Contacts of the helix formed by residues 1908 - 1927 (chain A) in PDB entry 2HC2
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 VAL1908 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1736A ILE* 3.5 32.1 - - + -
1904A CYS* 3.4 12.3 - - - -
1906A ALA* 3.7 18.8 - - + +
1907A GLY* 1.3 80.7 - - - +
1909A GLY* 1.3 75.0 + - - +
1910A ARG* 3.4 2.2 - - + +
1911A THR* 3.1 3.1 + - - -
1912A GLY 3.0 18.2 + - - -
1944A VAL 4.5 1.8 - - - +
1945A HIS* 3.2 35.0 - - + -
1946A MET* 3.4 6.7 - - - +
1948A GLN* 3.2 18.2 - - - +
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Residues in contact with GLY1909 (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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1908A VAL* 1.3 81.1 - - - +
1910A ARG* 1.3 57.7 + - - +
1912A GLY* 3.2 1.2 + - - -
1913A THR* 2.8 32.7 + - - -
1945A HIS 3.2 10.8 + - - -
1947A VAL 4.0 1.5 + - - -
1948A GLN* 3.0 16.7 + - - -
1952A GLN* 3.4 25.5 - - - +
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Residues in contact with ARG1910 (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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1801A VAL* 3.0 38.6 + - + +
1802A THR* 3.6 9.6 + - - +
1806A GLU* 3.2 37.1 + - - -
1868A TRP* 3.6 53.7 - - + +
1869A PRO 3.2 24.6 + - - -
1870A ASP 3.4 12.7 + - - -
1871A HIS* 5.3 0.2 - - - +
1872A GLY 5.4 0.4 + - - -
1904A CYS* 4.1 14.4 - - + -
1908A VAL* 3.4 1.2 - - + +
1909A GLY* 1.3 74.2 - - - +
1911A THR* 1.3 59.1 + - - +
1913A THR* 3.3 2.1 + - - -
1914A PHE* 2.9 28.2 + - - +
1952A GLN* 3.6 6.4 - - - +
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Residues in contact with THR1911 (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 VAL* 3.2 43.5 - - + -
1801A VAL* 4.0 2.0 - - - +
1902A VAL* 3.5 22.5 - - + +
1903A HIS* 3.3 8.7 + - - -
1904A CYS* 3.2 29.7 + - - +
1907A GLY* 4.1 0.7 - - - -
1908A VAL 3.1 14.6 + - - -
1910A ARG* 1.3 79.8 - - - +
1912A GLY* 1.3 62.5 + - - +
1914A PHE* 3.3 3.0 + - - +
1915A ILE* 3.0 23.8 + - + +
1946A MET* 4.7 0.7 - - - -
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Residues in contact with GLY1912 (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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1908A VAL 3.0 12.0 + - - -
1909A GLY 3.7 3.4 - - - -
1911A THR* 1.3 76.8 - - - +
1913A THR* 1.3 56.9 + - - +
1915A ILE* 4.7 1.6 - - - -
1916A ALA* 2.8 32.6 + - - +
1939A LEU* 3.5 9.9 - - - +
1946A MET* 4.1 16.3 - - - -
1947A VAL* 3.6 21.5 - - - +
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Residues in contact with THR1913 (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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1868A TRP* 4.0 20.0 - - + -
1880A LEU* 4.3 5.6 - - + -
1909A GLY 2.8 20.2 + - - -
1910A ARG 3.6 4.7 - - - -
1912A GLY* 1.3 74.3 - - - +
1914A PHE* 1.3 65.9 + - - +
1917A LEU* 2.9 24.4 + - - +
1947A VAL* 3.9 9.8 - - - +
1952A GLN* 3.4 29.0 + - + +
1955A TYR* 4.2 20.0 - - + -
1956A LEU* 3.7 22.4 - - + +
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Residues in contact with PHE1914 (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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1772A TYR* 5.1 3.8 - + - -
1799A VAL* 3.9 29.6 - - + -
1801A VAL* 4.6 9.6 - - + -
1868A TRP* 5.4 0.7 - - + -
1880A LEU* 4.7 11.6 - - + +
