +
1585B ALA* 1.4 77.5 - - - +
1587B LEU* 1.4 56.9 + - - +
1589B GLU* 3.3 1.6 + - - +
1590B THR* 2.9 47.4 + - - -
1805B PX4 3.3 23.5 - - - +
1806B 5P2 3.2 58.2 + - + +
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Residues in contact with LEU1587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1583B PHE 2.8 17.1 + - - +
1584B LEU* 3.4 21.3 - - + +
1586B ASP* 1.4 77.2 - - - +
1588B ILE* 1.4 62.0 + - + +
1590B THR* 4.8 2.9 - - - -
1591B TYR* 3.1 51.3 + - + +
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Residues in contact with ILE1588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1584B LEU* 3.2 22.7 - - + +
1585B ALA 3.4 5.1 + - - +
1586B ASP 3.4 0.4 - - - -
1587B LEU* 1.4 81.2 - - + +
1589B GLU* 1.4 60.4 + - - +
1591B TYR* 2.8 22.7 - - - +
1592B PHE* 3.8 1.0 + - - -
1593B VAL* 3.3 46.5 + - + +
1594B SER 4.5 0.9 - - - +
1597B LEU* 3.9 32.5 - - + +
1598B PHE* 4.6 10.5 - - + +
1601B ILE* 3.7 30.1 - - + -
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Residues in contact with GLU1589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1533B THR* 5.3 1.6 - - - +
1537B TYR* 3.7 16.3 + - - -
1585B ALA 3.0 17.8 + - - +
1586B ASP* 3.6 5.4 - - - +
1588B ILE* 1.4 75.8 - - - +
1590B THR* 1.4 62.2 + - - +
1592B PHE* 4.0 27.5 - - - -
1598B PHE* 3.4 36.7 - - + -
1806B 5P2 3.7 38.8 - - + +
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Residues in contact with THR1590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1586B ASP* 2.9 30.4 + - - -
1587B LEU* 4.1 4.5 - - - -
1589B GLU* 1.4 74.5 - - - +
1591B TYR* 1.3 78.2 + - + +
1592B PHE* 3.3 24.1 + - - -
1805B PX4 6.0 0.5 - - - -
1806B 5P2 4.5 10.1 - - - -
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Residues in contact with TYR1591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1587B LEU* 3.1 37.8 + - + +
1588B ILE* 2.8 12.9 - - - +
1590B THR* 1.3 90.2 - - + +
1592B PHE* 1.4 52.5 + - - +
1593B VAL* 2.8 31.5 + - + +
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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