Contacts of the helix formed by residues 2002 - 2026 (chain B) in PDB entry 1V9P
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 THR2002 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2001B MET* 1.3 77.4 - - - +
2003B ARG* 1.3 65.2 + - - +
2004B GLU* 3.4 14.1 + - + +
2005B GLU* 3.0 50.6 + - + +
2006B ALA* 2.9 26.7 + - - +
2051B PHE* 4.4 1.6 - - - -
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Residues in contact with ARG2003 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2002B THR* 1.3 78.9 + - - +
2004B GLU* 1.3 59.6 + - - +
2006B ALA* 3.1 2.7 + - - +
2007B ARG* 2.9 32.2 + - - +
2051B PHE* 4.2 15.5 - - + -
2053B GLU* 3.7 34.0 + - - +
2054B PHE* 3.6 17.7 - - + -
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Residues in contact with GLU2004 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2002B THR* 3.2 12.4 + - + +
2003B ARG* 1.3 83.0 - - - +
2005B GLU* 1.3 56.9 + - + +
2007B ARG* 2.4 45.5 + - - +
2008B ARG* 3.2 28.7 + - - +
2130B GLU* 5.7 0.4 - - - +
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Residues in contact with GLU2005 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2001B MET* 3.3 20.6 - - + +
2002B THR* 3.0 42.9 + - + +
2004B GLU* 1.3 76.7 - - + +
2006B ALA* 1.3 60.8 + - - +
2008B ARG* 3.7 6.7 + - - +
2009B ARG* 2.8 30.7 + - - +
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Residues in contact with ALA2006 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2001B MET* 3.6 12.0 - - - -
2002B THR 2.9 13.2 + - - +
2003B ARG 3.4 8.1 - - - +
2005B GLU* 1.3 72.5 - - - +
2007B ARG* 1.3 68.2 + - - +
2009B ARG* 2.7 14.0 + - - +
2010B ILE* 2.8 20.5 + - + +
2047B LEU* 4.9 2.9 - - + -
2051B PHE* 3.4 44.6 - - + -
2054B PHE* 4.1 2.9 - - + -
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Residues in contact with ARG2007 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2003B ARG 2.9 11.0 + - - +
2004B GLU* 2.4 41.6 + - - +
2006B ALA* 1.3 74.1 - - - +
2008B ARG* 1.3 56.3 + - - +
2010B ILE* 2.8 22.4 + - - +
2011B ASN* 2.7 29.1 + - - +
2054B PHE* 3.5 46.3 - - + -
2129B GLU* 3.1 36.0 + - - +
2130B GLU* 3.0 48.1 + - - +
2168B ARG* 6.1 0.6 - - - +
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Residues in contact with ARG2008 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2004B GLU* 3.2 19.4 + - - +
2005B GLU* 3.9 5.8 - - - +
2006B ALA 3.2 0.4 - - - -
2007B ARG* 1.3 82.9 - - - +
2009B ARG* 1.3 60.0 + - - +
2011B ASN* 3.1 12.8 + - - +
2012B GLU* 3.1 43.1 + - - +
2130B GLU* 3.7 52.5 + - + +
2132B VAL* 6.4 0.4 - - + -
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Residues in contact with ARG2009 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2001B MET* 4.7 11.5 - - + +
2005B GLU 2.8 18.7 + - - +
2006B ALA* 2.7 10.7 + - - +
2008B ARG* 1.3 71.4 - - - +
2010B ILE* 1.3 63.7 + - - +
2012B GLU* 3.4 16.4 + - - +
2013B LEU* 2.9 34.6 + - + +
2043B GLU* 2.4 43.0 + - - +
2047B LEU* 3.4 28.1 - - + +
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Residues in contact with ILE2010 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2006B ALA* 2.8 15.7 + - + +
2007B ARG* 2.8 7.5 + - - +
2009B ARG* 1.3 74.1 - - - +
2011B ASN* 1.3 67.4 + - - +
2012B GLU 3.0 0.2 + - - -
2013B LEU* 3.0 7.2 + - - +
2014B ARG* 3.0 57.6 + - - +
2044B LEU* 3.9 11.2 - - + -
2047B LEU* 4.3 20.2 - - + +
2048B GLU* 4.2 26.5 - - + +
2051B PHE* 4.9 1.3 - - + +
2054B PHE* 3.4 39.3 - - + +
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Residues in contact with ASN2011 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2007B ARG* 2.7 38.8 + - - +
