Contacts of the helix formed by residues 1712 - 1733 (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 SER1712 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1709B ASP 5.7 0.8 + - - -
1710B MET* 3.4 3.6 + - - -
1711B CYS* 1.3 76.6 - - - +
1713B TRP* 1.3 65.8 + - - +
1714B SER* 3.7 9.6 + - - -
1715B LYS* 3.3 27.2 + - - +
1716B GLY 3.2 16.8 + - - -
1754B LEU* 3.5 10.3 - - - +
1786B TYR* 3.6 11.0 - - - -
1787B THR* 4.0 14.1 - - - -
1788B PRO 5.5 4.5 - - - -
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Residues in contact with TRP1713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1712B SER* 1.3 73.9 - - - +
1714B SER* 1.3 70.3 + - - +
1716B GLY* 3.5 2.1 + - - -
1717B MET* 3.2 50.3 + - + +
1754B LEU 3.4 9.0 - - - +
1755B GLN* 3.4 49.1 + - + +
1786B TYR* 3.6 21.5 + - - +
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Residues in contact with SER1714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1633B GLU* 4.4 16.3 + - - -
1712B SER* 3.1 9.1 + - - -
1713B TRP* 1.3 90.6 - - - +
1715B LYS* 1.3 61.4 + - - +
1717B MET* 3.2 13.0 + - - +
1718B GLN* 3.0 30.1 + - - +
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Residues in contact with LYS1715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1630B LEU* 2.4 40.6 + - + +
1631B GLU* 3.5 13.1 + - - +
1633B GLU* 4.6 4.5 - - - +
1709B ASP 4.8 3.1 - - - +
1710B MET* 3.2 57.4 - - + +
1712B SER* 3.3 17.9 + - - +
1714B SER* 1.3 76.4 - - - +
1716B GLY* 1.3 61.7 + - - +
1718B GLN* 3.1 25.7 + - + +
1719B ILE* 2.9 41.1 + - + +
1754B LEU* 4.7 1.3 - - + -
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Residues in contact with GLY1716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1712B SER 3.2 11.0 + - - -
1713B TRP 3.8 4.3 - - - -
1714B SER 3.3 0.4 - - - -
1715B LYS* 1.3 76.3 - - - +
1717B MET* 1.3 60.4 + - - +
1719B ILE* 4.6 0.4 - - - -
1720B ARG* 3.1 21.0 + - - +
1751B ALA* 3.7 27.9 - - - +
1754B LEU* 3.9 13.9 - - - +
1755B GLN* 3.0 14.4 - - - +
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Residues in contact with MET1717 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1635B ILE* 4.2 32.8 - - + -
1713B TRP* 3.2 48.0 + - + +
1714B SER* 3.2 15.1 + - - +
1715B LYS 3.1 0.4 - - - -
1716B GLY* 1.3 74.3 - - - +
1718B GLN* 1.3 66.0 + - + +
1720B ARG* 3.4 3.5 + - - +
1721B TYR* 3.1 22.2 + - - +
1755B GLN* 3.2 13.9 + - - +
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Residues in contact with GLN1718 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1629B MET 4.1 9.1 + - - +
1630B LEU 3.0 23.6 + - - -
1632B HIS 3.3 16.4 + - - -
1633B GLU* 3.3 35.0 - - - +
1634B THR* 3.9 18.7 - - + +
1635B ILE* 5.0 7.0 - - + +
1714B SER* 3.0 19.1 + - - +
1715B LYS* 3.1 34.6 + - + +
1717B MET* 1.3 80.9 - - + +
1719B ILE* 1.3 57.5 + - - +
1721B TYR* 3.1 5.6 + - - +
1722B ASN* 2.8 35.2 + - - +
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Residues in contact with ILE1719 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1629B MET* 4.3 8.3 - - + +
1630B LEU* 3.8 31.0 - - + -
1700B THR* 4.7 2.5 - - + -
