Contacts of the helix formed by residues 1993 - 2023 (chain A) in PDB entry 4D0O
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 LYS1993 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1992A GLN* 1.3 78.1 + - - +
1994A LYS* 1.3 67.6 + - - +
1995A ASP* 3.3 4.9 - - + +
1996A VAL* 3.1 19.9 + - + +
1997A VAL* 3.0 20.8 + - - +
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Residues in contact with LYS1994 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1992A GLN 3.8 0.6 + - - -
1993A LYS* 1.3 72.5 - - - +
1995A ASP* 1.3 58.1 + - - +
1997A VAL* 3.4 8.9 + - - +
1998A LYS* 3.0 30.6 + - - +
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Residues in contact with ASP1995 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1993A LYS* 3.3 3.9 - - + +
1994A LYS* 1.3 78.4 - - - +
1996A VAL* 1.3 61.7 + - + +
1998A LYS* 3.9 6.7 - - - +
1999A ARG* 3.1 27.0 + - - +
2167A CYS* 4.1 16.3 - - - +
2169A LYS* 5.7 7.4 - - + -
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Residues in contact with VAL1996 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1989A LEU* 5.3 0.4 - - + -
1992A GLN* 4.3 17.0 - - + +
1993A LYS* 3.1 23.0 + - + +
1995A ASP* 1.3 77.2 - - + +
1997A VAL* 1.3 59.9 + - - +
1998A LYS 3.2 0.2 - - - -
1999A ARG* 3.2 6.2 + - + +
2000A GLN* 2.9 46.1 + - + +
2077A LEU* 4.2 22.7 - - + -
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Residues in contact with VAL1997 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1989A LEU* 3.2 45.2 - - + +
1990A LYS* 4.5 8.1 - - - +
1992A GLN* 3.9 11.7 - - + +
1993A LYS 3.0 17.9 + - - +
1994A LYS* 3.4 11.6 + - - +
1996A VAL* 1.3 75.3 - - - +
1998A LYS* 1.3 59.3 + - - +
2000A GLN* 4.0 1.4 - - - +
2001A GLU* 3.0 48.9 + - - +
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Residues in contact with LYS1998 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1994A LYS 3.0 18.8 + - - +
1995A ASP* 3.9 7.6 - - - +
1997A VAL* 1.3 78.5 - - - +
1999A ARG* 1.3 61.8 + - - +
2001A GLU* 3.2 13.3 + - + +
2002A VAL* 3.1 31.3 + - + +
2163A ARG* 6.1 2.0 - - - +
2167A CYS* 3.9 18.6 - - - -
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Residues in contact with ARG1999 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1995A ASP 3.1 18.6 + - - +
1996A VAL* 3.2 6.9 + - - +
1998A LYS* 1.3 77.4 - - - +
2000A GLN* 1.3 66.8 + - - +
2002A VAL* 3.4 3.7 + - - +
2003A ILE* 3.1 39.8 + - + +
2078A ILE 2.7 30.3 + - - -
2079A LYS* 3.5 17.7 + - - +
2081A ILE* 4.3 0.8 - - - +
2164A ILE* 4.2 9.2 - - + +
2167A CYS* 3.8 20.1 - - + +
2168A THR* 2.9 37.8 + - - +
2171A ASN* 5.7 0.7 - - - -
2174A GLU* 2.6 43.5 + - - +
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Residues in contact with GLN2000 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1980A TRP* 5.0 2.9 + - - -
1984A ILE* 3.9 6.2 - - + +
1989A LEU* 3.9 31.0 - - + -
1996A VAL* 2.9 26.7 + - + +
1997A VAL 4.0 0.7 - - - +
1999A ARG* 1.3 86.7 - - - +
2001A GLU* 1.3 58.0 + - - +
2003A ILE* 3.6 7.2 + - - +
2004A TYR* 3.0 27.9 + - - +
2076A PHE* 4.6 4.0 - - - -
2077A LEU* 3.6 20.4 - - + +
2078A ILE* 2.7 60.5 + - - +
2079A LYS* 6.0 0.4 - - - +
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Residues in contact with GLU2001 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1984A ILE* 4.2 34.9 - - + +
