Contacts of the helix formed by residues 1681 - 1705 (chain B) in PDB entry 4J5L
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 ASP1681 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1562B CYS* 4.1 16.2 - - - +
1563B ARG* 3.7 12.3 + - - -
1566B HIS* 2.9 29.4 + - - -
1679B GLY 4.4 3.5 - - - +
1680B MET* 1.3 77.7 - - - +
1682B PRO* 1.3 68.5 - - + +
1683B GLU* 4.4 4.5 - - + +
1684B LEU* 3.0 20.0 + - + +
1685B ILE* 2.9 24.8 + - - +
1829B PHE* 5.6 4.0 - - - +
1830B PRO* 4.8 5.9 - - + +
1832B ASN* 3.0 25.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1682 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1680B MET 3.4 4.5 - - - +
1681B ASP* 1.3 85.8 - - + +
1683B GLU* 1.3 60.3 + - + +
1685B ILE* 3.2 11.5 + - + +
1686B LYS* 2.9 38.2 + - + +
1832B ASN* 4.2 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1683 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1681B ASP* 3.3 3.5 - - + +
1682B PRO* 1.3 82.0 - - + +
1684B LEU* 1.3 59.9 + - - +
1686B LYS* 2.7 43.5 + - - +
1687B GLN* 3.0 33.2 + - - +
1830B PRO* 4.0 31.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1684 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1558B LEU* 3.9 17.9 - - + -
1559B SER* 5.9 0.2 - - - -
1562B CYS* 4.0 15.5 - - + -
1610B TYR* 4.1 9.2 - - + -
1680B MET* 3.7 24.2 - - + -
1681B ASP* 3.0 23.0 + - + +
1683B GLU* 1.3 78.0 - - - +
1685B ILE* 1.3 65.3 + - - +
1687B GLN* 3.2 10.0 + - - +
1688B VAL* 3.0 26.1 + - - +
1827B VAL* 3.8 21.8 - - + -
1828B THR 4.3 2.0 + - - +
1829B PHE* 3.6 38.8 - - + -
1830B PRO* 5.8 1.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1685 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1672B HIS* 3.9 27.4 - - + +
1675B MET* 4.2 23.6 - - + +
1676B CYS* 4.2 23.6 - - - -
1680B MET* 3.5 39.3 - - + +
1681B ASP 2.9 14.5 + - - +
1682B PRO* 3.6 11.7 - - + +
1684B LEU* 1.3 76.0 - - - +
1686B LYS* 1.3 56.7 + - - +
1688B VAL* 3.2 8.2 + - - +
1689B VAL* 2.9 33.5 + - + +
1735B LEU* 5.3 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1686 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1682B PRO* 2.9 23.5 + - + +
1683B GLU* 2.7 36.6 + - - +
1685B ILE* 1.3 77.2 - - - +
1687B GLN* 1.3 56.8 + - + +
1689B VAL* 3.4 2.9 + - - +
1690B LYS* 3.0 28.2 + - - +
1735B LEU* 4.0 23.8 - - + +
1737B ASN* 3.8 32.4 + - - +
1738B SER* 3.6 23.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1687 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1610B TYR* 3.6 16.6 + - + +
1683B GLU* 3.0 28.4 + - - +
1684B LEU* 3.2 10.5 + - - +
1686B LYS* 1.3 74.6 - - + +
1688B VAL* 1.3 64.7 + - - +
1690B LYS* 3.5 11.2 + - + +
1691B GLN* 3.0 22.9 + - - +
1738B SER 5.6 0.4 - - - -
1826B PRO 4.0 5.0 - - - +
1827B VAL* 3.3 15.0 - - - +
1828B THR* 3.0 52.0 + - - -
1830B PRO* 4.9 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1688 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1610B TYR* 3.6 27.6 - - + -
1613B LEU* 4.3 11.0 - - + -
1614B VAL* 5.8 1.3 - - + -
1617B LEU* 3.6 27.3 - - + +
1675B MET* 3.7 37.0 - - + -
1680B MET* 4.6 4.3 - - - -
1684B LEU 3.0 19.9 + - - +
1685B ILE 3.2 7.2 + - - +
1687B GLN* 1.3 77.8 - - - +
1689B VAL* 1.3 56.8 + - - +
1691B GLN* 3.2 5.5 + - - +
1692B MET* 2.9 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1689 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1672B HIS* 4.7 2.9 - - + +
1675B MET* 5.1 3.1 - - + -
1685B ILE* 2.9 28.2 + - + +
1686B LYS* 3.8 4.7 - - - +
1687B GLN 3.3 0.2 - - - -
1688B VAL* 1.3 72.9 - - - +
1690B LYS* 1.3 65.5 + - - +
1692B MET* 3.0 23.3 + - + +
1693B PHE* 3.0 27.5 + - + -
