Contacts of the helix formed by residues 1928 - 1954 (chain A) in PDB entry 5MQF
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 SER1928 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1924A LEU* 5.7 0.4 - - - -
1927A ILE* 1.3 78.7 - - - +
1929A SER* 1.3 62.1 + - - +
1930A TYR* 3.1 10.5 + - - -
1931A THR* 3.3 10.8 + - - -
1932A ALA* 2.9 27.3 + - - +
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Residues in contact with SER1929 (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 PHE* 3.7 24.2 - - - +
1812A PRO 4.2 6.0 - - - +
1813A ARG* 3.7 28.5 - - - -
1924A LEU* 5.8 3.0 - - - +
1927A ILE 4.0 0.4 + - - -
1928A SER* 1.3 74.5 - - - +
1930A TYR* 1.3 57.0 + - - +
1932A ALA* 3.8 8.4 - - - +
1933A PHE* 2.9 28.9 + - - +
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Residues in contact with TYR1930 (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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1768A TYR 5.6 6.3 - - - +
1769A GLY* 6.1 3.8 - - - -
1772A PHE* 4.5 10.3 - - + +
1928A SER* 3.1 7.4 - - - -
1929A SER* 1.3 77.2 - - - +
1931A THR* 1.3 61.1 + - - +
1933A PHE* 3.1 6.6 + - - +
1934A SER* 2.9 31.4 + - - -
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Residues in contact with THR1931 (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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1927A ILE* 4.5 14.8 - - - -
1928A SER* 3.3 15.2 + - - -
1930A TYR* 1.3 77.0 - - - +
1932A ALA* 1.3 57.8 + - - +
1934A SER* 4.7 2.7 - - - +
1935A ARG* 2.9 36.5 + - - +
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Residues in contact with ALA1932 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1920A TYR* 4.7 11.7 - - + -
1923A TRP* 4.1 26.2 - - + -
1924A LEU* 5.6 0.9 - - - +
1927A ILE* 5.2 2.3 - - + +
1928A SER 2.9 18.3 + - - +
1929A SER* 3.8 8.7 - - - +
1931A THR* 1.3 76.9 - - - +
1933A PHE* 1.3 51.3 + - - +
1935A ARG* 4.5 3.1 - - - -
1936A LEU* 2.6 36.2 + - - +
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Residues in contact with PHE1933 (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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1768A TYR 5.9 2.7 - - - +
1771A LEU* 6.3 1.6 - - + -
1812A PRO* 5.1 13.9 - - + +
1929A SER 2.9 20.1 + - - +
1930A TYR* 3.1 8.2 + - - +
1932A ALA* 1.3 76.7 - - - +
1934A SER* 1.3 60.5 + - - +
1936A LEU* 3.2 5.7 - - - +
1937A ILE* 2.9 28.2 + - - +
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Residues in contact with SER1934 (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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1930A TYR 2.9 13.7 + - - -
1931A THR* 4.4 2.9 - - - -
1933A PHE* 1.3 73.3 - - - +
1935A ARG* 1.3 66.7 + - - +
1937A ILE* 3.1 5.0 + - - +
1938A LEU* 2.9 27.0 + - - +
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Residues in contact with ARG1935 (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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1931A THR* 2.9 21.9 + - - +
1932A ALA* 4.3 3.8 - - - +
1934A SER* 1.3 75.4 - - - +
1936A LEU* 1.3 62.2 + - - +
1938A LEU* 4.1 4.2 - - - +
1939A ILE* 3.0 28.8 + - - +
1980A GLU* 6.1 5.6 - - + -
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Residues in contact with LEU1936 (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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1932A ALA 2.6 25.6 + - - +
1933A PHE* 3.2 9.6 - - - +
1934A SER 3.1 0.4 - - - -
1935A ARG* 1.3 76.5 - - - +
1937A ILE* 1.3 57.0 + - - +
1939A ILE* 3.4 5.1 + - - +
1940A LEU* 2.8 26.4 + - - +
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Residues in contact with ILE1937 (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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1890A GLN 5.0 11.7 - - - +
