Contacts of the helix formed by residues 2006 - 2018 (chain B) in PDB entry 5G1N
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 SER2006 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2187A ARG 5.1 2.0 + - - -
1970B TYR* 5.2 0.4 - - - -
2004B GLY 3.5 3.3 + - - -
2005B GLU* 1.3 75.1 - - - +
2007B LEU* 1.3 57.0 + - - +
2008B ALA* 4.0 7.8 + - - +
2009B ASP* 3.2 29.3 + - - +
2010B SER* 2.7 34.4 + - - -
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Residues in contact with LEU2007 (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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1970B TYR* 3.8 35.7 - - + +
2006B SER* 1.3 71.0 - - - +
2008B ALA* 1.3 63.1 + - - +
2010B SER* 3.0 1.4 + - - -
2011B VAL* 2.8 49.3 + - + +
2023B LEU* 4.2 9.6 - - + -
2025B HIS* 4.0 26.5 - - + +
2030B ALA* 3.7 33.9 - - + +
2033B LEU* 5.6 5.4 - - + -
2034B ALA* 3.9 9.6 - - + -
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Residues in contact with ALA2008 (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* 4.2 7.6 - - - +
2007B LEU* 1.3 81.3 - - - +
2009B ASP* 1.3 61.0 + - - +
2011B VAL* 3.9 3.6 - - - +
2012B GLN* 3.0 32.0 + - - +
2033B LEU* 5.0 15.7 - - + +
2034B ALA* 5.1 9.7 - - - +
2037B HIS* 4.9 18.8 - - + +
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Residues in contact with ASP2009 (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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2185A MET* 4.4 3.5 - - - +
2187A ARG* 3.0 53.4 + - - +
2196A ASP* 4.7 1.4 - - - +
2204A PHE* 3.8 22.7 - - + -
2005B GLU* 3.7 19.9 - - + +
2006B SER* 3.2 20.7 + - - +
2007B LEU 3.2 0.6 - - - -
2008B ALA* 1.3 81.2 - - - +
2010B SER* 1.3 56.5 + - - +
2012B GLN* 4.8 2.1 - - - +
2013B THR* 2.5 37.6 + - - -
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Residues in contact with SER2010 (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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1974A THR* 4.8 1.9 - - - +
1968B MET* 4.2 2.9 - - - -
1970B TYR* 3.7 17.0 + - - -
1994B PHE* 4.1 15.0 - - - -
2001B VAL* 3.8 13.3 - - - +
2005B GLU* 3.5 20.5 + - - +
2006B SER 2.7 22.3 + - - -
2007B LEU 3.6 3.8 - - - -
2009B ASP* 1.3 77.4 - - - +
2011B VAL* 1.3 58.4 + - - +
2013B THR* 3.4 5.7 - - - -
2014B MET* 3.1 32.6 + - - +
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Residues in contact with VAL2011 (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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1968B MET* 3.6 23.1 - - + -
2007B LEU* 2.8 40.5 + - + +
2008B ALA 4.1 2.2 - - - +
2010B SER* 1.3 74.1 - - - +
2012B GLN* 1.3 64.0 + - - +
2013B THR 3.1 1.3 - - - -
2014B MET* 4.0 1.2 - - - +
2015B SER* 2.9 30.2 + - - +
2021B VAL* 4.7 7.2 - - + -
2023B LEU* 4.5 7.9 - - + -
2034B ALA* 3.8 32.5 - - + +
2037B HIS 5.5 0.2 - - - +
2038B CYS* 3.9 16.4 - - + -
2042B VAL* 4.4 9.0 - - + -
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Residues in contact with GLN2012 (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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2196A ASP* 4.4 8.8 - - - +
2204A PHE* 3.4 49.2 - - + +
2008B ALA 3.0 19.7 + - - +
2009B ASP* 4.8 2.3 - - - +
2011B VAL* 1.3 76.5 - - - +
2013B THR* 1.3 61.9 + - - +
2015B SER* 3.5 12.1 + - - -
2016B CYS* 3.2 15.4 + - - -
2037B HIS* 3.6 37.3 + - - +
2039B ARG* 5.7 8.9 - - - +