2008B ARG* 3.1 20.7 - - - +
2010B ILE* 1.3 78.0 - - - +
2012B GLU* 1.3 61.5 + - + +
2014B ARG* 3.6 7.6 + - - +
2015B ASP* 3.3 24.1 + - - +
2129B GLU* 3.3 23.4 + - - +
2130B GLU* 4.8 3.4 - - - +
2132B VAL* 4.1 20.7 - - + +
2133B LEU 4.6 3.4 - - - +
2134B VAL* 3.9 22.9 - - + +
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Residues in contact with GLU2012 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2008B ARG* 3.1 36.8 + - - +
2009B ARG* 3.4 20.7 + - - +
2010B ILE 3.1 0.6 - - - -
2011B ASN* 1.3 79.1 - - - +
2013B LEU* 1.3 66.2 + - + +
2015B ASP* 3.9 1.6 - - - +
2016B LEU* 3.0 33.0 + - + +
2132B VAL* 4.2 21.9 - - + +
2161B ARG* 4.0 24.0 + - - +
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Residues in contact with LEU2013 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2009B ARG* 2.9 60.4 + - + +
2010B ILE* 3.0 4.5 + - - +
2012B GLU* 1.3 76.3 - - + +
2014B ARG* 1.3 58.3 + - - +
2016B LEU* 3.4 9.5 + - + +
2017B ILE* 2.9 36.5 + - - +
2040B LEU* 3.8 45.1 - - + +
2043B GLU* 3.2 22.4 - - + +
2044B LEU* 3.9 23.1 - - + +
2047B LEU* 5.3 2.0 - - + -
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Residues in contact with ARG2014 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2010B ILE* 3.0 32.0 + - - +
2011B ASN* 3.9 7.1 + - - +
2013B LEU* 1.3 71.7 - - - +
2015B ASP* 1.3 67.7 + - - +
2017B ILE* 2.9 5.2 + - - +
2018B ARG* 2.7 63.2 + - - +
2044B LEU* 3.9 21.1 - - + -
2048B GLU* 2.8 26.8 + - - -
2054B PHE 2.6 30.1 + - - -
2055B LYS 3.9 1.4 - - - -
2056B SER* 3.7 25.4 + - - -
2058B ASP* 5.1 2.2 - - - +
2059B SER* 3.5 13.9 - - - +
2060B PRO* 4.0 4.0 - - + -
2134B VAL* 5.1 13.1 - - - +
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Residues in contact with ASP2015 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2011B ASN 3.3 15.4 + - - +
2012B GLU 3.9 2.5 - - - +
2014B ARG* 1.3 78.2 - - - +
2016B LEU* 1.3 63.0 + - - +
2018B ARG* 3.5 12.9 - - - +
2019B TYR* 2.9 22.3 + - - +
2132B VAL* 4.2 11.7 - - + -
2133B LEU* 4.4 12.0 - - - +
2153B LEU* 4.9 4.2 - - - +
2160B ARG* 2.9 44.8 + - - +
2161B ARG* 2.3 37.9 + - - +
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Residues in contact with LEU2016 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2012B GLU* 3.0 31.2 + - + +
2013B LEU* 3.5 11.4 - - + +
2015B ASP* 1.3 76.9 - - - +
2017B ILE* 1.3 62.8 + - - +
2019B TYR* 3.1 6.3 + - + +
2020B HIS* 3.0 49.5 + - + +
2040B LEU* 4.5 23.3 - - + -
2160B ARG* 5.0 4.7 - - - +
2161B ARG* 4.1 25.8 - - - +
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Residues in contact with ILE2017 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2013B LEU 2.9 16.6 + - - +
2014B ARG 2.9 4.9 + - - +
2016B LEU* 1.3 74.2 - - - +
2018B ARG* 1.3 56.4 + - - +
2020B HIS* 5.1 1.1 - - - -
2021B ASN* 3.0 30.8 + - - +
2037B TYR* 3.6 34.0 - - + +
2040B LEU* 3.5 51.8 - - + +
2041B LEU* 3.6 19.5 - - + +
2044B LEU* 3.7 16.6 - - + -
2060B PRO* 3.9 20.9 - - + -
2069B LEU* 4.7 0.7 - - + -
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Residues in contact with ARG2018 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2014B ARG* 2.7 73.7 + - - +
2015B ASP* 3.5 8.7 - - - +
2017B ILE* 1.3 71.8 - - - +
2019B TYR* 1.3 65.8 + - - +
2021B ASN* 3.1 1.9 + - - +
2022B TYR* 3.0 20.5 + - - +
2058B ASP* 3.4 29.7 + - - +
2060B PRO* 4.1 14.5 - - + +
2069B LEU* 4.3 5.2 - - + -
2133B LEU* 4.7 4.8 + - - +
2134B VAL* 2.6 32.5 + - - +
2149B THR* 3.8 27.1 + - - +
2150B GLN* 3.3 28.8 - - + +
2153B LEU* 4.0 14.4 - - + -
