Contacts of the helix formed by residues 2006 - 2018 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2187D ARG 5.1 1.2 + - - -
1970E TYR* 5.4 0.2 - - - -
2001E VAL* 6.1 0.2 - - - -
2004E GLY 3.4 4.8 + - - -
2005E GLU* 1.3 79.3 - - - +
2007E LEU* 1.3 66.0 + - - +
2008E ALA* 3.7 6.1 + - - +
2009E ASP* 3.6 26.0 + - - +
2010E SER* 3.2 21.1 + - - -
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Residues in contact with LEU2007 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1970E TYR* 3.6 39.7 - - + +
2006E SER* 1.3 75.8 - - - +
2008E ALA* 1.3 65.3 + - - +
2010E SER* 3.2 2.9 + - - -
2011E VAL* 3.0 39.3 + - + +
2023E LEU* 4.3 6.3 - - + -
2025E HIS* 3.9 22.2 - - + +
2030E ALA* 3.6 39.3 - - + +
2034E ALA* 4.0 10.1 - - + -
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Residues in contact with ALA2008 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2006E SER* 3.4 5.9 + - - +
2007E LEU* 1.3 78.5 - - - +
2009E ASP* 1.3 57.0 + - - +
2011E VAL* 3.3 4.9 + - - +
2012E GLN* 2.7 49.4 + - - +
2033E LEU 5.8 1.6 - - - +
2034E ALA* 4.8 16.2 - - - +
2037E HIS* 6.3 1.6 - - + -
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Residues in contact with ASP2009 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2185D MET* 4.3 8.1 - - + +
2187D ARG* 3.1 55.1 + - - +
2193D VAL* 5.8 0.2 - - - +
2204D PHE* 3.6 11.2 - - - -
2005E GLU* 3.4 24.5 - - + +
2006E SER* 3.5 15.2 + - - +
2007E LEU 3.3 0.4 - - - -
2008E ALA* 1.3 81.5 - - - +
2010E SER* 1.3 50.8 + - - +
2012E GLN* 3.6 6.2 + - - +
2013E THR* 2.5 42.9 + - - -
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Residues in contact with SER2010 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1974D THR* 5.1 2.4 + - - -
1968E MET* 3.9 11.2 - - - -
1970E TYR* 3.5 22.9 + - - -
1994E PHE* 4.1 6.6 - - - -
2001E VAL* 3.8 13.3 + - - +
2005E GLU* 3.7 19.4 + - - +
2006E SER 3.2 10.1 + - - -
2007E LEU 3.2 9.2 + - - -
2009E ASP* 1.3 77.1 - - - +
2011E VAL* 1.3 63.4 + - - +
2013E THR* 3.0 8.3 + - - -
2014E MET* 2.9 26.4 + - - +
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Residues in contact with VAL2011 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1968E MET* 4.0 18.1 - - + +
2007E LEU* 3.0 26.0 + - + +
2008E ALA 3.7 3.4 - - - +
2010E SER* 1.3 75.2 - - - +
2012E GLN* 1.3 60.9 + - - +
2014E MET* 3.2 2.1 + - - +
2015E SER* 2.9 27.2 + - - -
2021E VAL* 4.5 8.1 - - + +
2023E LEU* 3.9 26.2 - - + -
2034E ALA* 4.0 28.0 - - + +
2038E CYS* 4.0 19.5 - - + -
2042E VAL* 4.2 12.8 - - + -
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Residues in contact with GLN2012 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2196D ASP* 5.6 2.3 + - - +
2204D PHE* 2.8 44.0 - - + -
2008E ALA* 2.7 31.9 + - - +
2009E ASP* 3.8 4.8 + - - +
2011E VAL* 1.3 74.2 - - - +
2013E THR* 1.3 57.2 + - - +
2015E SER* 3.0 17.5 + - - +
2016E CYS* 3.1 20.4 - - - -
2037E HIS* 3.5 36.5 + - - +
2038E CYS* 4.9 3.8 - - - -
2039E ARG* 5.1 6.4 - - - +