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Residues in contact with THR2013 (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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1974A THR* 3.8 19.7 - - + -
1975A ARG* 3.3 46.4 + - + +
2204A PHE* 3.7 10.7 - - - -
2207A ALA* 5.2 1.8 - - + -
2005B GLU* 3.8 0.2 + - - -
2009B ASP 2.5 24.0 + - - -
2010B SER* 3.4 7.9 - - - -
2012B GLN* 1.3 74.1 - - - +
2014B MET* 1.3 65.6 + - - +
2016B CYS* 3.0 28.7 + - - +
2017B TYR* 3.7 14.5 - - + +
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Residues in contact with MET2014 (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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1974A THR* 3.9 13.5 - - - -
1978A SER* 3.5 36.1 - - - +
1966B ALA* 3.8 25.8 - - + -
1968B MET* 3.6 27.4 - - + -
1992B LEU* 4.4 16.2 - - + +
1993B SER 6.2 0.7 - - - -
1994B PHE* 3.8 24.2 - - + -
2010B SER 3.1 17.3 + - - +
2011B VAL 3.5 2.7 + - - +
2012B GLN 3.5 0.2 - - - -
2013B THR* 1.3 79.7 - - - +
2015B SER* 1.3 57.4 + - - +
2017B TYR* 3.0 14.8 + - + +
2018B ALA* 3.0 28.3 + - - +
2021B VAL* 4.9 2.0 - - + -
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Residues in contact with SER2015 (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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2011B VAL 2.9 12.5 + - - -
2012B GLN* 3.7 8.3 - - - -
2013B THR 3.1 0.8 - - - -
2014B MET* 1.3 76.2 - - - +
2016B CYS* 1.3 54.5 + - - +
2017B TYR 3.4 0.2 - - - -
2018B ALA 3.7 15.8 - - - +
2021B VAL* 3.3 13.0 - - - +
2038B CYS* 2.5 38.0 - - - -
2039B ARG* 2.8 36.1 + - - -
2040B ARG* 3.8 11.7 - - - +
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Residues in contact with CYS2016 (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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2204A PHE* 3.8 31.0 - - - -
2207A ALA* 4.4 6.1 - - - -
2208A GLU* 4.0 42.1 - - + +
2211A MET* 4.3 7.8 - - - +
2012B GLN* 3.2 19.5 - - - -
2013B THR* 3.0 19.0 + - - +
2015B SER* 1.3 77.8 - - - +
2017B TYR* 1.3 70.2 + - + +
2018B ALA 5.1 0.2 - - - -
2039B ARG* 4.3 7.7 + - - +
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Residues in contact with TYR2017 (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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1975A ARG* 3.2 39.8 + - + +
1978A SER* 3.6 29.2 - - - -
1979A SER* 4.0 13.4 - - - -
1982A ALA* 3.9 10.9 - - + +
1986A ARG* 3.0 27.9 + - - -
2207A ALA* 3.6 34.1 + - + +
2208A GLU* 5.0 0.2 - - - -
2211A MET* 4.0 21.8 - - + +
2214A ARG* 5.1 1.0 + - - -
1964B VAL* 4.1 5.9 - - - +
1992B LEU* 3.9 16.8 - - + -
2013B THR* 3.7 28.0 - - + -
2014B MET* 3.0 13.0 + - + +
2016B CYS* 1.3 87.2 - - + +
2018B ALA* 1.3 57.7 + - - +
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Residues in contact with ALA2018 (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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1986A ARG* 4.4 1.3 - - - -
1964B VAL* 3.3 16.6 - - + +
1965B MET 4.0 0.4 - - - -
1966B ALA* 3.5 30.7 - - + +
1992B LEU* 4.8 4.3 - - + -
2014B MET 3.0 15.5 + - - +
2015B SER* 3.7 9.0 - - - +
2017B TYR* 1.3 79.1 - - - +
2019B ASP* 1.3 64.3 + - - +
2020B VAL 3.6 7.2 - - - +
2021B VAL* 5.1 0.2 - - + -
2040B ARG* 3.5 21.3 + - - +
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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