1989A LEU* 5.0 3.2 - - + +
1997A VAL* 3.0 36.7 + - - +
1998A LYS* 3.4 13.5 - - + +
1999A ARG 3.2 0.4 - - - -
2000A GLN* 1.3 77.2 - - - +
2002A VAL* 1.3 62.7 + - + +
2004A TYR* 3.5 7.9 - - + +
2005A GLU* 3.3 19.2 + - - +
2201B LYS* 5.9 6.1 - - - +
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Residues in contact with VAL2002 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1998A LYS* 3.1 20.0 + - + +
1999A ARG* 3.9 4.7 - - - +
2001A GLU* 1.3 76.2 - - + +
2003A ILE* 1.3 66.0 + - - +
2005A GLU* 3.2 8.0 + - + +
2006A LEU* 3.2 20.4 + - - +
2160A LEU* 3.8 7.9 - - + +
2163A ARG* 3.6 53.6 - - + +
2164A ILE* 3.5 26.4 - - + +
2167A CYS* 4.1 16.2 - - - -
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Residues in contact with ILE2003 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1980A TRP* 4.0 22.2 - - + -
1999A ARG* 3.1 51.6 + - + +
2000A GLN* 4.0 8.1 - - - +
2002A VAL* 1.3 73.1 - - - +
2004A TYR* 1.3 66.1 + - - +
2006A LEU* 3.4 7.4 + - + +
2007A MET* 3.2 19.6 + - - +
2060A ILE* 5.8 2.5 - - + +
2078A ILE* 3.9 30.7 - - + +
2081A ILE* 4.0 19.1 - - + -
2164A ILE* 3.9 26.5 - - + -
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Residues in contact with TYR2004 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1977A ALA 4.7 4.3 - - - -
1980A TRP* 3.6 30.7 - + + +
1981A SER* 3.1 40.6 - - - -
1984A ILE* 3.6 30.3 - - + -
2000A GLN 3.0 18.5 + - - +
2001A GLU* 3.5 9.9 - - + +
2003A ILE* 1.3 77.7 - - - +
2005A GLU* 1.3 62.2 + - + +
2007A MET* 2.9 10.3 + - + +
2008A GLN* 2.8 74.6 + - + +
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Residues in contact with GLU2005 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2001A GLU 3.3 10.5 + - - +
2002A VAL* 3.2 13.8 + - - +
2004A TYR* 1.3 85.4 - - + +
2006A LEU* 1.3 62.8 + - - +
2008A GLN* 4.0 7.8 - - - +
2009A THR* 3.0 40.9 + - + +
2160A LEU* 4.2 17.9 - - + -
2163A ARG* 4.8 11.9 - - - +
2200B GLU* 5.4 8.7 - - - +
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Residues in contact with LEU2006 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2002A VAL 3.2 8.8 + - - +
2003A ILE* 3.6 12.8 - - + +
2005A GLU* 1.3 79.1 - - - +
2007A MET* 1.3 61.0 + - - +
2009A THR* 3.3 4.8 + - - -
2010A GLU* 3.1 23.1 + - - +
2056A PHE* 4.9 6.5 - - + -
2060A ILE* 4.6 14.1 - - + -
2081A ILE* 5.1 8.1 - - + -
2085A LEU* 3.9 26.5 - - + -
2153A ARG* 4.3 1.1 - - - +
2157A TYR* 4.2 14.8 - - + -
2160A LEU* 3.8 29.3 - - + +
2161A PHE* 4.0 20.2 - - + -
2164A ILE* 4.2 17.5 - - + -
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Residues in contact with MET2007 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1977A ALA* 3.2 43.5 - - + +
1980A TRP* 3.8 39.3 - - + -
2003A ILE 3.2 9.2 + - - +
2004A TYR* 2.9 13.3 + - - +
2006A LEU* 1.3 78.4 - - - +
2008A GLN* 1.3 80.8 + - + +
2010A GLU* 3.0 8.4 + - - +
2011A PHE* 2.9 25.6 + - + -
2057A PHE* 3.3 26.3 - - + -
2060A ILE* 4.2 20.0 - - + -
2061A LEU* 4.7 1.6 - - + -
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Residues in contact with GLN2008 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1977A ALA* 6.3 0.4 - - + -
2004A TYR* 2.8 62.9 + - + +
2005A GLU* 4.0 7.9 - - - +
2007A MET* 1.3 85.5 - - + +
2009A THR* 1.3 67.5 + - - +
2011A PHE* 3.3 6.5 + - + +
