Contacts of the helix formed by residues 2010 - 2018 (chain B) in PDB entry 3NBN
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 GLY2010 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1975B GLN* 4.7 5.2 - - - -
2008B VAL 4.0 1.2 + - - -
2009B GLU* 1.3 68.5 - - - +
2011B MET* 1.3 50.8 + - - -
2012B LEU* 3.2 3.1 - - - +
2013B GLU* 2.7 44.0 + - - +
2014B ASP* 3.2 13.7 + - - -
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Residues in contact with MET2011 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1969B ALA 4.2 1.8 - - - +
1970B VAL* 3.9 29.8 - - + +
1973B ASP* 3.1 52.0 - - - +
1974B ALA 3.7 4.9 - - - +
1975B GLN* 4.4 11.2 + - - +
1978B PHE* 3.6 40.9 - - + -
2003B ALA* 4.6 7.2 - - + -
2008B VAL* 3.7 17.3 - - + -
2009B GLU 2.7 18.3 + - - +
2010B GLY* 1.3 68.1 - - - +
2012B LEU* 1.3 63.7 + - - +
2014B ASP* 3.2 1.5 + - - +
2015B LEU* 2.9 29.1 + - + +
22C ARG* 4.1 4.9 - - - +
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Residues in contact with LEU2012 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2000B LEU* 3.6 33.5 - - + +
2003B ALA* 4.1 13.8 - - + +
2004B ALA* 4.0 18.2 - - + +
2008B VAL* 5.1 4.4 + - - +
2009B GLU 5.3 0.2 - - - -
2010B GLY 2.8 4.4 + - - +
2011B MET* 1.3 76.4 - - - +
2013B GLU* 1.3 56.7 + - + +
2015B LEU* 3.3 3.3 + - - +
2016B ILE* 2.9 35.6 + - + +
2044B ALA* 3.6 24.9 - - + +
2047B VAL* 4.0 20.0 - - + -
2048B LEU* 3.4 34.5 - - + -
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Residues in contact with GLU2013 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2010B GLY* 2.7 17.9 + - - +
2012B LEU* 1.3 73.4 - - + +
2014B ASP* 1.3 65.4 + - - +
2016B ILE* 2.9 9.6 + - - +
2017B ASN* 2.8 52.6 + - - +
2047B VAL* 3.9 36.0 - - + +
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Residues in contact with ASP2014 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1975B GLN* 3.2 17.0 + - - +
1978B PHE* 3.9 6.5 - - + -
1979B GLN* 3.0 21.3 - - - +
1982B ILE* 3.4 17.7 - - + +
2010B GLY* 3.2 15.8 + - - +
2011B MET 3.2 6.8 + - - +
2013B GLU* 1.3 78.7 - - - +
2015B LEU* 1.3 57.4 + - - +
2017B ASN* 3.5 9.2 + - - +
2018B SER* 2.9 34.0 + - - -
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Residues in contact with LEU2015 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1966B LEU* 4.5 11.9 - - + -
1970B VAL* 5.0 1.1 - - + -
1978B PHE* 3.9 25.4 - - + -
1982B ILE* 4.3 6.7 - - + -
1989B LEU* 4.4 30.6 - - + +
1999B PRO* 3.7 14.1 - - + +
2000B LEU* 3.5 43.5 - - + +
2003B ALA* 4.4 5.4 - - + -
2011B MET 2.9 15.5 + - - +
2012B LEU 3.6 6.7 - - - +
2014B ASP* 1.3 73.0 - - - +
2016B ILE* 1.3 66.3 + - - +
2018B SER* 3.5 4.2 + - - +
2019B HIS 3.3 4.5 + - - -
2020B ALA* 3.1 28.0 + - + +
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Residues in contact with ILE2016 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2000B LEU* 4.3 15.9 - - + -
2012B LEU* 2.9 29.9 + - + +
2013B GLU* 2.9 10.2 + - - +
2015B LEU* 1.3 76.3 - - - +
2017B ASN* 1.3 57.3 + - - +
2019B HIS* 2.6 32.6 + - - -
2020B ALA* 3.7 6.5 + - - +
2022B VAL* 5.0 14.5 - - + +
2047B VAL* 3.4 29.2 - - + +
2048B LEU* 4.1 19.1 - - + -
2051B ASN* 3.6 38.1 - - + +
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Residues in contact with ASN2017 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2013B GLU* 2.8 41.6 + - - +
2014B ASP* 3.9 8.4 + - - +
2016B ILE* 1.3 76.4 - - - +
2018B SER* 1.3 57.5 + - - +
2019B HIS* 3.0 28.6 + - - -
2051B ASN* 5.1 5.2 + - - -
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Residues in contact with SER2018 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1982B ILE* 3.3 23.2 + - - +
1989B LEU* 3.5 27.0 - - - +
2014B ASP 2.9 19.1 + - - -
2015B LEU 3.7 1.1 - - - -
2016B ILE 3.2 0.6 + - - -
2017B ASN* 1.3 73.8 - - - +
2019B HIS* 1.3 72.0 + - - +
2020B ALA 3.6 1.3 - - - -
1985E ARG* 4.0 23.0 + - - +
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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