Contacts of the helix formed by residues 2002 - 2021 (chain X) in PDB entry 3HM6
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 SER2002 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1718X VAL* 5.8 2.9 - - - +
1723X VAL* 6.6 0.2 - - - -
2001X THR* 1.3 77.9 + - - +
2003X ASP* 1.3 61.5 + - - +
2004X ASN* 4.2 5.3 + - - +
2005X MET* 3.4 21.4 + - - +
2006X ASP* 2.8 33.9 + - - -
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Residues in contact with ASP2003 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1728X GLY* 5.5 4.7 - - - +
1738X ARG* 3.5 34.6 + - - +
2002X SER* 1.3 74.5 - - - +
2004X ASN* 1.3 57.2 + - - +
2006X ASP* 3.5 13.5 - - - +
2007X ALA* 3.0 26.2 + - - +
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Residues in contact with ASN2004 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1718X VAL* 3.7 20.7 - - + +
1723X VAL* 5.6 5.2 - - + -
1728X GLY 4.1 12.8 - - - +
1730X ALA* 3.3 18.6 - - + +
1732X TYR 3.3 24.7 + - - -
1733X THR* 3.0 22.1 + - - -
1738X ARG* 3.4 21.7 - - - +
2002X SER* 3.2 5.1 + - - +
2003X ASP* 1.3 77.2 - - - +
2005X MET* 1.3 65.7 + - - +
2007X ALA* 3.2 2.3 + - - +
2008X VAL* 2.9 30.4 + - - +
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Residues in contact with MET2005 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1711X PHE* 3.4 54.3 - - + +
1714X ILE* 3.5 31.9 - - + -
1715X LYS* 3.8 24.9 - - + +
1718X VAL* 5.4 2.6 - - + +
2000X GLN 5.6 0.4 - - - +
2001X THR* 3.2 19.5 - - - +
2002X SER* 3.4 26.1 + - - +
2004X ASN* 1.3 76.3 - - - +
2006X ASP* 1.3 56.0 + - - +
2008X VAL* 3.2 2.6 + - - +
2009X LEU* 2.9 51.6 + - + +
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Residues in contact with ASP2006 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1991X LYS* 4.4 14.3 - - - +
1994X GLN* 5.1 1.4 - - - +
2001X THR* 2.5 39.3 + - - +
2002X SER 2.8 27.7 + - - +
2003X ASP* 3.5 14.3 - - - +
2004X ASN 3.2 0.2 - - - -
2005X MET* 1.3 71.8 - - - +
2007X ALA* 1.3 58.0 + - - +
2009X LEU* 3.5 6.6 + - - +
2010X LEU* 2.9 30.9 + - - +
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Residues in contact with ALA2007 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X UNX 2.3 32.4 - - - -
1733X THR* 5.1 0.9 - - - +
1735X ASN* 4.5 6.9 - - + +
1738X ARG* 3.8 31.9 - - + +
2003X ASP 3.0 17.0 + - - +
2004X ASN* 3.2 6.2 + - - +
2006X ASP* 1.3 74.7 - - - +
2008X VAL* 1.3 61.0 + - - +
2010X LEU* 3.6 4.0 - - - +
2011X VAL* 3.3 13.5 + - - +
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Residues in contact with VAL2008 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1714X ILE* 3.5 39.0 - - + -
1718X VAL* 5.1 0.2 - - + -
1733X THR* 4.0 23.6 - - - +
1734X LEU* 3.8 32.5 - - + +
1925X MET* 4.4 9.0 - - + -
1929X LEU* 4.3 4.3 - - + -
2004X ASN* 2.9 24.2 + - - +
2005X MET 3.5 7.6 - - - +
2007X ALA* 1.3 74.3 - - - +
2009X LEU* 1.3 64.8 + - - +
2011X VAL* 3.2 14.6 + - - +
2012X ILE* 3.3 15.8 + - + +
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Residues in contact with LEU2009 (chain X).
