Contacts of the helix formed by residues 1905 - 1934 (chain r) in PDB entry 6FF7
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 SER1905 (chain r).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1904r LEU* 1.3 76.9 - - - +
1906r ALA* 1.3 59.4 + - - +
1907r GLU* 3.1 13.7 + - - -
1908r LEU* 3.2 7.0 + - - +
1909r GLN* 2.8 26.9 + - - +
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Residues in contact with ALA1906 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1623r GLY* 5.3 16.2 - - - +
1904r LEU 3.8 1.4 + - - -
1905r SER* 1.3 72.4 - - - +
1907r GLU* 1.3 57.3 + - - +
1909r GLN* 3.6 10.1 - - - -
1910r SER* 2.9 30.5 + - - -
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Residues in contact with GLU1907 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1622r GLU* 6.4 1.6 - - - -
1905r SER* 3.1 9.6 - - - -
1906r ALA* 1.3 82.1 - - - +
1908r LEU* 1.3 61.6 + - + +
1910r SER* 3.7 13.5 + - - -
1911r ASP* 3.7 4.9 + - - +
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Residues in contact with LEU1908 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1894r LEU* 5.5 4.3 - - + +
1904r LEU* 5.0 10.8 - - + -
1905r SER* 3.2 9.4 + - - +
1907r GLU* 1.3 77.2 - - + +
1909r GLN* 1.3 60.1 + - - +
1910r SER 3.4 0.2 - - - -
1911r ASP* 3.3 11.7 - - + +
1912r THR* 2.9 26.5 + - - -
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Residues in contact with GLN1909 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1904r LEU* 4.7 10.0 - - + +
1905r SER 2.8 19.9 + - - +
1906r ALA* 3.6 11.9 - - + +
1907r GLU 3.3 0.2 - - - -
1908r LEU* 1.3 74.6 - - - +
1910r SER* 1.3 65.7 + - - +
1912r THR* 3.2 9.6 + - - -
1913r GLU* 3.0 22.5 + - - +
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Residues in contact with SER1910 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1622r GLU* 6.4 2.5 - - - -
1906r ALA 2.9 17.1 + - - -
1907r GLU* 3.7 6.7 - - - -
1909r GLN* 1.3 74.2 - - - +
1911r ASP* 1.3 64.1 + - - +
1913r GLU* 3.1 11.4 + - - +
1914r GLU* 3.0 20.9 + - - +
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Residues in contact with ASP1911 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1858r ILE* 6.2 3.6 - - + -
1894r LEU* 5.9 2.7 - - + -
1907r GLU 3.7 3.0 + - - +
1908r LEU* 3.3 20.3 + - + +
1909r GLN 3.2 0.2 - - - -
1910r SER* 1.3 78.5 - - - +
1912r THR* 1.3 62.9 + - - +
1914r GLU* 3.0 10.3 + - - +
1915r ILE* 2.9 21.9 + - - +
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Residues in contact with THR1912 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1894r LEU* 4.8 25.2 - - - +
1898r HIS* 5.4 8.1 - - - -
1908r LEU 2.9 14.2 + - - -
1909r GLN* 3.2 12.8 + - - -
1911r ASP* 1.3 74.0 - - - +
1913r GLU* 1.3 63.4 + - - +
1915r ILE* 3.1 9.3 + - - +
1916r LEU* 2.9 25.0 + - - +
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Residues in contact with GLU1913 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1909r GLN 3.0 12.6 + - - +
1910r SER* 3.3 11.9 - - - +
1912r THR* 1.3 75.9 - - - +
1914r GLU* 1.3 61.9 + - - +
1916r LEU* 3.4 7.9 + - - +
1917r SER* 3.0 22.3 + - - -
2057r PRO* 4.6 19.5 - - + +
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Residues in contact with GLU1914 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1910r SER 3.0 13.0 + - - +
1911r ASP* 3.0 9.8 + - - +
1913r GLU* 1.3 77.0 - - - +
1915r ILE* 1.3 64.1 + - - +
1917r SER* 3.2 21.0 + - - -
1918r LYS* 3.7 4.9 + - - +
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Residues in contact with ILE1915 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1891r THR* 5.3 14.8 - - - +
1894r LEU* 6.0 3.8 - - + -
1895r LEU* 6.4 1.6 - - + -
1911r ASP 2.9 11.1 + - - +
