Contacts of the helix formed by residues 1772 - 1788 (chain A) in PDB entry 4W8F
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 THR1772 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1770A ILE* 3.4 12.7 + - + +
1771A TYR* 1.3 79.0 - - - +
1773A PRO* 1.3 76.6 - - - +
1774A LEU* 3.4 16.3 + - - +
1775A LEU* 3.0 24.9 + - + +
1776A LEU* 3.1 16.1 + - - +
1924A PRO 4.5 2.8 + - - -
1925A GLN* 3.8 11.9 - - + +
1928A THR* 3.4 19.7 - - - +
1929A ILE* 3.5 27.1 - - + -
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Residues in contact with PRO1773 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1710A ASN* 6.0 3.4 - - - +
1714A GLN* 5.6 8.3 - - - +
1771A TYR 4.8 0.2 - - - +
1772A THR* 1.3 84.8 - - - +
1774A LEU* 1.3 56.0 + - - +
1776A LEU* 3.3 15.3 + - + +
1777A ILE* 2.9 38.7 + - + +
1925A GLN* 3.2 31.2 - - - +
1928A THR* 5.7 2.2 - - + -
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Residues in contact with LEU1774 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1772A THR* 3.1 9.2 + - - +
1773A PRO* 1.3 74.9 - - - +
1775A LEU* 1.3 62.2 + - - +
1777A ILE* 3.3 9.0 + - + +
1778A GLY* 2.9 24.9 + - - -
1800A THR* 4.2 8.5 - - - +
1919A PHE* 5.0 6.1 - - + -
1920A SER 4.7 2.5 - - - +
1921A MET* 3.6 39.9 - - + +
1922A LYS* 4.5 20.9 - - + +
1923A SER* 3.8 27.8 - - - +
1924A PRO* 4.0 15.7 - - + +
1925A GLN* 3.8 8.8 - - + +
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Residues in contact with LEU1775 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1769A LEU* 3.7 40.6 - - + +
1770A ILE 4.3 8.5 - - - +
1771A TYR* 4.4 24.0 - - + -
1772A THR* 3.0 20.0 + - - +
1774A LEU* 1.3 80.5 - - - +
1776A LEU* 1.3 59.0 + - - +
1778A GLY* 3.4 0.9 + - - -
1779A PHE* 2.9 73.7 + - + -
1805A THR* 4.2 20.8 - - + +
1808A ALA* 4.8 3.1 - - + -
1921A MET* 5.4 1.1 - - - -
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Residues in contact with LEU1776 (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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1707A HIS* 4.3 11.7 - - + +
1711A VAL* 5.8 0.2 - - + -
1714A GLN* 6.1 3.1 - - - +
1730A LYS* 4.4 9.6 - - + +
1731A VAL* 4.0 39.5 - - + -
1732A GLN* 4.7 4.9 - - + +
1751A GLN* 3.3 14.2 + - - +
1771A TYR* 3.9 29.8 - - + -
1772A THR 3.1 17.8 + - - +
1773A PRO* 3.6 15.7 - - + +
1774A LEU 3.2 0.2 - - - -
1775A LEU* 1.3 75.1 - - + +
1777A ILE* 1.3 65.1 + - + +
1779A PHE* 3.3 13.6 + - + -
1780A ALA* 3.0 16.5 + - - +
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Residues in contact with ILE1777 (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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1730A LYS* 6.4 1.8 - - + -
1773A PRO* 2.9 25.2 + - + +
1774A LEU* 3.7 9.0 - - + +
1776A LEU* 1.3 73.2 - - + +
1778A GLY* 1.3 58.2 + - - +
1780A ALA* 2.8 27.2 + - + +
1781A THR* 2.9 16.3 + - + +
1919A PHE* 3.3 34.1 - - + -
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Residues in contact with GLY1778 (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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1774A LEU 2.9 14.8 + - - -
1775A LEU* 3.7 4.7 - - - -
1777A ILE* 1.3 77.7 - - - +
1779A PHE* 1.3 63.3 + - - +
1781A THR* 3.2 9.6 + - - -
1782A LEU* 3.1 28.3 + - - +
1794A PHE* 4.2 15.7 - - - -
1805A THR* 5.1 3.1 - - - -
1919A PHE* 4.5 8.9 - - - -
1921A MET* 5.0 3.4 - - - -
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Residues in contact with PHE1779 (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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1732A GLN* 3.6 22.4 - - + +
1751A GLN* 3.4 15.0 - - - +
1768A ARG* 5.6 0.9 - - - -
1771A TYR* 4.8 4.7 - + - -
1775A LEU* 2.9 51.5 + - + -
1776A LEU* 3.4 17.7 - - + +
1777A ILE 3.2 0.2 - - - -
1778A GLY* 1.3 78.9 - - - +
1780A ALA* 1.3 57.5 + - - +
1782A LEU* 5.3 0.9 - - + -
1783A THR* 3.0 30.7 + - - +
1805A THR* 3.6 26.2 - - + -
1808A ALA* 4.2 5.6 - - + -
1809A PHE* 3.7 40.4 - + + -
1812A ASN* 3.3 25.8 - - - -
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Residues in contact with ALA1780 (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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1730A LYS* 5.3 2.0 - - - +
1751A GLN* 3.8 10.5 + - - +
1752A SER* 4.2 16.6 + - - +
