Contacts of the helix formed by residues 2000 - 2014 (chain r) 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 THR2000 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1994r ASN* 5.3 0.4 - - - +
1998r GLN* 3.9 6.1 + - - -
1999r LEU* 1.3 74.8 - - - +
2001r ASP* 1.3 55.9 + - - +
2002r SER* 3.3 2.2 - - - -
2003r GLN* 3.2 16.7 + - - +
2004r ILE* 2.7 39.8 + - - +
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Residues in contact with ASP2001 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1999r LEU 4.4 0.4 - - - -
2000r THR* 1.3 70.7 - - - +
2002r SER* 1.3 57.6 - - - +
2004r ILE* 4.0 6.0 - - - +
2005r ALA* 2.9 30.8 + - - +
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Residues in contact with SER2002 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2000r THR* 3.3 2.1 - - - -
2001r ASP* 1.3 76.5 - - - +
2003r GLN* 1.3 58.7 + - - +
2005r ALA* 3.4 6.2 + - - +
2006r ASP* 2.9 27.7 + - - +
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Residues in contact with GLN2003 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1964r PRO* 5.1 3.5 - - - +
1965r HIS* 4.0 24.6 - - + +
2000r THR* 3.2 18.1 + - - +
2002r SER* 1.3 77.2 - - - +
2004r ILE* 1.3 59.6 + - - +
2006r ASP* 3.3 9.1 + - - +
2007r VAL* 2.9 29.3 + - - +
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Residues in contact with ILE2004 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1994r ASN* 4.9 15.9 - - + -
2000r THR 2.7 27.3 + - - +
2001r ASP* 4.0 5.6 - - - +
2003r GLN* 1.3 70.2 - - - +
2005r ALA* 1.3 59.5 + - - +
2007r VAL* 3.4 8.1 + - - +
2008r ALA* 2.9 27.4 + - - +
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Residues in contact with ALA2005 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2001r ASP 2.9 20.3 + - - +
2002r SER* 3.6 5.8 - - - +
2004r ILE* 1.3 75.0 - - - +
2006r ASP* 1.3 59.4 + - - +
2008r ALA* 3.0 9.2 + - - +
2009r ARG* 2.9 30.3 + - - +
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Residues in contact with ASP2006 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1964r PRO* 4.8 18.5 - - + +
2002r SER 2.9 15.4 + - - +
2003r GLN* 3.5 13.2 - - - +
2005r ALA* 1.3 75.7 - - - +
2007r VAL* 1.3 59.3 + - - +
2009r ARG* 3.9 6.1 + - - +
2010r PHE* 3.7 16.1 + - - +
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Residues in contact with VAL2007 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1963r LEU* 5.1 10.7 - - + +
1964r PRO* 4.7 16.6 - - - +
2003r GLN 2.9 15.9 + - - +
2004r ILE* 3.7 8.3 - - - +
2006r ASP* 1.3 74.8 - - - +
2008r ALA* 1.3 60.1 + - - +
2009r ARG 3.3 0.4 - - - -
2010r PHE* 3.2 9.5 + - - +
2011r CYS* 2.9 28.0 + - - +
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Residues in contact with ALA2008 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2004r ILE 2.9 14.6 + - - +
2005r ALA* 3.0 13.4 + - - +
2007r VAL* 1.3 77.0 - - - +
2009r ARG* 1.3 56.2 + - - +
2011r CYS* 3.3 9.2 + - - +
2012r ASN* 2.9 28.2 + - - +
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Residues in contact with ARG2009 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2005r ALA 2.9 14.9 + - - +
2006r ASP* 4.3 7.0 - - - +
2007r VAL 3.3 0.2 - - - -
2008r ALA* 1.3 73.4 - - - +
2010r PHE* 1.3 60.6 + - - +
2012r ASN* 3.3 7.0 + - - +
2013r ARG* 2.9 29.5 + - - +
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Residues in contact with PHE2010 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1962r GLN 5.9 1.1 - - - +
1963r LEU* 5.4 12.8 - - + -
1964r PRO* 5.6 2.2 - - + -
2006r ASP 3.7 11.1 + - - +
2007r VAL* 3.2 12.9 + - - +
2009r ARG* 1.3 77.1 - - - +
2011r CYS* 1.3 54.8 + - - +
2013r ARG* 3.1 7.5 + - - +
2014r TYR* 2.7 36.5 + - - +
2052r ILE* 5.2 12.8 - - + -
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Residues in contact with CYS2011 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1982r VAL* 6.5 1.1 - - - -
1985r ILE 6.2 0.4 - - - +
1986r MET* 6.4 2.0 - - - -
2007r VAL 2.9 12.8 + - - +
2008r ALA* 3.3 12.1 + - - +
2010r PHE* 1.3 78.3 - - - +
2012r ASN* 1.3 62.1 + - - +
2014r TYR* 3.5 18.4 + - - +
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Residues in contact with ASN2012 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2008r ALA 2.9 13.1 + - - +
2009r ARG* 3.7 9.9 - - - +
2011r CYS* 1.3 79.8 - - - +
2013r ARG* 1.3 60.6 + - - +
2014r TYR 3.3 7.1 + - - +
2045r GLU* 4.4 13.9 - - - +
2046r GLU* 5.2 7.9 + - + +
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Residues in contact with ARG2013 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2009r ARG 2.9 18.4 + - - +
2010r PHE* 3.6 7.0 - - - +
2012r ASN* 1.3 74.0 - - - +
2014r TYR* 1.3 65.0 + - - +
2015r PRO* 3.5 3.3 - - - +
2046r GLU 5.9 2.0 - - - -
2048r THR 5.7 4.5 - - - +
2050r PRO 5.1 9.2 - - - +
2051r VAL* 6.2 0.4 - - - -
2052r ILE* 5.0 14.4 - - + +
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Residues in contact with TYR2014 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1982r VAL* 5.4 12.1 - - + -
2010r PHE 2.7 18.9 + - - +
2011r CYS* 3.7 15.7 - - - +
2012r ASN 3.2 9.3 - - - +
2013r ARG* 1.3 74.9 - - - +
2015r PRO* 1.3 66.1 - - - +
2016r ASN* 3.4 5.0 + - - +
2045r GLU* 4.7 2.6 - - - +
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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