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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1707X LEU* 5.9 2.0 - - + -
1710X LEU* 4.1 20.0 - - + -
1711X PHE* 5.1 3.6 - - + -
1714X ILE* 3.6 25.8 - - + -
1990X ILE* 3.5 25.7 - - + +
1991X LYS* 4.2 9.2 - - - +
1993X PRO* 3.5 39.3 - - + -
2001X THR* 4.9 0.2 - - - +
2005X MET* 2.9 35.4 + - + +
2006X ASP* 3.9 4.9 - - - +
2008X VAL* 1.3 73.5 - - - +
2010X LEU* 1.3 59.1 + - - +
2012X ILE* 3.5 5.1 + - + -
2013X ALA* 2.8 30.8 + - - +
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Residues in contact with LEU2010 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X UNX 3.6 11.4 - - - -
1735X ASN* 5.8 0.4 - - - +
1991X LYS* 3.9 34.0 - - + +
2006X ASP 2.9 18.7 + - - +
2007X ALA* 3.6 8.5 - - - +
2008X VAL 3.2 0.2 - - - -
2009X LEU* 1.3 75.1 - - - +
2011X VAL* 1.3 60.4 + - - +
2013X ALA* 3.2 3.6 + - + +
2014X GLN* 2.8 56.3 + - + +
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Residues in contact with VAL2011 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X UNX 3.3 20.9 - - - -
1734X LEU* 4.0 38.4 - - + +
1735X ASN* 4.4 4.3 - - + +
2007X ALA 3.3 6.0 + - - +
2008X VAL 3.2 8.1 + - - +
2010X LEU* 1.3 74.1 - - - +
2012X ILE* 1.3 57.1 + - - +
2014X GLN* 3.2 15.8 + - - +
2015X THR* 2.9 31.8 + - - -
2033X ILE* 5.7 2.2 - - + -
2034X ASN* 3.6 28.6 - - + +
2037X LEU* 4.6 2.2 - - + -
2038X TYR* 3.9 17.0 - - + -
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Residues in contact with ILE2012 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1710X LEU* 4.2 22.0 - - + -
1714X ILE* 4.1 15.5 - - + -
1734X LEU* 4.0 6.1 - - + -
1929X LEU* 5.0 2.0 - - + -
1933X VAL* 4.2 17.3 - - + -
1936X LEU* 5.4 0.4 - - + -
1937X PHE* 3.6 29.6 - - + -
1990X ILE* 4.4 10.3 - - + -
2008X VAL* 3.3 33.5 + - + +
2009X LEU* 3.8 7.9 - - - +
2011X VAL* 1.3 75.2 - - - +
2013X ALA* 1.3 57.6 + - - +
2015X THR* 3.3 8.7 + - - -
2016X PHE* 3.0 22.7 + - - +
2038X TYR* 3.8 20.9 - - - +
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Residues in contact with ALA2013 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1987X ILE* 3.3 21.0 - - + +
1990X ILE* 3.8 13.9 - - + +
1991X LYS* 3.4 34.1 - - + -
2009X LEU 2.8 22.0 + - - +
2010X LEU* 3.5 3.8 - - + +
2012X ILE* 1.3 74.6 - - - +
2014X GLN* 1.3 57.3 + - - +
2016X PHE* 3.1 6.2 + - - +
2017X MET 2.9 23.7 + - - -
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Residues in contact with GLN2014 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1987X ILE* 5.1 0.4 - - - -
2010X LEU* 2.8 42.6 + - + +
2011X VAL* 3.4 25.6 + - - +
2013X ALA* 1.3 72.8 - - - +
2015X THR* 1.3 57.4 + - - +
2017X MET* 3.4 13.9 - - - +
2018X ASP* 2.9 35.8 + - - +
2032X PRO* 5.7 5.6 - - - +
2034X ASN* 3.5 25.1 + - - +
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Residues in contact with THR2015 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1937X PHE* 4.1 5.1 - - + -
2011X VAL 2.9 14.4 + - - -
2012X ILE* 3.4 11.0 - - - -
2014X GLN* 1.3 75.0 - - - +
2016X PHE* 1.3 58.7 + - - +
2018X ASP* 3.3 4.9 + - - +
2019X ALA* 3.0 26.3 + - - +
2034X ASN* 3.4 15.2 + - - +
2038X TYR* 3.1 53.0 - - + +
2042X ILE* 4.0 10.9 - - + +
2045X TYR* 4.1 18.4 - - + -
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Residues in contact with PHE2016 (chain X).