1883A PHE* 3.5 33.2 - + - -
1884A VAL* 3.6 31.1 - - + +
1887A VAL* 4.0 17.0 - - + -
1891A ILE* 5.9 0.9 - - + -
1900A THR* 5.7 1.1 - - + -
1902A VAL* 3.9 24.7 - - + -
1910A ARG 2.9 14.2 + - - +
1911A THR 3.3 7.2 + - - +
1913A THR* 1.3 78.1 - - - +
1915A ILE* 1.3 65.1 + - + +
1917A LEU* 3.3 4.5 + - - +
1918A ASP* 2.9 41.2 + - + +
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Residues in contact with ILE1915 (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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1763A ILE* 4.5 6.1 - - + -
1772A TYR* 3.5 52.3 - - + -
1774A VAL* 3.4 33.0 - - + -
1902A VAL* 4.0 12.8 - - + -
1911A THR* 3.0 21.8 + - + +
1912A GLY* 4.0 3.8 - - - +
1914A PHE* 1.3 76.8 - - + +
1916A ALA* 1.3 69.2 + - - +
1918A ASP* 3.2 6.0 + - - +
1919A ARG* 2.9 25.0 + - - +
1939A LEU* 3.7 26.5 - - + -
1946A MET* 5.4 1.1 - - - -
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Residues in contact with ALA1916 (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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1912A GLY 2.8 18.8 + - - +
1913A THR 3.9 0.4 - - - +
1915A ILE* 1.3 76.3 - - - +
1917A LEU* 1.3 58.3 + - - +
1919A ARG* 3.2 7.1 + - - +
1920A ILE* 2.9 42.0 + - + +
1935A ALA* 4.6 5.6 - - + -
1936A VAL* 4.4 6.5 - - + -
1939A LEU* 3.8 14.1 - - + +
1947A VAL* 4.4 3.6 - - + -
1956A LEU* 3.8 26.5 - - + -
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Residues in contact with LEU1917 (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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1880A LEU* 3.8 37.9 - - + +
1881A ILE* 4.1 4.5 - - - +
1884A VAL* 3.8 15.9 - - + -
1913A THR 2.9 18.3 + - - +
1914A PHE 3.7 3.4 - - - +
1916A ALA* 1.3 74.5 - - - +
1918A ASP* 1.3 66.3 + - - +
1920A ILE* 4.5 6.5 - - + +
1921A LEU* 2.9 54.9 + - + +
1956A LEU* 3.8 16.1 - - + +
1959A CYS* 3.7 36.8 - - + -
1960A VAL* 5.2 2.5 - - + -
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Residues in contact with ASP1918 (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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1772A TYR* 2.5 28.9 + - - +
1884A VAL* 3.5 18.2 - - + +
1888A ARG* 2.8 52.7 + - - +
1891A ILE* 4.4 4.8 - - - +
1914A PHE* 2.9 24.9 + - + +
1915A ILE* 3.2 10.7 + - - +
1917A LEU* 1.3 75.5 - - - +
1919A ARG* 1.3 62.1 + - - +
1921A LEU* 4.1 1.0 - - - +
1922A GLN* 3.0 28.2 + - - +
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Residues in contact with ARG1919 (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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1764A PRO 3.0 23.2 + - - -
1765A GLY* 3.7 22.4 + - - -
1766A ASN* 2.8 49.5 + - - +
1772A TYR* 3.8 13.7 - - - +
1915A ILE* 2.9 22.7 + - + +
1916A ALA* 3.6 4.5 - - - +
1918A ASP* 1.3 78.0 - - - +
1920A ILE* 1.3 61.8 + - - +
1922A GLN* 3.8 1.8 - - - +
1923A GLN* 3.2 18.7 + - - +
1934A GLY 5.0 1.2 + - - -
1935A ALA* 4.4 20.9 - - + +
1938A ASP* 2.9 42.4 + - - +
1939A LEU* 3.7 17.4 - - - +
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Residues in contact with ILE1920 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1916A ALA* 2.9 37.6 + - + +
1917A LEU* 4.0 7.4 - - + +
1919A ARG* 1.3 73.4 - - - +
1921A LEU* 1.3 63.2 + - + +
1923A GLN* 3.1 13.9 + - - +
1924A LEU* 3.0 27.5 + - + +
1930A VAL* 3.3 17.9 - - + -
1932A ILE* 3.7 43.5 - - + -
