Contacts of the helix formed by residues 2000 - 2018 (chain B) in PDB entry 4ILG
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 SER2000 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1996B LEU* 3.9 0.9 - - - -
1999B ILE* 1.3 79.9 - - - +
2001B SER* 1.3 59.2 + - - +
2002B TYR* 3.7 8.3 + - - +
2003B THR* 2.9 31.0 + - - -
2004B ALA* 2.9 26.0 + - - +
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Residues in contact with SER2001 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1844B PHE* 3.7 12.0 - - - -
1884B PRO 4.2 0.9 - - - -
1885B LYS* 2.7 64.0 + - - +
1992B TYR* 4.2 2.1 + - - -
1996B LEU* 3.7 14.6 - - - +
2000B SER* 1.3 74.7 - - - +
2002B TYR* 1.3 57.1 + - - +
2004B ALA* 3.4 1.7 + - - +
2005B PHE* 2.8 31.5 + - - +
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Residues in contact with TYR2002 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1840B TYR* 3.6 34.0 - + - -
1841B ALA* 6.3 2.0 - - - -
1844B PHE* 3.5 40.7 - + + +
2000B SER* 3.2 7.6 + - - +
2001B SER* 1.3 78.5 - - - +
2003B THR* 1.3 62.3 + - - +
2005B PHE* 3.3 1.4 + - + +
2006B SER* 2.8 46.2 + - - -
2080B LYS* 6.1 1.0 - - - +
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Residues in contact with THR2003 (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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1999B ILE* 4.0 26.0 - - + +
2000B SER* 2.9 23.3 + - - -
2002B TYR* 1.3 84.5 - - - +
2004B ALA* 1.3 57.2 + - - +
2006B SER* 3.3 7.2 + - - -
2007B ARG* 2.9 32.3 + - - +
2052B GLU* 5.3 5.1 - - - +
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Residues in contact with ALA2004 (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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1992B TYR* 3.7 23.0 - - + -
1995B TRP* 3.7 9.2 - - + -
1996B LEU* 3.7 20.9 - - + -
1999B ILE* 3.6 16.5 - - + +
2000B SER 2.9 16.6 + - - +
2001B SER 3.6 4.7 - - - +
2003B THR* 1.3 77.0 - - - +
2005B PHE* 1.3 56.9 + - - +
2007B ARG* 3.2 3.4 + - - +
2008B LEU* 2.9 29.3 + - - +
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Residues in contact with PHE2005 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1840B TYR* 3.6 35.7 - + - -
1843B LEU* 4.3 3.4 - - + -
1844B PHE* 3.6 21.8 - + + -
1851B PHE* 3.8 30.5 - + - -
1882B LEU* 4.5 3.1 - - + -
1884B PRO* 3.9 11.9 - - + -
1963B LEU* 4.2 11.9 - - + -
1965B PHE* 3.9 20.9 - + - -
1992B TYR* 3.3 24.2 + - - +
2001B SER 2.8 19.7 + - - +
2002B TYR 3.8 1.1 - - - +
2004B ALA* 1.3 72.4 - - - +
2006B SER* 1.3 58.6 + - - +
2008B LEU* 3.4 6.9 + - + +
2009B THR* 2.9 52.4 + - + +
2084B LEU* 4.6 1.8 - - + -
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Residues in contact with SER2006 (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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1840B TYR* 4.2 5.1 + - - -
2002B TYR* 2.8 41.2 + - - -
2003B THR* 3.6 7.4 - - - -
2004B ALA 3.2 0.2 - - - -
2005B PHE* 1.3 75.7 - - - +
2007B ARG* 1.3 64.0 + - - +
2009B THR* 3.6 7.4 + - - -
2010B LEU* 3.0 25.9 + - - +
2083B ILE* 5.3 2.2 - - - +
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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
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1995B TRP* 3.5 47.7 - - + +
1998B ARG* 5.4 1.4 - - - +
1999B ILE* 3.7 27.2 - - - +
2003B THR* 2.9 17.0 + - - +
2004B ALA* 3.5 8.7 - - - +
2006B SER* 1.3 77.2 - - - +
2008B LEU* 1.3 56.5 + - - +
2010B LEU* 3.3 6.4 + - - +
2011B LEU* 2.9 41.5 + - + +
2045B ASP* 5.8 2.6 + - - +
2048B TRP* 3.4 62.1 - - + +
2052B GLU* 2.8 35.0 + - + +
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Residues in contact with LEU2008 (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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1882B LEU* 4.2 18.6 - - + -
1965B PHE* 4.5 13.0 - - + -
1991B ILE* 3.8 53.6 - - + +
1992B TYR* 4.0 14.1 - - + -
1995B TRP* 4.1 3.5 - - + -
2004B ALA 2.9 17.0 + - - +
2005B PHE* 3.6 9.9 - - + +
2007B ARG* 1.3 75.4 - - - +
2009B THR* 1.3 59.3 + - - +
2011B LEU* 3.3 8.8 + - - +
2012B LEU* 3.0 39.3 + - + +
2040B TRP* 3.9 19.5 - - + -
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Residues in contact with THR2009 (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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1840B TYR* 5.5 0.3 + - - -
1963B LEU* 4.4 5.4 - - + -
1964B PRO* 3.7 27.4 - - + +
1965B PHE* 4.5 7.6 - - + -
2005B PHE* 2.9 53.9 + - + +
2006B SER* 3.6 8.0 + - - -
2008B LEU* 1.3 74.4 - - + +
2010B LEU* 1.3 66.3 + - - +
2012B LEU* 4.6 0.4 - - - -
2013B ARG* 3.0 27.5 + - - +
2083B ILE* 3.8 19.1 - - - +
2084B LEU* 4.5 8.9 - - + +
