Contacts of the helix formed by residues 2004 - 2012 (chain A) in PDB entry 4M6W
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 SER2004 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2002A ASN 3.9 2.0 + - - -
2003A SER* 1.3 72.9 - - - +
2005A LEU* 1.3 69.2 + - - +
2006A GLN* 2.9 18.2 + - - +
2007A GLU* 2.9 30.7 + - - +
2008A ILE* 3.2 10.2 + - - +
2023A TYR* 4.9 4.5 - - - -
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Residues in contact with LEU2005 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2003A SER 3.8 1.4 + - - -
2004A SER* 1.3 72.6 - - - +
2006A GLN* 1.3 83.8 + - + +
2008A ILE* 4.0 8.1 - - - -
2009A SER* 3.2 24.4 + - - -
2016A HIS 5.9 0.9 - - - +
2019A ALA* 3.5 24.4 - - + +
2020A GLU* 4.5 21.5 - - + +
2023A TYR* 4.5 26.0 - - + -
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Residues in contact with GLN2006 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2004A SER* 2.9 10.2 + - - +
2005A LEU* 1.3 95.4 - - + +
2007A GLU* 1.3 59.5 + - + +
2009A SER* 3.6 6.4 - - - -
2010A MET* 3.5 39.5 + - + +
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Residues in contact with GLU2007 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1994A PHE* 4.8 0.4 - - - -
1999A ARG* 4.7 11.8 + - - +
2003A SER* 3.1 31.9 + - - -
2004A SER* 2.9 27.8 + - - +
2006A GLN* 1.3 76.8 - - + +
2008A ILE* 1.3 61.9 + - - +
2009A SER 3.3 0.4 - - - -
2010A MET* 3.8 4.3 - - - +
2011A TYR* 2.9 61.2 + - + +
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Residues in contact with ILE2008 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1990A MET* 5.3 2.7 - - + -
1994A PHE* 3.9 15.5 - - + -
2000A MET* 4.9 5.4 - - - +
2003A SER* 3.6 28.0 - - - +
2004A SER 3.2 18.8 + - - +
2005A LEU* 4.1 2.2 - - - +
2007A GLU* 1.3 73.4 - - - +
2009A SER* 1.3 63.5 + - - +
2012A ALA* 2.9 44.0 + - + +
2014A VAL* 4.0 10.3 - - + -
2019A ALA* 3.7 29.8 - - + +
2022A ILE* 3.5 37.0 - - + -
2023A TYR* 5.5 3.6 - - + +
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Residues in contact with SER2009 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2005A LEU 3.2 19.9 + - - -
2006A GLN* 3.6 8.1 - - - -
2008A ILE* 1.3 79.2 - - - +
2010A MET* 1.3 65.9 + - - +
2013A GLN* 3.4 1.7 + - - -
2014A VAL* 2.9 49.6 + - - +
2015A THR 3.3 9.7 + - - -
2016A HIS* 4.1 6.2 + - - -
2019A ALA* 3.6 15.5 - - - -
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Residues in contact with MET2010 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1993A GLN* 4.1 3.3 - - - +
2006A GLN* 3.5 33.8 + - + +
2007A GLU* 4.2 5.4 - - - +
2008A ILE 3.2 0.2 - - - -
2009A SER* 1.3 84.4 - - - +
2011A TYR* 1.3 72.6 + - + +
2013A GLN* 3.3 20.3 + - - +
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Residues in contact with TYR2011 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1989A ASN 3.0 18.3 - - - +
1993A GLN* 3.2 50.1 + - + +
1994A PHE* 3.7 27.8 - + + -
2007A GLU* 2.9 51.2 + - + +
2010A MET* 1.3 81.7 - - + +
2012A ALA* 1.3 58.3 + - - +
2013A GLN 3.2 0.8 + - - -
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Residues in contact with ALA2012 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1986A THR* 3.8 6.7 - - + +
1989A ASN* 3.0 23.9 - - - +
1990A MET* 3.7 25.8 - - + -
1994A PHE* 4.0 5.5 - - + -
2008A ILE* 2.9 33.9 + - + +
2011A TYR* 1.3 75.4 - - - +
2013A GLN* 1.3 67.4 + - - +
2014A VAL* 3.6 16.1 + - + +
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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