1704B LEU* 3.9 27.6 - - + -
1715B LYS* 2.9 25.0 + - + +
1716B GLY* 4.0 4.5 - - - +
1718B GLN* 1.3 75.3 - - + +
1720B ARG* 1.3 59.4 + - - +
1722B ASN* 3.1 8.4 + - - +
1723B VAL* 2.8 37.7 + - + +
1747B LEU* 3.7 39.3 - - + +
1748B ILE 5.5 0.2 - - - +
1751B ALA* 3.9 16.8 - - + -
1754B LEU* 4.8 2.0 - - + -
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Residues in contact with ARG1720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1716B GLY 3.1 17.4 + - - +
1717B MET* 3.9 3.6 - - - +
1719B ILE* 1.3 79.3 - - - +
1721B TYR* 1.3 62.1 + - - +
1723B VAL* 3.7 9.7 + - + +
1724B SER* 3.3 20.4 + - - -
1748B ILE* 3.6 21.7 - - + +
1751B ALA* 4.3 13.0 - - + -
1752B GLN* 2.9 41.5 + - - +
1755B GLN* 4.2 18.1 - - - +
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Residues in contact with TYR1721 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1634B THR* 3.7 25.6 - - + -
1635B ILE* 3.7 27.4 - - + -
1661B LEU* 4.5 2.7 - - + -
1717B MET 3.1 14.6 + - - +
1718B GLN 3.6 6.1 - - - +
1720B ARG* 1.3 75.5 - - - +
1722B ASN* 1.3 75.9 + - - +
1724B SER* 2.3 29.2 + - - -
1725B GLN* 3.2 44.0 + - + +
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Residues in contact with ASN1722 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1628B GLY 3.5 9.5 + - - -
1629B MET* 3.2 56.6 + - + +
1632B HIS 5.6 0.2 + - - -
1634B THR* 3.1 30.5 - - - +
1661B LEU* 3.3 24.9 - - + +
1718B GLN* 2.8 15.2 + - - +
1719B ILE 3.5 8.1 - - - +
1721B TYR* 1.3 76.8 - - - +
1723B VAL* 1.3 62.5 + - - +
1725B GLN* 3.1 6.1 + - - +
1726B LEU* 3.0 26.2 + - - +
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Residues in contact with VAL1723 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1629B MET* 4.7 4.7 - - + -
1719B ILE* 2.8 34.5 + - + +
1720B ARG* 3.9 9.9 - - + +
1721B TYR 3.3 0.2 - - - -
1722B ASN* 1.3 75.8 - - - +
1724B SER* 1.3 58.3 + - - +
1726B LEU* 3.0 11.2 + - + +
1727B GLU* 2.8 43.4 + - + +
1744B LEU* 4.2 15.3 - - + -
1747B LEU* 4.3 13.0 - - + -
1748B ILE* 3.7 39.3 - - + -
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Residues in contact with SER1724 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1720B ARG 3.3 10.0 + - - -
1721B TYR* 2.3 36.0 + - - -
1723B VAL* 1.3 79.7 - - - +
1725B GLN* 1.3 67.2 + - - +
1727B GLU* 3.6 16.0 + - - +
1728B GLU* 3.1 28.8 + - - +
1731B ARG* 4.8 1.2 + - - -
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Residues in contact with GLN1725 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1661B LEU* 3.7 25.6 - - + -
1665B LEU* 4.2 12.9 - - + +
1721B TYR* 3.2 50.2 + - + +
1722B ASN 3.1 6.7 + - - +
1724B SER* 1.3 85.1 + - - +
1726B LEU* 1.3 65.0 + - - +
1728B GLU* 3.4 11.6 + - - +
1729B TRP* 3.1 22.2 + - - +
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Residues in contact with LEU1726 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1629B MET* 4.3 13.9 - - + -
1661B LEU* 4.8 4.5 - - + -
1664B ILE* 4.7 5.6 - - + -
1665B LEU* 4.2 26.7 - - + -
1668B LEU* 4.2 17.9 - - + -
1693B PHE* 3.6 18.5 - - + -
1696B ILE* 4.1 32.5 - - + -