1729B TRP* 3.9 17.0 - - + -
1730B LEU* 3.9 28.7 - - + -
1735B LEU* 3.7 23.8 - - + -
1738B SER* 4.3 2.9 - - - +
1740B ALA* 4.0 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1690 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1686B LYS 3.0 17.6 + - - +
1687B GLN* 3.7 10.3 - - + +
1689B VAL* 1.3 76.7 - - - +
1691B GLN* 1.3 62.3 + - - +
1693B PHE* 3.4 2.6 + - - +
1694B TYR* 3.1 21.7 + - - +
1738B SER 3.7 22.8 + - - +
1739B GLY* 4.1 9.2 - - - -
1740B ALA* 3.8 13.9 - - + +
1743B THR* 4.0 25.9 + - + -
1825B PHE* 4.3 35.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1691 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1610B TYR* 4.3 6.3 + - - +
1614B VAL* 3.6 35.3 - - + +
1617B LEU* 5.6 2.9 - - + -
1618B GLU* 4.7 1.0 + - - -
1687B GLN 3.0 14.4 + - - +
1688B VAL* 3.4 12.6 - - - +
1689B VAL 3.1 0.2 - - - -
1690B LYS* 1.3 80.0 - - - +
1692B MET* 1.3 61.6 + - + +
1694B TYR* 3.3 17.5 + - - +
1695B ILE* 3.2 36.0 + - + +
1823B HIS 2.9 25.0 + - - -
1824B ILE* 3.7 4.5 - - - +
1825B PHE* 3.1 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1692 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1617B LEU* 3.8 23.3 - - + -
1621B LEU* 4.1 13.6 - - + +
1668B LEU* 3.8 23.1 - - + +
1671B PHE* 3.5 41.7 - - + -
1672B HIS 5.6 0.7 - - - +
1675B MET* 5.0 2.2 - - + -
1688B VAL* 2.9 19.9 + - + +
1689B VAL* 3.0 38.6 + - + +
1691B GLN* 1.3 75.3 - - - +
1693B PHE* 1.3 64.6 + - + +
1695B ILE* 3.4 11.9 + - + +
1696B ILE* 3.2 26.8 + - - +
1729B TRP* 4.7 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1693 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1668B LEU* 3.9 19.5 - - + -
1689B VAL* 3.0 21.9 + - + +
1690B LYS 3.9 2.9 - - - +
1692B MET* 1.3 78.8 - - + +
1694B TYR* 1.3 59.7 + - - +
1696B ILE* 3.3 8.8 + - + +
1697B GLY 2.9 24.4 + - - -
1726B LEU* 3.6 46.7 - - + -
1729B TRP* 3.9 24.7 - + - -
1730B LEU* 3.7 23.6 - - + -
1740B ALA* 3.6 28.5 - - + +
1743B THR* 3.6 4.0 - - - +
1744B LEU* 3.4 33.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1694 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1690B LYS 3.1 14.0 + - - +
1691B GLN* 3.5 24.0 - - - +
1692B MET 3.3 0.2 - - - -
1693B PHE* 1.3 77.8 - - - +
1695B ILE* 1.3 60.0 + - - +
1697B GLY* 3.8 0.3 - - - -
1698B ALA* 2.8 37.9 + - + +
1743B THR* 3.6 22.0 + - - +
1816B GLN* 5.7 0.7 + - - -
1819B MET* 4.4 17.7 - - + +
1820B ASP* 2.7 39.4 + - - +
1821B ALA* 4.2 9.2 - - - -
1823B HIS* 3.8 25.8 - + + +
1825B PHE* 3.6 31.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1695 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1614B VAL 4.9 0.2 - - - +
1617B LEU* 4.9 6.3 - - + -
1618B GLU* 3.6 53.4 - - + +
1621B LEU* 4.7 15.3 - - + -
1622B GLN* 5.2 1.1 - - + +
1625B ILE* 3.8 15.9 - - + -
1691B GLN* 3.2 31.1 + - + +
1692B MET* 3.6 13.9 - - - +
1694B TYR* 1.3 79.5 - - + +
1696B ILE* 1.3 62.0 + - - +
1698B ALA* 4.6 2.7 - - - -
1699B ILE* 3.1 39.6 + - + +
1821B ALA 4.2 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1696 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1621B LEU* 4.6 7.6 - - + -
1625B ILE* 3.6 23.6 - - + +
1629B MET* 4.2 25.4 - - + -
1664B ILE* 4.1 23.8 - - + -
1668B LEU* 4.3 20.9 - - + -
1692B MET 3.2 16.5 + - - +
1693B PHE* 3.3 14.6 + - + +
1695B ILE* 1.3 75.5 - - - +
1697B GLY* 1.3 60.9 + - - +
1700B THR* 2.7 33.7 + - - +
1726B LEU* 4.1 26.7 - - + -
1744B LEU* 5.0 3.1 - - + -
1747B LEU* 5.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1697 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1693B PHE 2.9 16.5 + - - -
1694B TYR 3.9 0.4 - - - -
1696B ILE* 1.3 78.9 - - - +