2012A HIS* 3.1 49.4 + - + +
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Residues in contact with THR2009 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2005A GLU* 3.0 30.2 + - + +
2006A LEU 3.3 2.3 + - - -
2008A GLN* 1.3 83.7 - - - +
2010A GLU* 1.3 60.8 + - - +
2012A HIS* 3.5 11.6 + - - +
2013A HIS* 3.0 25.8 + - - +
2153A ARG* 3.0 32.6 + - - -
2160A LEU* 3.8 10.8 - - + +
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Residues in contact with GLU2010 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2006A LEU* 3.1 19.4 + - + +
2007A MET* 3.0 7.3 + - - +
2009A THR* 1.3 75.3 + - - +
2011A PHE* 1.3 61.1 + - - +
2013A HIS* 3.4 3.9 + - - +
2014A VAL* 3.0 28.6 + - - +
2053A HIS* 2.7 39.2 + - - +
2056A PHE* 3.5 22.0 - - + -
2057A PHE* 3.8 25.8 - - + -
2060A ILE* 4.6 4.7 - - + -
2153A ARG* 2.9 14.4 + - - +
2157A TYR* 2.5 27.3 + - - -
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Residues in contact with PHE2011 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1970A LEU* 3.8 24.9 - - + -
1973A GLN* 4.2 3.6 - - + -
1974A SER* 3.2 46.2 - - - -
1977A ALA* 4.3 10.1 - - + -
2007A MET* 2.9 31.3 + - + -
2008A GLN* 3.4 5.4 - - + +
2009A THR 3.3 0.2 - - - -
2010A GLU* 1.3 78.0 - - - +
2012A HIS* 1.3 72.5 + + - +
2014A VAL* 3.3 6.5 + - + +
2015A ARG* 2.8 55.7 + - - +
2057A PHE* 3.5 19.2 - + + -
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Residues in contact with HIS2012 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2008A GLN* 3.1 41.9 + - + +
2009A THR* 3.8 12.9 - - - +
2010A GLU 3.3 0.2 - - - -
2011A PHE* 1.3 87.4 - + - +
2013A HIS* 1.3 61.2 + - - +
2015A ARG* 3.0 43.7 + - - +
2016A THR* 2.8 34.4 + - - +
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Residues in contact with HIS2013 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2009A THR 3.0 18.1 + - - +
2010A GLU* 3.5 6.1 - - - +
2012A HIS* 1.3 76.7 - - - +
2014A VAL* 1.3 57.2 + - - +
2016A THR* 3.3 7.6 + - - -
2017A LEU* 3.0 42.6 + - + +
2053A HIS* 3.4 37.3 + + + -
2101A TYR* 3.0 22.4 + - - -
2149A LEU* 4.7 2.4 + - - +
2150A VAL* 4.0 30.0 + - + +
2153A ARG* 3.3 43.7 - - + +
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Residues in contact with VAL2014 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1970A LEU* 4.3 5.6 - - + -
1973A GLN* 3.9 20.0 - - - +
2010A GLU 3.0 21.8 + - - +
2011A PHE* 3.6 7.6 - - + +
2013A HIS* 1.3 74.6 - - - +
2015A ARG* 1.3 63.3 + - - +
2017A LEU* 3.4 9.7 + - + +
2018A LYS* 3.0 35.6 + - + +
2050A ILE* 5.5 1.6 - - + +
2053A HIS* 3.6 42.4 - - + +
2054A SER* 3.8 18.6 - - - +
2057A PHE* 4.5 6.7 - - + -
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Residues in contact with ARG2015 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1970A LEU* 4.5 25.6 - - + +
2011A PHE* 2.8 37.1 + - + +
2012A HIS* 3.0 45.9 + - - +
2014A VAL* 1.3 77.8 - - - +
2016A THR* 1.3 57.0 + - - +
2018A LYS* 3.3 1.7 + - - +
2019A ILE* 2.9 52.5 + - + +
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Residues in contact with THR2016 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2012A HIS* 2.8 28.8 + - - +
2013A HIS* 3.5 9.2 - - - -
2015A ARG* 1.3 73.7 + - - +
2017A LEU* 1.3 64.5 + - - +
2019A ILE* 3.4 6.9 + - - +
2020A MET* 3.0 27.6 + - - +
2141A LEU* 4.4 13.6 - - + +