1776A LEU 3.0 11.7 + - - +
1777A ILE* 2.8 17.8 + - + +
1779A PHE* 1.3 76.5 - - - +
1781A THR* 1.3 58.2 + - + -
1783A THR* 3.1 11.1 - - - +
1784A ASP* 2.9 29.1 + - - +
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Residues in contact with THR1781 (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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1777A ILE* 2.9 22.1 + - + +
1778A GLY 3.2 7.4 + - - -
1780A ALA* 1.3 73.7 - - + +
1782A LEU* 1.3 64.4 + - - +
1784A ASP* 3.3 7.8 + - - +
1785A SER* 2.8 34.0 + - - -
1794A PHE* 3.7 19.1 - - - -
1917A ARG 6.2 0.2 - - - -
1919A PHE* 3.5 47.8 - - + +
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Residues in contact with LEU1782 (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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1778A GLY 3.1 16.2 + - - +
1779A PHE* 4.0 3.4 - - + +
1781A THR* 1.3 81.7 + - - +
1783A THR* 1.3 64.9 + - - +
1785A SER* 3.2 3.2 + - - -
1786A LEU* 3.0 30.7 + - - +
1792A GLY* 3.8 19.7 - - - -
1794A PHE* 3.5 35.4 - - + -
1805A THR* 5.3 0.9 - - + +
1806A VAL* 4.3 14.6 - - + -
1809A PHE* 3.9 37.5 - - + -
1895A PHE* 3.5 32.1 - - + -
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Residues in contact with THR1783 (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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1732A GLN* 5.8 0.4 - - - -
1749A ILE* 6.0 0.5 - - - +
1751A GLN* 3.8 30.0 + - + +
1752A SER* 5.0 2.2 - - - -
1754A TYR* 3.8 17.0 + - + +
1756A LEU* 3.2 36.9 - - - +
1779A PHE 3.0 18.9 + - - +
1780A ALA* 3.1 25.8 - - - +
1782A LEU* 1.3 76.7 - - - +
1784A ASP* 1.3 62.3 + - - +
1786A LEU* 4.1 1.2 - - - +
1787A HIS* 3.2 25.1 + - - +
1809A PHE* 4.1 3.3 - - - -
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Residues in contact with ASP1784 (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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1752A SER* 6.4 0.9 - - - -
1754A TYR* 3.3 33.5 + - + -
1780A ALA 2.9 20.2 + - - +
1781A THR* 3.4 9.9 - - - +
1782A LEU 3.1 0.2 - - - -
1783A THR* 1.3 79.7 - - - +
1785A SER* 1.3 63.4 + - - +
1787A HIS* 3.6 11.8 + - - +
1788A GLN* 4.2 6.2 + - - +
1917A ARG* 4.7 15.2 + - - -
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Residues in contact with SER1785 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1781A THR* 2.8 22.0 + - - -
1782A LEU 3.2 4.5 + - - -
1784A ASP* 1.3 76.0 + - - +
1786A LEU* 1.3 66.0 + - - +
1787A HIS 3.0 1.8 - - - -
1788A GLN* 3.0 15.8 + - - +
1789A LYS 3.1 7.6 + - - -
1790A TYR* 3.2 22.9 + - - +
1791A GLY 4.3 4.3 - - - -
1792A GLY* 4.2 11.1 - - - -
1917A ARG* 3.2 39.0 + - - +
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Residues in contact with LEU1786 (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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1756A LEU* 4.4 18.9 - - + +
1782A LEU 3.0 18.4 + - - +
1783A THR 4.2 2.9 - - - +
1785A SER* 1.3 77.8 - - - +
1787A HIS* 1.3 64.5 + - - +
1789A LYS* 2.9 22.8 + - - +
1790A TYR 3.7 15.0 - - - +
1791A GLY* 5.1 1.1 - - - -
1792A GLY 5.0 1.8 - - - +
1809A PHE* 3.9 16.6 - - + -
1844A TRP* 3.7 36.3 - - + -
1869A GLN* 5.9 0.9 - - - +
1893A ALA* 4.3 14.8 - - + -
1895A PHE* 3.9 25.1 - - + -
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Residues in contact with HIS1787 (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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1754A TYR* 3.4 56.4 + + + -
1755A LEU 4.7 10.1 - - - -
1756A LEU* 4.9 6.5 - - + +
1783A THR 3.2 19.0 + - - +
1784A ASP 3.6 8.1 - - - +
1786A LEU* 1.3 78.1 - - - +
1788A GLN* 1.3 70.1 + - + +
1789A LYS* 4.7 3.5 - - - +
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Residues in contact with GLN1788 (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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1754A TYR* 5.9 1.3 - - - +
1784A ASP 5.0 4.5 - - - +
1785A SER 3.0 7.5 + - - +
1787A HIS* 1.3 90.9 - - + +
1789A LYS* 1.3 72.7 + - - +
1790A TYR* 3.3 30.8 + - + -
1873A GLN* 4.4 4.7 - - - +
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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
------------------------------------------------------------
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