Contacts of the strand formed by residues 2009 - 2014 (chain A) in PDB entry 3PZD
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 THR2009 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2004A ALA* 3.2 29.5 - - - +
2005A PRO* 3.7 8.6 - - + +
2006A LEU* 3.7 28.2 + - + +
2007A ALA 3.0 14.8 + - - -
2008A ASN* 1.3 74.5 + - - +
2010A TYR* 1.3 65.3 + - - +
2011A LYS* 5.8 0.4 - - + -
2020A LEU* 4.6 11.2 - - + -
2021A PHE 3.4 21.8 - - - +
2022A GLU* 4.1 12.8 + - + +
2026A VAL* 3.6 3.5 - - - +
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Residues in contact with TYR2010 (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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1973A LEU* 5.1 4.9 - - + -
2002A PHE* 3.8 21.9 - + + -
2003A GLY 3.8 4.3 - - - -
2009A THR* 1.3 74.7 - - - +
2011A LYS* 1.3 68.0 + - - +
2012A ILE* 4.9 7.0 - - + -
2020A LEU* 4.6 0.2 - - - -
2021A PHE* 2.7 58.7 + + + +
2023A THR* 4.7 5.6 - - + -
2026A VAL* 3.7 46.4 - - + +
2029A VAL* 3.7 16.4 - - + -
2030A ALA* 3.8 10.7 - - + -
2033A MET* 3.1 39.8 - - + +
1437B LEU* 3.3 19.2 - - + +
1440B ILE* 4.5 8.1 - - + -
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Residues in contact with LYS2011 (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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2002A PHE* 3.6 3.1 - - - -
2003A GLY* 2.8 43.2 + - - +
2005A PRO* 3.7 24.2 - - + -
2009A THR* 4.1 1.2 + - + -
2010A TYR* 1.3 79.6 - - - +
2012A ILE* 1.3 61.3 + - - +
2013A VAL* 5.8 1.8 - - + -
2018A GLU* 5.5 7.0 - - - +
2019A LEU 3.4 10.1 - - - +
2020A LEU* 4.6 5.8 - - + +
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Residues in contact with ILE2012 (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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1973A LEU* 6.0 1.8 - - + -
1980A VAL* 4.8 10.5 - - + -
1994A PHE* 4.6 17.7 - - + -
1999A ILE* 3.7 29.4 - - + -
2001A SER 3.5 11.0 - - - +
2002A PHE* 3.6 26.9 - - + -
2010A TYR* 5.0 5.2 - - + -
2011A LYS* 1.3 75.4 - - - +
2013A VAL* 1.3 70.2 + - - +
2014A VAL* 4.6 2.2 - - + +
2017A ARG 3.9 0.2 - - - +
2018A GLU* 5.4 0.2 - - - -
2019A LEU* 3.0 42.1 + - + +
2021A PHE* 3.6 32.1 - - + -
2033A MET* 6.5 0.2 - - + -
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Residues in contact with VAL2013 (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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1999A ILE* 3.7 3.1 - - - +
2000A LEU* 2.8 50.3 + - + -
2001A SER* 3.0 30.7 + - - +
2011A LYS* 5.8 2.2 - - + -
2012A ILE* 1.3 78.0 - - - +
2014A VAL* 1.3 62.0 + - - +
2016A GLU 5.3 1.1 - - - +
2017A ARG 3.6 13.5 - - - +
2018A GLU* 3.3 28.0 - - - +
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Residues in contact with VAL2014 (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* 3.6 45.1 - - + -
1998A HIS* 3.3 30.7 - - + +
1999A ILE* 4.8 4.3 - - + -
2000A LEU 4.5 0.2 - - - +
2012A ILE* 4.0 4.5 + - + +
2013A VAL* 1.3 78.3 - - - +
2015A ASP* 1.3 77.3 + - - +
2016A GLU 3.1 0.3 + - - -
2017A ARG* 2.8 44.0 + - + +
2019A LEU* 4.1 7.6 - - + -
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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