2146A CYS* 4.3 36.1 - - - +
2149A LEU* 4.4 19.5 - - + +
2150A VAL* 4.4 6.5 - - + -
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Residues in contact with LEU2017 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2013A HIS* 3.0 40.3 + - + +
2014A VAL* 3.7 7.2 - - - +
2016A THR* 1.3 76.4 - - - +
2018A LYS* 1.3 57.8 + - - +
2020A MET* 3.2 7.9 + - - +
2021A SER* 3.0 27.4 + - - -
2046A LEU* 3.8 19.7 - - + +
2049A LEU* 3.8 39.0 - - + +
2050A ILE* 3.7 18.1 - - + +
2053A HIS* 4.1 5.4 - - + -
2150A VAL* 3.5 36.8 - - + -
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Residues in contact with LYS2018 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1968A GLU 3.2 24.9 + - - -
1970A LEU* 4.2 31.9 - - + +
1973A GLN* 3.3 16.6 + - - -
2014A VAL* 3.0 24.3 + - + +
2015A ARG 4.0 2.9 - - - +
2017A LEU* 1.3 74.4 - - - +
2019A ILE* 1.3 58.2 + - - +
2021A SER* 3.8 2.2 - - - +
2022A GLY* 2.7 31.7 + - - -
2023A VAL* 5.2 0.3 - - - +
2050A ILE* 3.8 37.2 - - + -
2054A SER* 3.7 12.0 + - - -
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Residues in contact with ILE2019 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2015A ARG* 2.9 42.0 + - + +
2016A THR* 3.7 5.2 - - - +
2018A LYS* 1.3 73.9 - - - +
2020A MET* 1.3 65.8 + - - +
2023A VAL* 3.0 32.3 + - + +
2024A TYR* 3.4 11.8 + - + -
2137A VAL* 4.2 27.1 - - + +
2138A VAL* 3.9 29.4 - - + -
2139A ARG* 5.3 1.3 - - + +
2141A LEU* 4.0 26.9 - - + -
2146A CYS* 5.2 1.1 - - - -
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Residues in contact with MET2020 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2016A THR* 3.0 18.7 + - - +
2017A LEU* 3.3 11.7 - - - +
2019A ILE* 1.3 75.5 - - - +
2021A SER* 1.3 57.1 + - - +
2024A TYR* 3.5 12.7 - - + +
2025A SER* 2.8 30.3 + - - -
2043A PHE* 3.4 38.7 - - + -
2046A LEU* 3.8 23.3 - - + -
2104A PHE* 4.1 18.4 - - + -
2146A CYS* 3.6 36.8 - - + -
2147A ILE* 5.0 1.3 - - + -
2150A VAL* 3.7 23.8 - - + -
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Residues in contact with SER2021 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2017A LEU 3.0 6.8 + - - -
2018A LYS* 4.0 2.9 - - - -
2020A MET* 1.3 77.8 - - - +
2022A GLY* 1.3 59.9 + - - +
2025A SER* 3.3 5.9 + - - -
2026A GLN* 2.9 39.8 + - - +
2046A LEU* 3.8 13.8 - - - +
2047A ASP* 4.5 9.2 + - - -
2050A ILE* 3.6 31.8 - - - +
----------------------------------------------------------
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Residues in contact with GLY2022 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2018A LYS 2.7 22.0 + - - -
2021A SER* 1.3 74.6 - - - +
2023A VAL* 1.3 61.0 + - - +
2026A GLN* 3.5 21.2 - - - +
----------------------------------------------------------
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Residues in contact with VAL2023 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2018A LYS 5.2 0.2 - - - +
2019A ILE* 3.0 27.3 + - + +
2022A GLY* 1.3 80.5 - - - +
2024A TYR* 1.3 62.9 + - + +
2027A GLY* 3.1 25.0 + - - -
2132A LYS* 3.6 40.6 - - + +
2135A SER* 5.9 2.5 - - - +
2137A VAL* 3.6 31.0 - - + -
2138A VAL* 3.7 14.8 - - + -
----------------------------------------------------------
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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