Contacts of the helix formed by residues 2002 - 2011 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2000D ARG 3.8 2.4 - - - +
2001D SER* 1.3 91.7 - - - +
2003D PRO* 1.3 72.3 - - + +
2004D GLN* 3.9 20.2 - - + +
2005D GLU* 3.4 19.6 + - + +
2006D GLN* 2.9 26.5 + - - +
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Residues in contact with PRO2003 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2001D SER 4.5 0.9 - - - +
2002D PRO* 1.3 86.7 - - + +
2004D GLN* 1.3 66.0 + - - +
2006D GLN* 3.2 13.4 + - + +
2007D ILE* 2.9 39.0 + - + +
3636D PRO* 5.3 13.7 - - + +
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Residues in contact with GLN2004 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2002D PRO* 3.9 21.0 - - + +
2003D PRO* 1.3 85.0 - - - +
2005D GLU* 1.3 65.9 + - + +
2007D ILE* 3.3 4.6 + - - +
2008D ASN* 2.9 41.7 + - - +
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Residues in contact with GLU2005 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2001D SER* 4.8 5.6 - - - -
2002D PRO* 3.4 27.7 + - + +
2003D PRO 3.4 0.2 - - - -
2004D GLN* 1.3 83.4 - - + +
2006D GLN* 1.3 57.4 + - - +
2008D ASN* 3.3 10.7 + - - +
2009D MET* 2.9 31.0 + - - +
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Residues in contact with GLN2006 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1974D GLN* 4.4 15.0 - - - +
1998D GLU* 3.7 24.3 + - + +
2001D SER* 4.5 12.5 - - - +
2002D PRO 2.9 17.5 + - - +
2003D PRO* 3.2 10.9 + - - +
2005D GLU* 1.3 77.1 - - - +
2007D ILE* 1.3 60.3 + - + +
2009D MET* 3.2 6.1 + - - +
2010D LEU* 2.9 42.3 + - + +
3636D PRO* 3.3 26.1 - - - +
3637D LEU* 3.2 36.5 + - - +
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Residues in contact with ILE2007 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1967D VAL* 5.9 7.0 - - + -
2003D PRO* 2.9 19.8 + - + +
2004D GLN* 3.9 5.8 - - - +
2006D GLN* 1.3 80.7 - - + +
2008D ASN* 1.3 63.2 + - - +
2010D LEU* 3.7 26.7 - - + -
2011D LEU* 3.1 29.9 + - + +
3637D LEU* 3.7 26.7 - - + -
3645D ALA* 5.5 6.3 - - + +
3648D MET* 4.6 32.1 - - + +
3649D PHE* 4.9 9.9 - - + +
3652D SER* 4.9 4.8 - - - -
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Residues in contact with ASN2008 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2004D GLN* 2.9 32.5 + - - +
2005D GLU* 3.7 8.7 - - - +
2007D ILE* 1.3 78.6 - - - +
2009D MET* 1.3 59.7 + - - +
2011D LEU* 4.3 0.6 - - - +
2012D HIS* 3.4 21.7 + - - +
3652D SER* 3.3 29.6 + - - -
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Residues in contact with MET2009 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2005D GLU 2.9 17.3 + - - +
2006D GLN* 3.7 5.2 - - - +
2008D ASN* 1.3 77.2 - - - +
2010D LEU* 1.3 63.8 + - - +
2012D HIS* 3.5 18.7 + - - +
2023D PRO* 4.6 15.3 - - + +
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Residues in contact with LEU2010 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1967D VAL* 6.4 1.3 - - + -
1970D LEU* 3.6 31.9 - - + -
1974D GLN* 5.0 12.1 - - - +
2006D GLN* 2.9 36.5 + - + +
2007D ILE* 3.7 34.3 - - + +
2009D MET* 1.3 77.5 - - - +
2011D LEU* 1.3 77.4 + - + +
2012D HIS 3.4 5.2 + - - +
2023D PRO* 4.9 14.0 - - + +
2024D LEU* 3.2 30.2 - - + +
3637D LEU* 3.8 18.6 - - + -
3649D PHE* 6.3 0.2 - - + -
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Residues in contact with LEU2011 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1966D TYR* 5.7 2.6 - - - -
1970D LEU* 4.8 5.6 - - + -
2007D ILE* 3.1 21.1 + - + +
2008D ASN 4.3 1.3 - - - +
2010D LEU* 1.3 82.9 - - + +
2012D HIS* 1.3 62.6 + - - +
2013D PHE* 3.5 6.1 + - - +
2024D LEU* 5.3 1.1 - - - -
2032D LEU* 4.9 9.5 - - - +
3649D PHE* 3.9 32.7 - - + -
3652D SER* 5.0 8.7 - - - -
3656D ALA* 5.3 6.6 - - - +
3657D TRP* 5.1 4.9 + - - -
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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