1698B ALA* 1.3 56.5 + - - +
1700B THR* 3.5 1.2 + - - -
1701B LEU* 3.0 31.9 + - - +
1743B THR 4.9 6.3 - - - -
1744B LEU* 3.9 15.5 - - - +
1747B LEU* 4.3 18.1 - - - +
1819B MET* 5.4 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1698 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1694B TYR* 2.8 29.2 + - + +
1695B ILE 4.0 2.7 - - - +
1697B GLY* 1.3 76.3 - - - +
1699B ILE* 1.3 57.3 + - - +
1701B LEU* 3.3 1.9 + - - +
1702B ASN* 2.9 36.4 + - - +
1819B MET* 4.1 31.8 - - + +
1821B ALA* 4.2 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1699 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1618B GLU* 5.7 0.2 - - - +
1622B GLN* 3.6 38.1 - - + +
1625B ILE* 3.6 32.5 - - + -
1626B VAL* 4.0 22.9 - - + -
1695B ILE* 3.1 25.5 + - + +
1698B ALA* 1.3 75.6 - - - +
1700B THR* 1.3 61.8 + - - +
1702B ASN* 3.4 7.5 + - + +
1703B ASN* 3.0 35.2 + - - +
1821B ALA* 3.9 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1700 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1625B ILE* 3.2 15.9 - - - +
1629B MET* 3.7 15.9 - - + +
1630B LEU* 3.6 33.8 - - + +
1696B ILE* 2.7 24.3 + - - +
1697B GLY 3.9 3.4 - - - -
1699B ILE* 1.3 75.3 - - - +
1701B LEU* 1.3 64.4 + - - +
1703B ASN* 3.3 5.9 + - - +
1704B LEU* 3.3 20.4 + - - +
1719B ILE* 4.5 4.9 - - + -
1747B LEU* 3.6 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1701 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1697B GLY 3.0 18.1 + - - +
1698B ALA* 3.7 4.5 - - - +
1700B THR* 1.3 73.7 - - - +
1702B ASN* 1.3 67.6 + - - +
1704B LEU* 3.1 20.4 + - + -
1705B LEU* 3.1 32.0 + - + +
1746B PRO* 3.9 26.7 - - + -
1747B LEU* 4.4 19.0 - - + +
1750B ALA* 4.0 21.8 - - + -
1774B LEU* 4.2 11.9 - - + -
1778B GLN* 4.2 12.8 - - + +
1782B VAL* 5.5 1.1 - - + -
1819B MET* 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1702 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1698B ALA 2.9 23.7 + - - +
1699B ILE* 3.7 8.3 - - - +
1700B THR 3.3 0.2 - - - -
1701B LEU* 1.3 78.7 - - - +
1703B ASN* 1.3 63.7 + - - +
1705B LEU* 3.3 6.2 + - - +
1706B LEU* 3.2 33.5 + - + +
1818B LEU* 3.5 25.2 - - + +
1819B MET* 2.8 49.4 + - - +
1821B ALA* 4.9 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1703 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1626B VAL* 3.3 32.1 - - + +
1630B LEU* 4.6 12.6 - - + -
1699B ILE* 3.0 29.6 + - - +
1700B THR 3.7 8.5 - - - +
1701B LEU 3.2 0.4 - - - -
1702B ASN* 1.3 77.4 - - - +
1704B LEU* 1.3 62.5 + - - +
1706B LEU* 4.6 7.2 - - - +
1707B ARG* 3.0 64.2 + - - +
1710B MET* 4.6 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1704 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1630B LEU* 4.0 22.7 - - + -
1700B THR 3.3 12.6 + - - +
1701B LEU* 3.1 15.6 + - + +
1703B ASN* 1.3 78.0 - - - +
1705B LEU* 1.3 62.7 + - + +
1706B LEU 3.1 1.3 + - - -
1707B ARG 3.6 3.2 - - - +
1710B MET* 3.9 24.7 - - + +
1711B CYS* 3.1 36.1 - - - -
1719B ILE* 3.9 21.1 - - + -
1747B LEU* 4.4 9.2 - - + -
1750B ALA* 4.3 23.6 - - + -
1754B LEU* 4.1 14.6 - - + -
1782B VAL* 5.3 6.0 - - + +
1785B LEU* 3.4 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1705 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1701B LEU* 3.1 31.1 + - + +
1702B ASN* 3.3 7.8 + - - +
1703B ASN 3.2 0.2 - - - -
1704B LEU* 1.3 77.1 - - - +
1706B LEU* 1.3 59.9 + - - +
1778B GLN* 3.8 36.1 - - + +
1781B LYS* 2.7 45.6 + - + +
1782B VAL* 3.9 16.8 - - + -
1785B LEU* 3.5 5.2 - - - -
1817B LEU* 3.3 38.0 - - + +
1818B LEU* 4.1 14.6 - - + -
----------------------------------------------------------
Back to top of page
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