Contacts of the helix formed by residues 2002 - 2011 (chain B) in PDB entry 6X34
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 PRO2002 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2000B ARG 3.8 3.3 - - - +
2001B SER* 1.3 91.7 - - - +
2003B PRO* 1.3 70.3 - - + +
2004B GLN* 3.4 19.5 + - + +
2005B GLU* 3.4 21.5 + - + +
2006B GLN* 2.9 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO2003 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2001B SER 3.8 1.1 - - - +
2002B PRO* 1.3 87.2 - - + +
2004B GLN* 1.3 67.6 - - - +
2006B GLN* 3.2 12.9 + - + +
2007B ILE* 2.9 39.5 + - + +
3636B PRO* 5.3 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2004 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2002B PRO* 3.9 21.9 - - + +
2003B PRO* 1.3 85.8 - - - +
2005B GLU* 1.3 66.4 + - + +
2007B ILE* 3.3 5.3 + - - +
2008B ASN* 2.9 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2005 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2001B SER* 4.8 4.9 - - - -
2002B PRO* 3.4 27.9 + - + +
2003B PRO 3.4 0.2 - - - -
2004B GLN* 1.3 82.5 - - + +
2006B GLN* 1.3 58.6 + - - +
2008B ASN* 3.7 10.8 - - - +
2009B MET* 2.9 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2006 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1974B GLN* 4.4 14.8 - - - +
1998B GLU* 3.7 24.0 + - - +
1999B PHE 5.1 0.2 - - - +
2001B SER* 4.5 13.3 - - - +
2002B PRO 2.9 17.3 + - - +
2003B PRO* 3.5 11.6 - - - +
2005B GLU* 1.3 76.3 - - - +
2007B ILE* 1.3 59.3 + - + +
2009B MET* 3.2 6.5 + - - +
2010B LEU* 2.9 41.7 + - + +
3636B PRO* 3.3 25.5 - - - +
3637B LEU* 3.2 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2007 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1967B VAL* 5.9 7.2 - - + -
2003B PRO* 2.9 21.6 + - + +
2004B GLN* 3.9 5.6 - - - +
2006B GLN* 1.3 80.8 - - + +
2008B ASN* 1.3 62.3 + - - +
2010B LEU* 3.7 27.1 - - + +
2011B LEU* 3.1 30.3 + - + +
3637B LEU* 3.7 26.0 - - + -
3645B ALA* 5.5 6.1 - - + +
3648B MET* 4.6 33.4 - - + +
3649B PHE* 4.9 10.1 - - + +
3652B SER* 4.9 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2008 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2004B GLN* 2.9 32.9 + - - +
2005B GLU* 3.7 8.4 - - - +
2006B GLN 3.2 0.2 - - - -
2007B ILE* 1.3 77.9 - - - +
2009B MET* 1.3 59.7 + - - +
2011B LEU* 4.3 0.9 - - - +
2012B HIS* 3.4 22.0 + - - +
3652B SER* 3.3 28.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET2009 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2005B GLU 2.9 17.9 + - - +
2006B GLN* 3.2 5.8 + - - +
2008B ASN* 1.3 76.1 - - - +
2010B LEU* 1.3 64.6 + - - +
2012B HIS* 3.5 18.4 + - - +
2023B PRO* 4.6 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2010 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1967B VAL* 6.4 1.8 - - + -
1970B LEU* 3.6 31.6 - - + -
1974B GLN* 5.0 11.4 - - - +
2006B GLN* 2.9 34.5 + - + +
2007B ILE* 3.7 33.9 - - + +
2009B MET* 1.3 77.9 - - - +
2011B LEU* 1.3 77.0 + - + +
2012B HIS 3.4 5.4 + - - +
2023B PRO* 5.0 15.2 - - + +
2024B LEU* 3.2 28.8 - - + +
3637B LEU* 3.8 19.7 - - + -
3649B PHE* 6.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2011 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1966B TYR* 5.7 2.7 - - - -
1970B LEU* 4.8 5.8 - - + -
2007B ILE* 3.1 21.4 + - + +
2008B ASN 4.3 1.3 - - - +
2010B LEU* 1.3 83.6 - - + +
2012B HIS* 1.3 60.6 + - - +
2013B PHE* 3.5 6.3 + - - +
2024B LEU* 5.3 0.4 - - - -
2032B LEU* 4.9 9.2 - - - +
3649B PHE* 3.9 32.8 - - + -
3652B SER* 5.0 9.0 - - - -
3656B ALA* 5.3 6.0 - - - +
3657B TRP* 5.1 5.4 + - - -
----------------------------------------------------------
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