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Residues in contact with TYR2019 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2015B ASP 2.9 17.1 + - - +
2016B LEU* 3.5 4.9 - - + +
2018B ARG* 1.3 76.6 - - - +
2020B HIS* 1.3 87.7 + + - +
2022B TYR* 2.9 40.8 + + - +
2023B ARG* 2.9 40.6 + - + +
2031B GLU* 2.9 29.6 + - - -
2153B LEU* 4.7 4.9 - - + +
2160B ARG* 3.1 51.4 - - - +
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Residues in contact with HIS2020 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2016B LEU* 3.0 44.8 + - + +
2017B ILE* 4.6 1.8 - - - +
2019B TYR* 1.3 100.8 - + - +
2021B ASN* 1.3 64.2 + - - +
2023B ARG* 3.7 9.6 - - + +
2024B TYR* 3.0 22.9 + - - +
2030B PRO* 5.6 1.8 - - + +
2031B GLU* 4.0 27.8 + - + +
2032B ILE* 3.3 44.8 - - + +
2037B TYR* 4.5 11.9 - - + -
2040B LEU* 4.4 4.0 - - + -
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Residues in contact with ASN2021 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2017B ILE 3.0 22.1 + - - +
2018B ARG 3.1 5.4 + - - +
2020B HIS* 1.3 76.1 - - - +
2022B TYR* 1.3 58.3 + - - +
2024B TYR* 3.3 3.1 + - - -
2025B TYR* 3.0 48.7 + - - +
2026B VAL* 6.1 0.2 - - - +
2037B TYR* 2.7 32.2 + - - +
2065B GLY 5.3 1.4 + - - -
2067B ARG 3.9 4.6 + - - -
2068B PRO* 4.0 1.7 - - - +
2069B LEU* 3.0 49.4 + - + +
2150B GLN* 4.3 2.3 - - - +
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Residues in contact with TYR2022 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2018B ARG 3.0 11.6 + - - +
2019B TYR* 2.9 33.6 + + - +
2021B ASN* 1.3 74.6 + - - +
2023B ARG* 1.3 68.5 + - + +
2024B TYR 3.0 1.6 - - - -
2026B VAL* 3.0 62.1 + - + +
2027B LEU* 3.0 42.0 + - + +
2150B GLN* 4.7 11.4 + - - +
2153B LEU* 3.9 19.8 + - + -
2154B THR* 3.9 30.4 + - + -
2156B PRO* 5.2 10.2 - - - +
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Residues in contact with ARG2023 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2019B TYR* 2.9 51.4 + - + +
2020B HIS* 3.4 13.7 + - - +
2022B TYR* 1.3 77.6 - - + +
2024B TYR* 1.3 52.7 + - - +
2027B LEU* 3.3 31.4 - - - +
2028B ALA 2.5 31.5 + - - -
2029B ASP* 2.9 50.4 + - - +
2030B PRO* 4.2 7.6 - - + -
2031B GLU* 2.6 49.7 + - - +
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Residues in contact with TYR2024 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2020B HIS 3.0 13.2 + - - +
2021B ASN* 3.3 9.6 - - - +
2022B TYR 3.0 1.6 - - - -
2023B ARG* 1.3 75.7 - - - +
2025B TYR* 1.3 103.7 + + + +
2028B ALA* 2.8 32.4 + - - +
2029B ASP 4.8 0.7 - - - +
2030B PRO* 4.8 22.9 - - + +
2034B ASP* 3.7 26.0 + - + -
2037B TYR* 5.9 5.6 - + + -
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Residues in contact with TYR2025 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2021B ASN* 3.0 41.1 + - - +
2024B TYR* 1.3 114.0 - + + +
2026B VAL* 1.3 61.0 + - + +
2028B ALA* 5.8 0.2 - - - -
2034B ASP* 5.7 0.7 + - - -
2037B TYR* 5.5 3.6 - + - -
2065B GLY 4.8 0.2 + - - -
2066B ALA* 2.9 43.5 + - - +
2067B ARG* 3.9 5.2 - - - -
2068B PRO* 3.7 35.0 - - + -
2214B ARG* 2.9 31.4 + - + +
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Residues in contact with VAL2026 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2021B ASN* 5.1 0.4 - - - +
2022B TYR* 3.0 49.7 + - + +
2025B TYR* 1.3 83.2 - - + +
2027B LEU* 1.3 65.6 + - + +
2068B PRO* 6.1 1.1 - - + -
2150B GLN* 6.1 1.1 - - - +
2154B THR* 4.4 1.8 - - + -
2213B PRO* 4.5 15.0 - - + -
2214B ARG* 3.3 38.9 + - + +
2217B ALA* 3.6 31.2 - - + -
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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