Contacts of the strand formed by residues 2008 - 2015 (chain A) in PDB entry 4ASI
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 VAL2008 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1972A ARG* 5.2 0.3 + - - -
1999A GLU* 5.2 0.2 - - - +
2005A ALA 3.1 22.9 + - - +
2006A GLN* 3.8 5.2 - - - -
2007A THR* 1.3 79.5 - - + +
2009A VAL* 1.3 66.2 + - - +
2010A VAL* 4.3 3.6 - - + -
2023A VAL* 3.7 20.4 - - + -
2024A ALA 3.1 19.5 - - - +
2055A TRP* 5.1 1.8 - - - +
2059A SER* 3.7 26.2 - - - +
2062A LYS* 3.2 31.2 + - + -
2063A THR* 3.6 17.7 - - - +
2083A TRP* 4.3 9.4 - - + +
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Residues in contact with VAL2009 (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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1971A PRO* 3.8 19.1 - - + -
1972A ARG* 3.4 38.6 - - + +
1975A LEU* 4.6 7.4 - - + +
1997A PHE* 3.9 23.6 - - + -
1999A GLU* 3.7 18.6 - - - +
2006A GLN 4.7 2.7 - - - +
2008A VAL* 1.3 77.2 - - - +
2010A VAL* 1.3 68.3 + - - +
2022A VAL* 3.9 1.0 - - - +
2023A VAL* 3.5 0.9 - - - -
2024A ALA* 2.8 43.9 + - + +
2026A GLU* 4.6 6.7 - - - +
2062A LYS* 4.5 0.2 - - - +
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Residues in contact with VAL2010 (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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1997A PHE* 4.5 4.9 - - - -
1999A GLU* 3.2 10.8 + - - +
2000A ILE* 3.1 50.0 + - + +
2001A MET* 3.9 12.8 - - + -
2008A VAL* 4.3 10.3 - - + -
2009A VAL* 1.3 81.8 - - - +
2011A GLY* 1.3 60.1 + - - +
2022A VAL 3.2 7.6 - - - +
2023A VAL* 4.2 11.4 - - + -
2062A LYS* 3.9 26.0 - - + +
2063A THR* 5.0 1.1 - - - -
2066A ALA* 3.9 25.6 - - + -
2070A PHE* 4.7 0.4 - - + -
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Residues in contact with GLY2011 (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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1997A PHE* 4.0 9.5 - - - -
1998A SER 3.3 13.9 - - - -
1999A GLU* 4.0 0.7 - - - -
2000A ILE* 4.2 5.8 - - - -
2010A VAL* 1.3 77.1 - - - +
2012A ARG* 1.3 61.7 + - - -
2022A VAL* 2.8 36.4 + - - -
2070A PHE* 3.1 14.4 - - - -
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Residues in contact with ARG2012 (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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1874A ARG* 4.2 10.3 - - - +
1919A HIS* 4.9 3.6 - - - -
1935A TRP* 3.8 27.7 - - - +
1938A TYR* 3.9 37.9 - - + -
1939A MET* 3.5 17.9 - - - +
1996A SER 3.3 1.0 - - - +
1997A PHE* 3.3 3.9 - - - -
1998A SER* 2.7 36.7 + - - +
2000A ILE* 3.8 26.9 - - - +
2011A GLY* 1.3 78.4 - - - +
2013A ALA* 1.3 59.8 + - - +
2020A VAL 3.3 9.0 - - - +
2021A GLY* 4.9 0.2 - - - -
2022A VAL* 4.3 1.1 - - - -
2069A ASP* 5.4 1.4 - - - +
2070A PHE* 3.8 18.1 - - + -
2073A GLU* 2.7 43.2 + - - -
2075A LEU* 3.9 13.0 - - + -
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Residues in contact with ALA2013 (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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1938A TYR* 3.8 5.1 - - - -
1992A PHE* 3.6 32.5 - - + -
1996A SER* 3.3 15.9 - - - +
1997A PHE* 3.8 13.2 - - + -
2012A ARG* 1.3 76.3 - - - +
2014A ARG* 1.3 66.2 + - - +
2019A PRO* 3.3 5.7 - - - +
2020A VAL* 2.9 31.4 + - - +
2022A VAL* 4.0 8.0 - - + +
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Residues in contact with ARG2014 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1653A MET* 3.9 9.0 - - - +
1656A GLN* 3.1 30.9 + - - +
1934A HIS* 6.0 0.2 - - - -
1937A SER* 2.8 51.9 + - - -
1938A TYR* 3.4 28.9 + - + +
1948A PRO 5.0 2.0 + - - -
1950A LEU* 3.4 27.3 - - - +
1952A SER* 6.2 0.2 - - - -
1992A PHE* 3.6 6.1 - - - +
1993A ASP* 2.9 42.6 + - - +
1996A SER* 3.1 13.1 + - - -
2013A ALA* 1.3 81.2 - - - +
2015A LEU* 1.3 58.5 + - - +
2017A GLY* 4.0 17.8 + - - -
2018A ILE 3.1 5.8 - - - +
2019A PRO* 3.9 14.7 - - + +
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Residues in contact with LEU2015 (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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1956A ILE* 5.9 0.2 - - + -
1991A PHE* 4.1 19.1 - - + +
1992A PHE* 4.0 12.8 - - + -
1993A ASP* 3.6 0.7 - - - -
2014A ARG* 1.3 71.2 - - - +
2016A GLY* 1.3 62.5 + - - +
2018A ILE* 2.8 42.2 + - + +
2020A VAL* 5.0 4.9 - - + -
2078A MET* 4.2 10.5 - - - -
2249A ARG* 3.8 42.2 - - + +
2252A PHE* 3.7 19.7 - - + +
2253A TYR* 3.6 34.0 - - + +
2256A LEU* 4.7 8.3 - - + -
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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