1722B ASN 3.0 16.5 + - - +
1723B VAL* 3.0 13.4 + - + +
1725B GLN* 1.3 76.7 - - - +
1727B GLU* 1.3 61.4 + - - +
1729B TRP* 3.3 8.2 + - - +
1730B LEU* 3.2 24.1 + - - +
1744B LEU* 4.3 18.4 - - + -
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Residues in contact with GLU1727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1723B VAL* 2.8 33.0 + - + +
1724B SER* 3.7 19.0 - - - +
1725B GLN 3.3 0.2 - - - -
1726B LEU* 1.3 75.8 - - - +
1728B GLU* 1.3 64.1 + - - +
1730B LEU* 3.2 17.0 + - + +
1731B ARG* 3.2 38.9 + - - +
1736B MET* 4.1 4.7 - - - +
1741B LYS* 2.4 50.2 + - + +
1744B LEU* 5.1 5.1 - - + +
1748B ILE* 4.2 8.3 - - - +
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Residues in contact with GLU1728 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1724B SER 3.1 18.0 + - - +
1725B GLN* 3.6 15.5 - - - +
1726B LEU 3.3 0.2 - - - -
1727B GLU* 1.3 74.4 - - - +
1729B TRP* 1.3 60.6 + - - +
1731B ARG* 2.4 44.6 + - - +
1732B ASP* 2.9 45.1 + - - +
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Residues in contact with TRP1729 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1665B LEU* 3.6 32.6 + - + -
1668B LEU* 3.7 34.5 - - + -
1669B ASN* 2.8 35.4 + - - +
1672B HIS* 4.0 13.7 - - + -
1689B VAL* 3.9 39.7 - - + -
1692B MET* 4.7 3.8 - - + -
1693B PHE* 3.9 16.4 - + - -
1725B GLN 3.1 7.1 + - - +
1726B LEU* 3.4 8.1 - - - +
1727B GLU 3.3 0.2 - - - -
1728B GLU* 1.3 77.4 - - - +
1730B LEU* 1.3 72.8 + - + +
1732B ASP* 3.3 13.2 + - + +
1733B LYS* 3.1 46.1 + - + +
1735B LEU* 4.2 6.1 - - + -
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Residues in contact with LEU1730 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1689B VAL* 3.9 23.6 - - + -
1693B PHE* 3.7 31.6 - - + -
1726B LEU 3.2 11.6 + - - +
1727B GLU* 3.3 15.7 - - + +
1729B TRP* 1.3 84.7 - - + +
1731B ARG* 1.3 50.7 + - - +
1733B LYS* 3.2 1.8 + - - -
1734B ASN 2.8 14.9 + - - -
1735B LEU* 2.7 51.2 + - + +
1736B MET* 3.9 15.3 - - - -
1740B ALA* 4.0 3.6 - - + -
1741B LYS* 4.1 31.0 - - + +
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Residues in contact with ARG1731 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1724B SER 4.8 1.4 + - - -
1727B GLU* 3.2 24.0 + - - +
1728B GLU* 2.4 57.5 + - - +
1730B LEU* 1.3 74.2 - - - +
1732B ASP* 1.3 69.3 + - - +
1734B ASN* 3.1 14.8 + - - +
1736B MET* 4.0 28.1 - - + +
1741B LYS* 5.6 3.0 - - - +
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Residues in contact with ASP1732 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1728B GLU* 2.9 31.6 + - - +
1729B TRP* 3.3 17.6 + - + +
1731B ARG* 1.3 78.1 - - - +
1733B LYS* 1.3 73.9 + - + +
1734B ASN* 3.8 0.3 + - - +
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Residues in contact with LYS1733 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1669B ASN* 3.2 29.0 + - - +
1672B HIS* 4.0 29.4 + - + +
1729B TRP* 3.1 44.3 + - + +
1732B ASP* 1.3 88.1 + - - +
1734B ASN* 1.3 70.9 + - - +
1735B LEU* 3.5 27.0 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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