1935A ALA* 4.3 10.3 - - + -
1956A LEU* 4.5 6.7 - - + -
1960A VAL* 3.1 36.8 - - + -
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Residues in contact with LEU1921 (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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1881A ILE* 4.1 25.8 - - + +
1884A VAL* 3.9 24.5 - - + -
1885A ARG* 4.3 17.5 - - + +
1917A LEU* 2.9 39.9 + - + +
1918A ASP 4.2 2.9 - - - +
1920A ILE* 1.3 78.8 - - + +
1922A GLN* 1.3 62.2 + - + +
1924A LEU* 3.3 26.7 + - + +
1925A ASP* 3.2 29.2 + - - +
1959A CYS 5.4 0.9 - - - +
1960A VAL* 5.1 2.2 - - + -
1963A VAL* 3.9 20.0 - - + -
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Residues in contact with GLN1922 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1766A ASN* 3.3 19.6 + - - +
1767A ASN* 3.0 29.1 + - - +
1771A GLU* 4.7 0.4 + - - -
1772A TYR* 4.2 3.2 + - - -
1888A ARG* 3.5 48.0 + - + +
1892A ASN* 5.2 0.3 - - - +
1918A ASP* 3.0 31.1 + - - +
1919A ARG* 3.6 6.6 - - - +
1921A LEU* 1.3 78.2 - - + +
1923A GLN* 1.3 62.3 + - - +
1925A ASP* 3.1 16.0 + - - +
1926A SER* 3.0 19.8 + - - +
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Residues in contact with GLN1923 (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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1766A ASN* 3.6 26.0 + - - +
1919A ARG* 3.2 21.0 + - - +
1920A ILE* 3.1 12.4 + - - +
1922A GLN* 1.3 78.3 - - - +
1924A LEU* 1.3 58.1 + - - +
1926A SER* 3.9 5.6 - - - -
1927A LYS* 2.8 45.1 + - + +
1929A SER 4.1 12.7 - - - +
1930A VAL* 3.5 9.2 - - + +
1931A ASP* 3.0 43.3 + - - +
1935A ALA* 4.9 4.0 - - - +
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Residues in contact with LEU1924 (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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1685A ILE* 3.7 30.2 - - + +
1920A ILE 3.0 16.2 + - - +
1921A LEU* 3.6 26.0 - - + +
1923A GLN* 1.3 76.2 - - - +
1925A ASP* 1.3 58.0 + - - +
1926A SER 3.7 0.2 + - - -
1927A LYS 4.0 7.7 - - - +
1930A VAL* 3.8 19.5 - - + -
1960A VAL* 4.1 26.2 - - + -
1963A VAL* 3.7 30.5 - - + -
1964A LEU* 4.2 9.9 - - + -
1967A ARG* 2.5 35.0 + - - +
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Residues in contact with ASP1925 (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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1885A ARG* 5.2 12.1 + - - +
1921A LEU* 3.2 15.0 + - - +
1922A GLN* 3.1 11.7 + - - +
1923A GLN 3.1 1.0 - - - -
1924A LEU* 1.3 80.1 - - - +
1926A SER* 1.3 57.8 + - - +
1967A ARG* 3.6 13.9 + - - +
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Residues in contact with SER1926 (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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1922A GLN 3.0 16.5 + - - -
1923A GLN* 3.1 0.5 + - - -
1925A ASP* 1.3 78.1 - - - +
1927A LYS* 1.3 93.8 + - - +
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Residues in contact with LYS1927 (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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1685A ILE* 3.3 16.5 - - - +
1923A GLN* 2.8 24.3 + - + +
1924A LEU 4.0 5.2 - - - +
1925A ASP 5.2 0.2 - - - -
1926A SER* 1.3 107.8 + - - +
1928A ASP* 1.3 65.7 + - - +
1929A SER* 3.3 19.1 - - - +
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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