Contacts of the helix formed by residues 2002 - 2022 (chain A) in PDB entry 3CMT
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 ILE2002 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2001A ALA* 1.3 85.8 - - + +
2003A ASP* 1.3 62.5 + - + +
2004A GLU 3.4 0.4 + - - -
2005A ASN* 3.9 13.9 + - - +
2006A LYS* 3.9 14.4 - - + +
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Residues in contact with ASP2003 (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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2001A ALA 4.2 3.6 + - - -
2002A ILE* 1.3 73.8 + - + +
2004A GLU* 1.3 89.8 + - - +
2005A ASN 3.3 0.9 - - - -
2006A LYS* 3.4 19.7 - - + +
2007A GLN* 3.4 26.7 + - - +
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Residues in contact with GLU2004 (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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2001A ALA* 3.2 35.6 + - - +
2002A ILE 3.4 0.6 - - - -
2003A ASP* 1.3 89.9 + - - +
2005A ASN* 1.3 62.8 + - - +
2006A LYS 3.2 0.4 - - - -
2007A GLN* 3.6 14.1 + - - +
2008A LYS* 3.3 21.1 + - - +
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Residues in contact with ASN2005 (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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2001A ALA 3.3 20.2 + - - -
2002A ILE* 3.9 9.7 + - - +
2004A GLU* 1.3 80.0 - - - +
2006A LYS* 1.3 62.1 + - + +
2008A LYS* 3.4 24.3 - - - +
2009A ALA* 3.2 22.2 + - - +
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Residues in contact with LYS2006 (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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1087A GLY 5.4 3.6 + - - -
1089A THR* 4.8 4.9 + - - -
1136A GLY 4.0 18.2 - - - +
1137A ALA* 3.5 27.5 + - + +
1139A ASP* 3.5 30.5 + - - -
2002A ILE* 3.9 12.8 - - + +
2003A ASP* 3.4 23.5 + - + +
2004A GLU 3.2 0.4 - - - -
2005A ASN* 1.3 78.2 - - + +
2007A GLN* 1.3 53.4 + - + +
2009A ALA* 3.2 5.2 + - - -
2010A LEU* 2.7 34.7 + - - +
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Residues in contact with GLN2007 (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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2003A ASP* 3.4 14.6 + - - +
2004A GLU* 3.6 15.6 + - - +
2005A ASN 3.4 0.2 - - - -
2006A LYS* 1.3 73.6 - - + +
2008A LYS* 1.3 64.9 + - - +
2010A LEU* 3.5 18.9 - - + +
2011A ALA* 2.9 28.4 + - - +
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Residues in contact with LYS2008 (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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2004A GLU 3.3 11.5 + - - +
2005A ASN* 3.4 26.5 - - - +
2007A GLN* 1.3 80.3 - - - +
2009A ALA* 1.3 60.0 + - + +
2011A ALA* 4.4 3.0 - - - +
2012A ALA* 3.4 20.1 + - - +
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Residues in contact with ALA2009 (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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1135A SER* 3.7 25.5 - - - +
1137A ALA* 4.5 2.5 - - + -
2005A ASN 3.2 9.3 + - - +
2006A LYS* 3.2 10.3 + - - +
2008A LYS* 1.3 78.5 - - + +
2010A LEU* 1.3 65.1 + - - +
2012A ALA* 3.5 7.7 - - - +
2013A ALA* 3.1 21.8 + - - +
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Residues in contact with LEU2010 (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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1089A THR* 4.6 10.1 - - + -
1115A LEU* 3.9 18.6 - - + -
1132A LEU* 5.5 0.7 - - + -
1135A SER* 5.5 0.4 - - - +
1137A ALA* 3.6 26.4 - - + +
1138A VAL* 4.3 9.6 - - + -
2006A LYS 2.7 21.0 + - - +
2007A GLN* 3.5 20.9 - - + +
2009A ALA* 1.3 70.2 - - - +
2011A ALA* 1.3 63.1 + - + +
2013A ALA* 2.9 7.2 + - + +
2014A LEU* 2.9 56.4 + - + +
2028A ARG* 6.3 1.3 - - - +
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Residues in contact with ALA2011 (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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2007A GLN 2.9 16.1 + - - +
2008A LYS* 4.4 3.1 - - - +
2010A LEU* 1.3 78.6 - - + +
2012A ALA* 1.3 57.1 + - - +
2014A LEU* 3.8 9.0 - - - +
2015A GLY* 2.9 28.2 + - - -
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Residues in contact with ALA2012 (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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2008A LYS 3.4 18.0 + - - +
2009A ALA* 3.5 9.9 - - - +
2010A LEU 3.2 0.4 - - - -
2011A ALA* 1.3 80.1 - - - +
2013A ALA* 1.3 55.4 + - - +
