Contacts of the helix formed by residues 2006 - 2015 (chain C) in PDB entry 5G1N
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 SER2006 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2187B ARG 5.0 0.8 + - - -
2001C VAL* 5.9 0.4 - - - -
2004C GLY 4.0 2.0 + - - -
2005C GLU* 1.3 76.2 - - - +
2007C LEU* 1.3 64.6 + - - +
2008C ALA* 3.8 7.7 + - - +
2009C ASP* 3.1 34.7 + - - +
2010C SER* 2.8 27.0 + - - -
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Residues in contact with LEU2007 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1970C TYR* 4.0 22.4 - - + -
2005C GLU 4.0 0.6 + - - -
2006C SER* 1.3 74.0 - - - +
2008C ALA* 1.3 62.1 + - - +
2010C SER* 3.4 4.2 + - - -
2011C VAL* 3.1 37.7 + - + +
2023C LEU* 4.2 8.1 - - + -
2025C HIS* 3.6 32.5 - - + +
2027C GLN* 5.9 0.4 - - - +
2030C ALA* 3.4 41.1 - - + +
2033C LEU* 5.4 7.4 - - + -
2034C ALA* 3.7 12.6 - - + +
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Residues in contact with ALA2008 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2006C SER* 3.2 7.2 + - - +
2007C LEU* 1.3 81.0 - - - +
2009C ASP* 1.3 62.5 + - - +
2011C VAL* 3.6 1.7 + - - +
2012C GLN* 3.0 32.7 + - - +
2033C LEU* 5.8 6.5 - - + -
2034C ALA* 4.7 16.3 - - - +
2037C HIS* 5.0 19.8 - - + +
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Residues in contact with ASP2009 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2185B MET* 5.9 2.0 - - - -
2187B ARG* 3.3 55.8 + - - +
2196B ASP* 4.9 0.2 - - - +
2204B PHE* 3.8 18.9 - - + -
2005C GLU* 3.4 22.9 - - + +
2006C SER* 3.1 24.7 + - - +
2008C ALA* 1.3 78.1 - - - +
2010C SER* 1.3 59.5 + - - +
2012C GLN* 3.3 1.7 + - - +
2013C THR* 2.8 35.0 + - - -
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Residues in contact with SER2010 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1974B THR* 5.3 0.2 - - - -
1968C MET* 4.1 4.3 - - - -
1970C TYR* 3.4 24.5 + - - -
1994C PHE* 4.1 16.6 - - - -
2001C VAL* 3.8 8.1 - - - +
2005C GLU* 3.5 24.2 + - - +
2006C SER 2.8 17.2 + - - -
2007C LEU 3.9 1.8 - - - -
2009C ASP* 1.3 75.0 - - - +
2011C VAL* 1.3 58.6 + - - +
2013C THR* 3.4 4.6 - - - -
2014C MET* 2.8 34.9 + - - +
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Residues in contact with VAL2011 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1968C MET* 3.4 28.7 - - + -
2007C LEU* 3.1 32.7 + - + +
2008C ALA 4.2 2.5 - - - +
2010C SER* 1.3 75.5 - - - +
2012C GLN* 1.3 63.2 + - - +
2014C MET* 3.7 1.4 + - - +
2015C SER* 3.2 21.0 + - - -
2021C VAL* 4.3 17.7 - - + +
2023C LEU* 4.2 12.3 - - + -
2034C ALA* 4.0 30.5 - - + +
2038C CYS* 4.1 11.9 - - + -
2042C VAL* 4.9 4.3 - - + -
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Residues in contact with GLN2012 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2196B ASP* 4.9 4.8 - - - +
2204B PHE* 3.3 53.2 - - + +
2008C ALA 3.0 18.7 + - - +
2009C ASP* 4.0 2.9 - - - +
2011C VAL* 1.3 72.3 - - - +
2013C THR* 1.3 63.8 + - - +
2015C SER* 2.3 29.5 + - - +
2016C CYS* 3.3 12.2 - - - -
2037C HIS* 3.7 37.6 + - - +
2038C CYS* 5.1 0.4 - - - -
2039C ARG* 5.4 9.7 - - - +
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Residues in contact with THR2013 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1974B THR* 4.0 13.2 - - + -
1975B ARG* 3.6 51.0 + - + +
2185B MET* 5.2 2.6 - - - -
2204B PHE* 3.5 15.6 - - - -
2207B ALA* 5.4 2.7 - - + +
2005C GLU* 3.9 1.6 + - - -
2009C ASP 2.8 21.6 + - - -
2010C SER 3.4 6.1 - - - +
2012C GLN* 1.3 77.5 - - - +
2014C MET* 1.3 58.9 + - - +
2016C CYS* 3.0 32.5 + - - +
2017C TYR* 3.6 12.9 - - + -
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Residues in contact with MET2014 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1974B THR* 4.0 15.7 - - + -
1978B SER* 3.7 32.1 - - - +
1966C ALA* 3.9 25.1 - - + +
1968C MET* 3.8 23.8 - - + -
1992C LEU* 4.1 28.7 - - + +
1993C SER 5.7 0.2 - - - -
1994C PHE* 4.1 23.6 - - + -
2010C SER 2.8 23.9 + - - +
2011C VAL 4.3 1.6 - - - +
2013C THR* 1.3 72.7 - - - +
2015C SER* 1.3 56.6 + - - +
2016C CYS 3.2 0.4 - - - -
2017C TYR* 3.4 10.6 + - - +
2018C ALA* 3.0 30.4 + - - +
2021C VAL* 4.8 2.2 - - + -
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Residues in contact with SER2015 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2011C VAL 3.2 12.8 + - - -
2012C GLN* 2.3 34.1 + - - +
2014C MET* 1.3 74.0 - - - +
2016C CYS* 1.3 60.5 + - - +
2017C TYR 3.2 0.9 - - - -
2018C ALA 3.3 16.4 - - - +
2021C VAL* 4.3 6.7 - - - +
2038C CYS* 3.5 23.4 - - - -
2039C ARG* 3.1 28.6 + - - -
2040C ARG* 3.4 18.5 + - - +
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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