1912r THR* 3.4 12.3 - - - +
1914r GLU* 1.3 75.0 - - - +
1916r LEU* 1.3 63.5 + - - +
1917r SER 3.2 0.7 + - - -
1918r LYS* 3.2 6.2 + - - +
1919r ALA* 3.0 21.9 + - - +
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Residues in contact with LEU1916 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1912r THR 2.9 13.2 + - - +
1913r GLU* 3.6 11.7 - - - +
1915r ILE* 1.3 77.2 - - - +
1917r SER* 1.3 64.9 + - - +
1919r ALA* 3.2 21.7 + - - +
1920r ILE* 4.4 3.8 + - - +
2056r PHE* 6.2 2.7 - - + -
2057r PRO* 5.6 8.7 - - + -
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Residues in contact with SER1917 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1913r GLU 3.0 13.7 + - - -
1914r GLU* 3.3 15.3 - - - -
1915r ILE 3.2 0.4 - - - -
1916r LEU* 1.3 77.7 - - - +
1918r LYS* 1.3 59.4 + - - +
1920r ILE* 5.1 3.5 + - - +
2057r PRO* 5.6 6.5 - - - +
2058r GLN* 5.6 8.3 - - - -
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Residues in contact with LYS1918 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1854r GLU* 5.5 11.2 - - + -
1914r GLU 3.7 4.2 + - - +
1915r ILE 3.2 7.0 + - - +
1917r SER* 1.3 77.1 - - - +
1919r ALA* 1.3 65.8 + - - +
1920r ILE 3.5 2.0 + - - -
1921r ARG* 3.6 15.9 + - + +
1922r LEU* 3.8 9.9 + - - +
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Residues in contact with ALA1919 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1915r ILE 3.0 14.0 + - - +
1916r LEU* 3.2 18.8 + - - +
1918r LYS* 1.3 77.2 - - - +
1920r ILE* 1.3 65.2 + - - +
1922r LEU* 3.0 11.3 + - - +
1923r ILE* 3.0 21.7 + - - +
1949r VAL* 5.5 11.2 - - + -
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Residues in contact with ILE1920 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1916r LEU 4.4 3.9 + - - +
1917r SER 5.1 3.1 + - - +
1918r LYS 3.5 0.6 - - - -
1919r ALA* 1.3 77.0 - - - +
1921r ARG* 1.3 63.5 + - - +
1923r ILE* 3.2 10.0 + - - +
1924r GLN* 2.9 24.8 + - - +
1946r ALA* 6.0 4.9 - - + +
1949r VAL* 6.4 1.3 - - - -
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Residues in contact with ARG1921 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1822r TYR* 4.4 27.9 - - + +
1918r LYS* 3.6 13.5 + - + +
1919r ALA 3.2 0.8 - - - -
1920r ILE* 1.3 77.0 - - - +
1922r LEU* 1.3 59.3 + - - +
1924r GLN* 3.2 7.4 + - - +
1925r ALA* 2.9 28.2 + - - +
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Residues in contact with LEU1922 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1849r ILE* 5.2 18.4 - - + +
1852r ALA* 5.5 8.5 - - + -
1918r LYS 3.8 6.5 + - - +
1919r ALA* 3.0 11.8 + - - +
1921r ARG* 1.3 79.1 - - - +
1923r ILE* 1.3 62.7 + - - +
1925r ALA* 3.0 10.7 + - - +
1926r CYS* 3.0 20.8 + - - +
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Residues in contact with ILE1923 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1849r ILE* 5.7 4.9 - - - +
1919r ALA 3.0 12.2 + - - +
1920r ILE* 3.2 13.7 + - - +
1922r LEU* 1.3 75.1 - - - +
1924r GLN* 1.3 62.8 + - - +
1926r CYS* 3.0 12.3 + - - +
1927r VAL* 2.9 19.1 + - - +
1942r ALA* 4.6 11.7 - - + +
1945r LEU* 5.6 4.0 - - + -
1946r ALA* 4.8 23.1 - - + +
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Residues in contact with GLN1924 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1920r ILE 2.9 13.1 + - - +
1921r ARG* 3.4 10.8 - - - +
1923r ILE* 1.3 75.1 - - - +
1925r ALA* 1.3 63.0 + - - +
1927r VAL* 3.0 12.1 + - - +
1928r ASP* 2.9 22.9 + - - +
1946r ALA* 6.0 0.6 - - - +
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Residues in contact with ALA1925 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1818r ILE* 5.6 11.7 - - + +
1822r TYR* 5.1 11.9 - - + +
1829r ILE* 6.0 6.7 - - + -