2015A GLY* 4.0 0.9 - - - -
2016A GLN* 3.1 26.7 + - - +
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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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1131A ALA* 4.4 10.3 - - + +
1132A LEU* 5.0 3.1 - - + -
1135A SER* 3.7 23.1 - - - +
2009A ALA 3.1 12.3 + - - +
2010A LEU* 2.9 9.6 + - - +
2012A ALA* 1.3 75.7 - - - +
2014A LEU* 1.3 58.7 + - + +
2016A GLN* 3.2 9.2 + - + +
2017A ILE* 2.8 48.1 + - + +
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Residues in contact with LEU2014 (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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1115A LEU* 3.8 31.9 - - + -
1132A LEU* 4.6 12.3 - - + -
2010A LEU* 2.9 51.6 + - + +
2011A ALA* 3.9 7.9 - - - +
2013A ALA* 1.3 75.7 - - - +
2015A GLY* 1.3 56.8 + - - +
2017A ILE* 3.4 7.7 + - - +
2018A GLU* 3.0 38.5 + - + +
2026A ILE* 4.4 18.4 - - + +
2027A MET* 5.9 1.8 - - - -
2028A ARG* 5.4 9.0 - - - +
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Residues in contact with GLY2015 (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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2011A ALA 2.9 17.1 + - - -
2012A ALA* 4.1 1.1 - - - -
2014A LEU* 1.3 75.4 - - - +
2016A GLN* 1.3 57.6 + - - +
2018A GLU* 3.4 4.8 + - - +
2019A LYS* 3.0 32.2 + - - +
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Residues in contact with GLN2016 (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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1131A ALA* 5.3 7.9 - - + +
1134A ARG* 5.1 10.7 - - - +
2012A ALA 3.1 19.3 + - - +
2013A ALA* 3.4 10.5 - - - +
2015A GLY* 1.3 76.0 - - - +
2017A ILE* 1.3 66.1 + - + +
2019A LYS* 3.5 12.2 + - - +
2020A GLN* 3.1 50.4 + - - +
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Residues in contact with ILE2017 (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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1128A ILE* 3.9 33.0 - - + -
1131A ALA* 3.9 26.7 - - + -
1132A LEU* 3.9 29.8 - - + -
2013A ALA* 2.8 25.8 + - + +
2014A LEU* 3.7 8.1 - - - +
2015A GLY 3.3 0.2 - - - -
2016A GLN* 1.3 75.4 - - + +
2018A GLU* 1.3 51.6 + - - +
2020A GLN* 3.1 4.6 + - - -
2021A PHE* 2.7 44.1 + - + +
2025A SER* 4.0 7.6 - - - +
2026A ILE* 3.7 24.7 - - + -
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Residues in contact with GLU2018 (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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2014A LEU* 3.0 23.7 + - + +
2015A GLY* 4.0 4.9 - - - +
2017A ILE* 1.3 75.9 - - - +
2019A LYS* 1.3 57.6 + - - +
2022A GLY* 2.9 39.0 + - - +
2023A LYS 2.9 22.9 - - - +
2024A GLY* 3.6 8.3 - - - -
2025A SER* 3.7 4.6 + - - +
2026A ILE* 2.9 35.1 - - + +
2027A MET* 5.1 1.2 - - - +
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Residues in contact with LYS2019 (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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2015A GLY 3.0 18.2 + - - +
2016A GLN* 3.8 12.6 - - - +
2018A GLU* 1.3 76.8 - - - +
2020A GLN* 1.3 63.2 + - - +
2022A GLY* 4.8 0.5 + - - -
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Residues in contact with GLN2020 (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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158A GLU* 3.4 27.3 + - - +
1127A GLU* 4.5 5.7 - - - +
2016A GLN* 3.1 44.0 + - - +
2017A ILE* 3.1 5.3 + - - +
2019A LYS* 1.3 83.2 - - + +
2021A PHE* 1.3 90.6 + - + +
2022A GLY 3.6 1.2 + - - -
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Residues in contact with PHE2021 (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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158A GLU* 3.9 12.1 - - - -
1120A ASP* 5.2 3.3 - - - +
1124A GLN* 3.6 41.0 + - + +
1127A GLU* 3.7 31.6 - - + -
1128A ILE* 4.3 14.1 - - + -
2017A ILE* 2.7 35.6 + - + +
2020A GLN* 1.3 104.0 - - + +
2022A GLY* 1.3 60.4 + - - +
2025A SER* 3.3 24.7 - - - +
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Residues in contact with GLY2022 (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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2018A GLU* 2.9 21.2 + - - +
2019A LYS 4.6 1.0 + - - -
2020A GLN 3.6 2.2 - - - -
2021A PHE* 1.3 80.0 - - - +
2023A LYS* 1.3 72.2 + - - +
2024A GLY 3.7 1.1 - - - -
2025A SER* 3.1 13.1 + - - -
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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