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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1937X PHE* 3.7 37.2 - + + -
1940X ILE* 3.9 32.3 - - + -
1941X LEU* 4.2 32.1 - - + -
1982X PRO* 3.8 31.2 - - + -
1983X LEU* 4.8 3.6 - - + -
1986X TRP* 3.8 15.5 - + + -
1987X ILE* 4.7 3.8 - - + -
1990X ILE* 4.0 16.6 - - + -
2012X ILE 3.0 12.9 + - - +
2013X ALA 3.3 9.4 - - - +
2015X THR* 1.3 74.2 - - - +
2017X MET* 1.3 65.4 + - - +
2019X ALA* 3.1 17.8 + - + +
2020X CYS* 3.3 23.6 + - - -
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Residues in contact with MET2017 (chain X).
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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1983X LEU* 3.4 38.1 - - + +
1987X ILE* 3.5 17.9 - - + -
2013X ALA 2.9 7.1 + - - +
2014X GLN* 3.4 17.5 - - - +
2016X PHE* 1.3 75.6 - - - +
2018X ASP* 1.3 64.4 + - - +
2020X CYS* 2.9 17.7 + - - +
2021X THR* 2.9 23.2 + - - +
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Residues in contact with ASP2018 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2014X GLN* 2.9 22.3 + - - +
2015X THR 3.6 5.6 - - - +
2016X PHE 3.2 0.4 - - - -
2017X MET* 1.3 85.0 - - - +
2019X ALA* 1.3 61.0 + - - +
2020X CYS 3.5 0.3 + - - -
2021X THR* 3.5 24.8 + - - +
2034X ASN* 2.9 18.8 + - - -
2035X LYS* 2.9 40.0 + - - +
2042X ILE* 3.8 21.1 - - + +
2046X LYS* 3.6 12.0 - - - -
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Residues in contact with ALA2019 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1941X LEU* 5.7 0.9 - - + -
1974X HIS* 5.2 1.6 + - - -
2015X THR 3.0 13.1 + - - +
2016X PHE* 3.1 19.7 + - + +
2018X ASP* 1.3 76.0 - - - +
2020X CYS* 1.3 58.0 + - - +
2021X THR 3.7 0.9 + - - +
2042X ILE* 4.2 3.7 - - + +
2045X TYR* 3.4 35.4 - - + -
2046X LYS* 3.4 25.7 - - - +
2049X VAL* 3.3 21.9 - - + +
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Residues in contact with CYS2020 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1941X LEU* 5.4 0.4 - - - -
1974X HIS* 2.9 23.8 + - - -
1975X ILE* 5.8 0.2 - - - -
1978X THR* 3.2 34.5 + - + +
1982X PRO* 3.5 30.5 - - - -
1983X LEU* 4.5 2.7 - - + -
2016X PHE* 3.5 26.0 - - - -
2017X MET 2.9 9.0 + - - +
2019X ALA* 1.3 77.2 - - - +
2021X THR* 1.3 59.2 + - - +
2049X VAL* 4.0 22.0 - - - -
2053X TYR* 4.4 1.1 - - - +
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Residues in contact with THR2021 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1974X HIS* 5.0 0.3 + - - -
1978X THR* 5.7 0.2 - - - -
1983X LEU* 4.6 5.0 - - - +
2017X MET* 2.9 26.6 + - - +
2018X ASP* 3.5 12.2 + - - +
2019X ALA 3.4 1.6 - - - +
2020X CYS* 1.3 79.7 - - - +
2022X LEU* 1.3 66.3 + - - +
2023X ALA* 3.6 25.6 - - + +
2046X LYS* 3.2 27.5 - - - +
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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