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Residues in contact with THR2013 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1974D THR* 4.3 10.1 - - + -
1975D ARG* 3.3 50.1 + - + +
2185D MET* 5.2 0.3 - - - +
2204D PHE* 4.0 11.9 - - + -
2207D ALA* 4.6 7.4 - - + -
2005E GLU* 3.7 0.5 + - - -
2009E ASP 2.5 29.8 + - - -
2010E SER* 3.0 6.9 + - - -
2012E GLN* 1.3 72.5 - - - +
2014E MET* 1.3 62.2 + - - +
2016E CYS* 3.1 24.6 + - - +
2017E TYR* 3.3 19.0 - - + +
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Residues in contact with MET2014 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1974D THR* 4.0 13.9 - - + -
1978D SER* 3.3 31.4 - - - +
1966E ALA* 3.9 16.8 - - + -
1968E MET* 3.6 31.9 - - + -
1992E LEU* 3.9 30.1 - - + -
1993E SER 5.3 1.3 - - - +
1994E PHE* 3.8 29.4 - - + -
2010E SER 2.9 19.6 + - - +
2011E VAL 3.2 1.5 + - - +
2013E THR* 1.3 76.2 - - - +
2015E SER* 1.3 58.2 + - - +
2017E TYR* 3.2 7.9 + - - +
2018E ALA* 2.9 31.6 + - - +
2021E VAL* 4.6 2.2 - - + -
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Residues in contact with SER2015 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2011E VAL 2.9 18.8 + - - -
2012E GLN* 3.0 17.9 + - - +
2014E MET* 1.3 72.7 - - - +
2016E CYS* 1.3 61.4 + - - +
2018E ALA 3.0 19.9 - - - +
2021E VAL* 3.9 11.1 - - - +
2038E CYS* 3.5 21.1 - - - -
2039E ARG* 3.3 23.1 + - - +
2040E ARG* 3.4 23.1 + - - +
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Residues in contact with CYS2016 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2204D PHE* 3.9 30.5 - - - -
2207D ALA* 4.8 4.9 - - + -
2208D GLU* 3.8 39.2 - - + +
2211D MET* 4.1 9.7 - - - +
2012E GLN 3.1 24.9 - - - -
2013E THR* 3.1 16.1 + - - +
2015E SER* 1.3 79.5 - - - +
2017E TYR* 1.3 64.2 + - + +
2039E ARG* 3.8 17.6 + - - +
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Residues in contact with TYR2017 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1974D THR 4.9 0.2 - - - -
1975D ARG* 3.4 31.5 + - - +
1978D SER* 3.6 26.9 - - - -
1979D SER* 3.5 26.7 + - - -
1982D ALA* 4.1 6.7 - - + +
1986D ARG* 2.8 27.8 + - - -
2207D ALA* 3.4 35.5 + - + +
2208D GLU* 4.9 0.7 - - - -
2211D MET* 3.6 30.0 - - + +
2214D ARG* 4.9 1.7 + - - -
1964E VAL* 4.1 4.0 - - - +
1992E LEU* 3.8 18.4 - - + -
2013E THR* 3.3 35.4 - - + -
2014E MET* 3.2 11.9 + - - +
2016E CYS* 1.3 81.0 - - + +
2018E ALA* 1.3 51.5 + - - +
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Residues in contact with ALA2018 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1986D ARG* 4.4 0.9 - - - -
1964E VAL* 3.6 23.6 - - + +
1966E ALA* 3.6 29.4 - - + +
1992E LEU* 4.2 2.9 - - + -
2014E MET 2.9 13.6 + - - +
2015E SER* 3.0 21.9 - - - +
2017E TYR* 1.3 81.3 - - - +
2019E ASP* 1.3 63.2 + - - +
2020E VAL 3.4 3.5 + - - +
2040E ARG* 3.4 9.2 + - - +
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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
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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