Contacts of the helix formed by residues 2000 - 2014 (chain D) in PDB entry 6AH0
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 THR2000 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1998D GLN 3.9 2.8 + - - -
1999D LEU* 1.3 75.1 - - - +
2001D ASP* 1.3 56.2 + - - +
2002D SER 3.3 2.5 - - - -
2003D GLN* 3.2 5.6 + - - +
2004D ILE* 2.7 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP2001 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1999D LEU 4.4 0.2 - - - -
2000D THR* 1.3 71.0 - - - +
2002D SER* 1.3 56.4 + - - +
2004D ILE* 3.9 1.3 - - - +
2005D ALA* 2.9 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER2002 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2000D THR 3.3 0.8 - - - -
2001D ASP* 1.3 75.0 - - - +
2003D GLN* 1.3 57.1 + - - +
2005D ALA* 3.4 2.1 + - - -
2006D ASP* 2.9 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2003 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1964D PRO 5.1 6.2 - - - +
1965D HIS* 6.5 1.6 - - - +
2000D THR* 3.2 6.2 + - - +
2002D SER* 1.3 72.8 - - - +
2004D ILE* 1.3 60.6 + - - +
2006D ASP* 3.3 2.9 + - - +
2007D VAL* 2.9 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2004 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2000D THR 2.7 21.0 + - - +
2001D ASP* 4.0 1.8 - - - +
2003D GLN* 1.3 69.8 - - - +
2005D ALA* 1.3 58.7 + - - +
2007D VAL* 3.4 1.7 + - - +
2008D ALA* 2.9 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2005 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2001D ASP 2.9 18.2 + - - -
2002D SER 3.7 1.3 - - - -
2004D ILE* 1.3 73.3 - - - +
2006D ASP* 1.3 58.8 + - - +
2008D ALA* 3.0 2.7 + - - +
2009D ARG* 2.9 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP2006 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1964D PRO* 5.6 4.2 - - - +
2002D SER 2.9 14.9 + - - -
2003D GLN* 3.3 5.6 + - - +
2005D ALA* 1.3 75.6 - - - +
2007D VAL* 1.3 58.4 + - - +
2009D ARG* 3.9 1.9 + - - +
2010D PHE* 3.7 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2007 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1963D LEU* 6.0 2.0 - - - +
1964D PRO 5.3 13.4 + - - -
2003D GLN 2.9 13.7 + - - -
2004D ILE* 3.8 3.4 - - - +
2006D ASP* 1.3 75.0 - - - +
2008D ALA* 1.3 60.3 + - - +
2009D ARG 3.3 0.2 - - - -
2010D PHE* 3.2 3.8 + - - +
2011D CYS* 2.9 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2008 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2004D ILE 2.9 15.3 + - - -
2005D ALA* 3.0 5.3 + - - +
2007D VAL* 1.3 77.8 - - - +
2009D ARG* 1.3 55.6 + - - +
2011D CYS* 3.2 2.9 + - - +
2012D ASN* 2.9 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2009 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2005D ALA 2.9 13.3 + - - -
2006D ASP* 3.9 2.2 + - - +
2008D ALA* 1.3 72.6 - - - +
2010D PHE* 1.3 59.3 + - - +
2012D ASN* 3.3 2.1 + - - +
2013D ARG* 2.9 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2010 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2006D ASP 3.7 9.2 + - - -
2007D VAL 3.2 7.2 + - - -
2009D ARG* 1.3 75.8 - - - +
2011D CYS* 1.3 52.2 + - - +
2013D ARG* 3.1 2.5 + - - +
2014D TYR* 2.7 34.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS2011 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2007D VAL 2.9 14.0 + - - -
2008D ALA* 3.2 4.7 + - - +
2010D PHE* 1.3 77.3 - - - +
2012D ASN* 1.3 61.6 + - - +
2014D TYR* 3.5 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2012 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2008D ALA 2.9 14.2 + - - -
2009D ARG* 3.3 3.1 + - - +
2011D CYS* 1.3 79.2 - - - +
2013D ARG* 1.3 59.9 + - - +
2014D TYR 3.3 7.3 + - - +
2045D GLU* 5.2 8.5 - - - -
2046D GLU 5.2 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2013 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2009D ARG 2.9 15.4 + - - -
2010D PHE* 3.1 4.2 + - - +
2012D ASN* 1.3 73.7 - - - +
2014D TYR* 1.3 64.3 + - - +
2015D PRO* 3.5 3.5 - - - +
2046D GLU 5.9 2.5 - - - -
2048D THR 6.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR2014 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2010D PHE 2.7 17.9 + - - -
2011D CYS* 3.5 8.8 + - - +
2012D ASN 3.2 10.1 - - - +
2013D ARG* 1.3 75.2 - - - +
2015D PRO* 1.3 65.4 - - - +
2016D ASN* 3.4 2.4 + - - -
----------------------------------------------------------
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