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Residues in contact with LEU2010 (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 SER 3.0 20.2 + - - +
2007B ARG* 3.4 4.5 - - - +
2009B THR* 1.3 79.3 + - - +
2011B LEU* 1.3 62.3 + - + +
2013B ARG* 3.7 3.2 - - - +
2014B ALA* 3.0 25.3 + - - +
2052B GLU* 3.5 49.4 - - + +
2055B MET* 3.9 8.3 - - + -
2056B ARG* 4.0 32.1 - - + +
2059B ILE* 3.5 27.1 - - + -
2083B ILE* 4.1 20.2 - - + -
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Residues in contact with LEU2011 (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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1995B TRP* 3.9 26.7 - - + -
2007B ARG* 2.9 27.3 + - + +
2008B LEU* 3.3 6.9 + - - +
2010B LEU* 1.3 77.8 - - + +
2012B LEU* 1.3 56.8 + - - +
2014B ALA* 3.3 6.6 + - - +
2015B LEU* 2.9 35.2 + - + +
2026B LEU* 4.2 14.8 - - + -
2040B TRP* 3.9 33.9 - - + -
2048B TRP* 4.2 14.4 - - + -
2051B ILE* 4.8 1.3 - - + -
2052B GLU* 6.3 1.6 - - + -
2055B MET* 3.7 34.7 - - + +
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Residues in contact with LEU2012 (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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1880B PHE* 5.2 5.4 - - + -
1964B PRO* 3.5 30.5 - - + +
1965B PHE* 3.9 26.7 - - + -
1967B ALA* 3.3 27.9 - - + +
1968B ALA* 4.4 3.1 - - - +
1971B ILE* 4.2 22.7 - - + -
1991B ILE* 5.2 0.9 - - + -
2008B LEU* 3.0 40.0 + - + +
2009B THR* 5.0 0.2 - - - -
2011B LEU* 1.3 71.7 - - - +
2013B ARG* 1.3 55.7 + - - +
2015B LEU* 3.2 11.1 + - + -
2016B LYS* 2.7 35.9 + - - +
2040B TRP* 4.4 4.3 - - + -
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Residues in contact with ARG2013 (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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1962B ARG* 2.9 51.2 + - - +
1964B PRO* 3.7 24.9 - - + +
2009B THR 3.0 20.5 + - - +
2010B LEU* 3.7 3.6 - - - +
2012B LEU* 1.3 75.5 - - - +
2014B ALA* 1.3 52.5 + - - +
2016B LYS* 3.3 18.6 + - - +
2017B THR* 2.7 44.0 + - - -
2059B ILE* 3.5 29.8 - - + -
2082B ILE* 3.6 12.4 + - - -
2083B ILE* 3.0 33.7 + - - +
2084B LEU 3.3 12.3 + - - -
2085B GLY* 3.8 3.2 - - - +
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Residues in contact with ALA2014 (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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2010B LEU 3.0 18.2 + - - +
2011B LEU 3.5 4.7 - - - +
2012B LEU 3.2 0.2 - - - -
2013B ARG* 1.3 75.3 - - - +
2015B LEU* 1.3 59.5 + - - +
2017B THR* 3.2 1.2 + - - -
2018B ASN 3.0 32.1 + - - +
2022B ALA* 3.6 5.1 - - + +
2055B MET* 3.5 34.5 - - + +
2058B LEU* 3.8 8.6 - - + +
2059B ILE* 3.9 19.1 - - + -
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Residues in contact with LEU2015 (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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1967B ALA* 4.3 4.3 - - + -
1970B SER* 4.2 35.2 + - - +
1971B ILE* 4.6 4.3 - - + -
2011B LEU 2.9 23.2 + - - +
2012B LEU* 3.7 14.4 - - + +
2014B ALA* 1.3 76.1 - - - +
2016B LYS* 1.3 62.2 + - - +
2019B GLU* 3.4 29.4 + - + +
2022B ALA* 3.9 21.3 - - + -
2023B LYS* 3.9 24.9 - - + +
2026B LEU* 5.0 7.6 - - + -
2040B TRP* 4.1 30.3 - - + -
2055B MET* 5.9 0.7 - - + -
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Residues in contact with LYS2016 (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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1962B ARG* 4.4 19.0 + - - +
1963B LEU 4.2 14.8 + - - -
1964B PRO* 4.3 11.7 - - + +
1966B SER* 3.1 28.9 + - - +
1967B ALA* 3.9 10.3 - - + +
1970B SER* 5.9 0.2 - - - -
2012B LEU 2.7 21.0 + - - +
2013B ARG* 3.5 24.4 - - - +
2015B LEU* 1.3 74.9 - - - +
2017B THR* 1.3 61.2 + - - +
2019B GLU 5.2 0.5 + - - -
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Residues in contact with THR2017 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2013B ARG* 2.7 33.9 + - - +
2014B ALA* 3.2 4.5 + - - -
2016B LYS* 1.3 80.5 - - - +
2018B ASN* 1.3 58.6 + - - +
2058B LEU* 4.0 9.4 - - + -
2059B ILE* 4.3 12.1 - - + +
2062B GLU* 3.5 39.1 - - + +
2063B TYR 5.5 0.2 - - - +
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Residues in contact with ASN2018 (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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2014B ALA 3.0 7.7 + - - +
2017B THR* 1.3 80.1 - - - +
2019B GLU* 1.3 64.6 + - - +
2020B GLU* 3.8 5.4 + - - +
2021B SER* 3.1 33.3 + - - -
2022B ALA* 3.0 23.6 + - - +
2058B LEU* 3.9 17.2 - - + +
2062B GLU* 3.1 28.1 + - - +
2297C PRO* 5.2 8.0 - - - +
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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
------------------------------------------------------------
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