1891A LEU* 6.4 0.4 - - - -
1933A PHE 2.9 16.2 + - - +
1934A SER* 3.1 5.6 + - - +
1936A LEU* 1.3 73.2 - - - +
1938A LEU* 1.3 60.5 + - - +
1940A LEU* 2.6 29.3 + - - +
1941A ARG* 3.0 12.8 + - - +
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Residues in contact with LEU1938 (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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1934A SER 2.9 16.6 + - - +
1935A ARG* 4.1 4.3 - - - +
1937A ILE* 1.3 75.8 - - - +
1939A ILE* 1.3 58.5 + - - +
1941A ARG* 3.4 5.1 + - - +
1942A ALA* 3.0 26.6 + - - +
1980A GLU* 5.9 2.2 - - - +
1983A LEU* 4.8 7.5 - - + +
1984A LYS* 5.5 15.9 - - + +
1987A ILE* 5.5 4.2 - - - +
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Residues in contact with ILE1939 (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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1935A ARG 3.0 20.2 + - - +
1936A LEU* 3.5 4.9 - - - +
1938A LEU* 1.3 76.0 - - - +
1940A LEU* 1.3 57.0 + - - +
1942A ALA* 3.2 11.9 - - + +
1943A LEU* 2.8 24.6 + - - +
1983A LEU* 5.0 4.9 - - + -
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Residues in contact with LEU1940 (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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1890A GLN 5.3 0.2 - - - +
1891A LEU* 5.1 3.1 - - - -
1892A PRO* 3.2 32.2 - - + +
1936A LEU 2.8 12.5 + - - +
1937A ILE* 2.6 25.1 + - - +
1939A ILE* 1.3 68.1 - - - +
1941A ARG* 1.3 56.1 + - - +
1942A ALA 3.1 0.9 - - - -
1943A LEU* 2.5 29.2 + - - +
1944A HIS 3.0 8.7 + - - -
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Residues in contact with ARG1941 (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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1890A GLN* 5.6 8.1 - - + +
1892A PRO* 3.6 12.7 - - + +
1937A ILE 3.0 9.5 + - - +
1938A LEU* 4.1 6.1 - - - +
1940A LEU* 1.3 70.7 - - - +
1942A ALA* 1.3 68.8 + - - +
1944A HIS* 3.0 12.8 + - - +
1945A VAL* 3.2 13.9 + - - +
1987A ILE* 5.2 13.7 - - + -
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Residues in contact with ALA1942 (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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1938A LEU 3.0 15.7 + - - +
1939A ILE* 3.2 14.6 - - + +
1941A ARG* 1.3 73.9 - - - +
1943A LEU* 1.3 50.9 + - - +
1944A HIS 2.6 8.7 + - - -
1945A VAL* 5.5 0.9 - - - -
1946A ASN* 2.5 49.4 + - + +
1950A ALA* 5.6 1.6 - - + -
1983A LEU* 3.5 32.8 + - + +
1986A LEU* 5.6 3.8 - - + -
1987A ILE* 5.7 2.2 - - - +
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Residues in contact with LEU1943 (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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1892A PRO 5.6 0.4 - - - +
1895A ALA* 3.4 20.0 - - + +
1896A CYS* 5.1 4.9 - - + +
1939A ILE 2.8 16.3 + - - +
1940A LEU* 2.5 19.9 + - - +
1942A ALA* 1.3 67.5 - - - +
1944A HIS* 1.3 50.5 + - - -
1946A ASN 3.2 7.9 - - - -
1947A ASN* 2.1 37.3 - - + +
1950A ALA* 4.3 5.6 - - + +
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Residues in contact with HIS1944 (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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1892A PRO* 4.7 7.4 - - + -
1895A ALA* 4.0 11.3 - - + +
1940A LEU 3.0 6.3 + - - +
1941A ARG* 3.4 10.8 - - - +
1942A ALA 2.6 5.5 + - - -
1943A LEU* 1.3 71.5 - - - +
1945A VAL* 1.3 62.2 + - - +
1947A ASN* 2.4 29.2 + - - +
1948A ASP* 3.2 3.3 + - - +
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Residues in contact with VAL1945 (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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1941A ARG 3.2 7.3 + - - +
1942A ALA* 3.0 3.8 + - - -
1944A HIS* 1.3 78.1 - - - +
1946A ASN* 1.3 62.3 + - - +
1948A ASP* 3.3 11.1 - - - +
