Contacts of the helix formed by residues 2003 - 2013 (chain A) in PDB entry 6FF7
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 THR2003 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2001A SER 4.0 1.6 + - - -
2002A LEU* 1.3 75.6 - - - +
2004A GLN* 1.3 60.9 + - - +
2005A SER* 3.2 8.7 - - - -
2006A GLU* 2.9 15.3 + - - +
2007A ILE* 2.8 24.3 + - - +
890u GLU* 4.9 11.7 - - - -
891u GLN* 5.8 2.2 - - - +
894u ASP* 4.1 24.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2004 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2002A LEU 3.9 0.8 + - - -
2003A THR* 1.3 70.6 - - - +
2005A SER* 1.3 60.6 + - - +
2007A ILE* 3.7 11.8 - - + +
2008A ARG* 2.9 26.5 + - - +
894u ASP* 5.0 4.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER2005 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2003A THR* 3.2 6.7 - - - -
2004A GLN* 1.3 77.9 - - - +
2006A GLU* 1.3 56.1 + - - +
2008A ARG* 3.3 8.5 + - - +
2009A ASP* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2006 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2002A LEU* 4.4 9.9 - - + -
2003A THR* 2.9 22.5 + - - +
2005A SER* 1.3 77.0 - - - +
2007A ILE* 1.3 58.7 + - - +
2009A ASP* 3.1 9.1 + - - +
2010A ILE* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2007 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2002A LEU* 4.8 8.9 - - + +
2003A THR 2.8 17.9 + - - +
2004A GLN* 3.8 12.8 - - + +
2006A GLU* 1.3 71.0 - - - +
2008A ARG* 1.3 58.1 + - - +
2010A ILE* 3.4 7.1 + - - +
2011A ILE* 2.9 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2008 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2004A GLN 2.9 18.5 + - - +
2005A SER* 3.4 9.4 - - - +
2006A GLU 3.2 0.2 - - - -
2007A ILE* 1.3 76.8 - - - +
2009A ASP* 1.3 56.6 + - - +
2011A ILE* 3.1 5.4 + - - +
2012A LEU* 2.9 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP2009 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2005A SER 2.9 13.6 + - - +
2006A GLU* 3.1 11.8 + - - +
2008A ARG* 1.3 75.4 - - - +
2010A ILE* 1.3 60.2 + - - +
2012A LEU* 5.2 1.6 - - - -
2013A GLY* 3.2 2.1 + - - -
2014A MET* 2.7 53.1 + - + +
2016A ILE* 5.8 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2010 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1987A ILE* 6.0 2.6 - - - +
1988A LEU* 6.2 2.9 - - - -
1991A TYR* 5.2 13.9 - - + -
2006A GLU 2.9 15.8 + - - +
2007A ILE* 3.8 6.7 - - - +
2009A ASP* 1.3 76.1 - - - +
2011A ILE* 1.3 61.5 + - - +
2013A GLY* 3.2 12.6 + - - -
2014A MET 5.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2011 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1937A ILE* 5.4 3.1 - - - +
1938A LEU* 5.3 11.6 + - + +
1941A ARG* 5.3 7.3 - - - +
1984A LYS* 5.7 9.2 - - + -
1987A ILE* 5.9 8.1 - - + -
2007A ILE 2.9 19.3 + - - +
2008A ARG* 3.1 5.8 + - - +
2010A ILE* 1.3 76.5 - - - +
2012A LEU* 1.3 58.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2012 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1888A GLU 5.2 3.3 - - - +
1889A LEU* 5.3 3.5 - - - +
1890A GLN 4.4 12.6 + - - +
2008A ARG 2.9 14.5 + - - +
2009A ASP* 4.7 1.8 - - - +
2011A ILE* 1.3 79.2 - - - +
2013A GLY* 1.3 59.1 + - - +
2014A MET* 4.9 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY2013 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1888A GLU 4.0 13.5 - - - +
1890A GLN* 5.5 5.9 + - - +
2009A ASP 3.2 4.7 + - - -
2010A ILE* 3.2 10.4 + - - -
2012A LEU* 1.3 80.2 - - - +
2014A MET* 1.3 65.6 + - - +
2015A GLU 3.7 1.2 + - - -
----------------------------------------------------------
Back to top of page
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