1921r ARG 2.9 12.7 + - - +
1922r LEU* 3.2 13.0 - - - +
1924r GLN* 1.3 76.8 - - - +
1926r CYS* 1.3 58.1 + - - +
1928r ASP* 3.1 8.2 + - - +
1929r VAL* 2.9 29.5 + - - +
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Residues in contact with CYS1926 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1845r LEU* 6.3 2.9 - - + -
1922r LEU 3.0 11.5 + - - +
1923r ILE* 3.0 12.8 + - - +
1925r ALA* 1.3 73.9 - - - +
1927r VAL* 1.3 65.1 + - - +
1929r VAL* 3.2 6.6 + - - +
1930r LEU* 2.9 27.6 + - - +
1942r ALA* 4.7 11.2 - - + -
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Residues in contact with VAL1927 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1923r ILE 2.9 9.5 + - - +
1924r GLN* 3.2 16.2 - - - +
1926r CYS* 1.3 76.9 - - - +
1928r ASP* 1.3 58.7 + - - +
1930r LEU* 3.4 3.6 + - - +
1931r SER* 2.9 32.7 + - - -
1939r ALA* 4.7 9.3 - - + +
1942r ALA* 4.4 16.0 - - + +
1943r MET* 5.3 7.2 - - + +
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Residues in contact with ASP1928 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1818r ILE* 5.3 11.2 - - + -
1924r GLN 2.9 11.8 + - - +
1925r ALA* 3.1 11.2 + - - +
1927r VAL* 1.3 74.7 - - - +
1929r VAL* 1.3 59.3 + - - +
1931r SER* 4.0 4.1 - - - -
1932r SER* 2.9 33.7 + - - -
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Residues in contact with VAL1929 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1818r ILE* 6.2 0.6 - - - +
1832r PHE* 5.3 15.0 - - + +
1833r SER* 5.9 3.4 - - - +
1836r LEU* 5.8 7.4 - - + -
1925r ALA 2.9 18.5 + - - +
1926r CYS* 3.8 7.6 - - - +
1928r ASP* 1.3 72.8 - - - +
1930r LEU* 1.3 58.1 + - - +
1932r SER* 3.8 4.1 - - - -
1933r ASN* 2.9 30.5 + - - +
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Residues in contact with LEU1930 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1836r LEU* 5.8 9.0 - - + -
1926r CYS 2.9 17.3 + - - +
1927r VAL 3.8 2.9 - - - +
1929r VAL* 1.3 76.6 - - - +
1931r SER* 1.3 58.2 + - - +
1933r ASN* 3.3 6.2 + - - +
1934r GLY 2.8 23.2 + - - -
1935r TRP* 3.2 17.2 + - + +
1938r PRO* 4.6 10.8 - - + -
1939r ALA* 4.2 25.1 - - - +
1942r ALA* 6.0 0.7 - - + -
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Residues in contact with SER1931 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1927r VAL 2.9 17.5 + - - -
1928r ASP* 4.1 4.5 - - - -
1930r LEU* 1.3 76.9 - - - +
1932r SER* 1.3 63.0 + - - +
1934r GLY* 3.1 14.3 + - - +
1939r ALA* 4.5 12.3 - - - +
2076r LEU* 4.4 15.4 - - - +
2079r ILE* 4.8 18.6 - - - -
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Residues in contact with SER1932 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1814r ASN* 5.5 10.1 - - - -
1928r ASP 2.9 20.2 + - - -
1929r VAL* 3.8 4.5 - - - -
1931r SER* 1.3 74.1 - - - +
1933r ASN* 1.3 61.8 + - - +
1934r GLY* 3.0 6.4 + - - -
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Residues in contact with ASN1933 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1929r VAL 2.9 19.8 + - - +
1930r LEU* 3.3 6.9 + - - +
1932r SER* 1.3 74.3 - - - +
1934r GLY* 1.3 60.1 + - - +
1935r TRP* 3.8 3.6 - - + +
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Residues in contact with GLY1934 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1930r LEU 2.8 7.1 + - - -
1931r SER 3.1 12.1 + - - -
1932r SER 3.0 5.3 - - - -
1933r ASN* 1.3 79.3 - - - +
1935r TRP* 1.3 56.0 + - - -
2074r ASN 3.7 5.9 - - - +
2075r SER* 3.8 4.0 - - - -
2076r LEU* 3.3 28.7 + - - -
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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
------------------------------------------------------------
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