1949A ARG* 3.3 11.8 + - - +
1986A LEU* 5.9 7.9 - - + +
1990A ASP* 4.4 18.2 - - - +
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Residues in contact with ASN1946 (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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1942A ALA* 2.5 32.8 + - + +
1945A VAL* 1.3 79.5 - - - +
1947A ASN* 1.3 48.3 + - - +
1949A ARG* 3.1 20.4 - - + +
1950A ALA* 2.3 47.8 - - + +
1953A ILE* 5.8 0.9 - - + -
1983A LEU* 6.2 1.6 - - + -
1986A LEU* 5.5 10.5 - - + +
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Residues in contact with ASN1947 (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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1895A ALA* 4.8 6.1 - - + +
1899A VAL* 6.0 4.3 - - + -
1942A ALA 3.0 1.2 + - - -
1943A LEU* 2.1 27.4 - - + +
1944A HIS* 2.4 24.5 + - - +
1946A ASN* 1.3 64.7 - - - +
1948A ASP* 1.3 68.5 + - - +
1950A ALA* 3.4 7.0 - - - -
1951A LYS* 2.8 22.3 + - - +
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Residues in contact with ASP1948 (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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1944A HIS 3.2 3.3 + - - +
1945A VAL 3.3 11.2 - - - +
1947A ASN* 1.3 85.2 - - - +
1949A ARG* 1.3 61.2 + - + +
1951A LYS* 3.3 5.1 + - - +
1952A VAL* 3.2 16.5 + - - +
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Residues in contact with ARG1949 (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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1945A VAL 3.3 1.5 + - - +
1946A ASN* 3.1 22.6 - - + +
1948A ASP* 1.3 77.8 - - + +
1950A ALA* 1.3 59.8 + - - +
1952A VAL* 3.5 14.6 - - + -
1953A ILE* 2.8 29.6 + - + +
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Residues in contact with ALA1950 (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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1942A ALA* 4.9 2.0 - - + -
1943A LEU* 4.3 8.1 - - + +
1946A ASN* 2.3 37.2 + - + +
1947A ASN* 3.6 6.1 - - - -
1949A ARG* 1.3 75.2 - - - +
1951A LYS* 1.3 61.1 + - - +
1952A VAL 3.1 1.1 - - - -
1953A ILE* 4.1 2.5 - - - +
1954A LEU* 2.8 41.6 + - + +
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Residues in contact with LYS1951 (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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1947A ASN 2.8 18.7 + - - +
1948A ASP* 3.6 4.7 - - - +
1950A ALA* 1.3 75.4 - - - +
1952A VAL* 1.3 61.9 + - - +
1954A LEU 5.0 0.3 + - - -
1955A LYS* 5.3 5.2 + - - +
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Residues in contact with VAL1952 (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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1948A ASP 3.2 7.7 + - - +
1949A ARG* 3.6 22.7 - - + +
1950A ALA 3.1 0.6 - - - -
1951A LYS* 1.3 80.0 - - - +
1953A ILE* 1.3 63.1 + - + +
1955A LYS* 4.2 12.0 + - - +
1956A PRO* 5.6 0.2 - - - +
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Residues in contact with ILE1953 (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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1946A ASN* 5.8 0.7 - - + -
1949A ARG* 2.8 22.3 + - + +
1950A ALA* 4.6 2.0 - - - -
1952A VAL* 1.3 71.5 - - + +
1954A LEU* 1.3 54.9 + - - +
1955A LYS 2.7 18.1 + - - -
1956A PRO* 3.1 22.2 - - - +
1982A GLN* 6.3 2.5 - - + -
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Residues in contact with LEU1954 (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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1950A ALA* 2.8 30.3 + - + +
1953A ILE* 1.3 71.4 - - - +
1955A LYS* 1.3 55.5 + - - +
1956A PRO* 3.3 10.6 - - - +
1960A THR* 4.8 1.0 - - - -
1969A PRO* 3.9 27.9 - - + +
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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