Contacts of the helix formed by residues 2002 - 2022 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2001D ALA* 1.3 86.2 - - + +
2003D ASP* 1.3 61.7 + - + +
2004D GLU 3.4 1.0 + - - -
2005D ASN* 3.9 13.3 + - - +
2006D LYS* 3.9 14.7 - - + +
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Residues in contact with ASP2003 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2001D ALA 4.2 4.0 + - - -
2002D ILE* 1.3 75.1 - - + +
2004D GLU* 1.3 89.0 + - - +
2005D ASN 3.3 0.9 - - - -
2006D LYS* 3.4 20.1 - - + +
2007D GLN* 3.4 27.3 + - - +
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Residues in contact with GLU2004 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2001D ALA* 3.2 35.8 + - - +
2002D ILE 3.4 0.6 - - - -
2003D ASP* 1.3 90.3 + - - +
2005D ASN* 1.3 63.0 + - - +
2006D LYS 3.2 0.2 - - - -
2007D GLN* 3.6 13.7 + - - +
2008D LYS* 3.3 20.3 + - - +
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Residues in contact with ASN2005 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2001D ALA 3.3 19.8 + - - -
2002D ILE* 3.9 10.0 + - - +
2003D ASP 3.3 0.2 - - - -
2004D GLU* 1.3 79.2 - - - +
2006D LYS* 1.3 62.0 + - + +
2008D LYS* 3.4 24.4 - - - +
2009D ALA* 3.2 22.0 + - - +
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Residues in contact with LYS2006 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087D GLY 5.3 4.4 + - - -
1089D THR* 4.7 5.1 + - - -
1136D GLY 4.0 18.4 - - - +
1137D ALA* 3.4 28.4 + - + +
1139D ASP* 3.3 32.1 + - - -
2002D ILE* 3.9 13.2 - - + +
2003D ASP* 3.4 23.7 + - + +
2004D GLU 3.2 0.8 - - - -
2005D ASN* 1.3 78.6 - - + +
2007D GLN* 1.3 52.5 + - + +
2009D ALA* 3.2 5.0 + - - -
2010D LEU* 2.7 35.1 + - - +
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Residues in contact with GLN2007 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2003D ASP* 3.4 14.5 + - - +
2004D GLU* 3.6 14.6 + - - +
2005D ASN 3.4 0.2 - - - -
2006D LYS* 1.3 74.3 - - + +
2008D LYS* 1.3 60.1 + - - +
2010D LEU* 3.5 18.1 - - + +
2011D ALA* 2.9 33.8 + - - +
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Residues in contact with LYS2008 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2004D GLU 3.3 12.2 + - - +
2005D ASN* 3.4 26.9 - - - +
2007D GLN* 1.3 79.1 - - - +
2009D ALA* 1.3 60.3 + - - +
2011D ALA* 4.4 2.9 - - - +
2012D ALA* 3.4 19.4 + - - +
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Residues in contact with ALA2009 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135D SER* 3.6 25.5 - - - +
1136D GLY 5.9 0.2 - - - -
1137D ALA* 4.4 1.8 - - + -
2005D ASN 3.2 8.6 + - - +
2006D LYS* 3.2 10.1 + - - +
2008D LYS* 1.3 78.0 - - - +
2010D LEU* 1.3 64.7 + - - +
2012D ALA* 3.5 7.0 - - - +
2013D ALA* 3.1 22.7 + - - +
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Residues in contact with LEU2010 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089D THR* 4.5 11.0 - - + +
1115D LEU* 3.8 20.2 - - + -
1132D LEU* 5.4 0.7 - - + -
1135D SER* 5.5 0.2 - - - +
1137D ALA* 3.6 24.0 - - + +
1138D VAL* 4.2 10.3 - - + -
2006D LYS 2.7 20.0 + - - +
2007D GLN* 3.2 22.4 + - + +
2009D ALA* 1.3 70.7 - - - +
2011D ALA* 1.3 62.5 + - + +
2013D ALA* 2.9 7.5 + - + +
2014D LEU* 2.9 55.9 + - + +
2028D ARG* 6.3 1.3 - - - +
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Residues in contact with ALA2011 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2007D GLN 2.9 16.6 + - - +
2008D LYS* 4.4 3.1 - - - +
2010D LEU* 1.3 78.3 - - + +
2012D ALA* 1.3 57.6 + - - +
2014D LEU* 3.8 8.6 - - - +
2015D GLY* 2.9 28.1 + - - -
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Residues in contact with ALA2012 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2008D LYS 3.4 18.8 + - - +
2009D ALA* 3.5 9.9 - - - +
2010D LEU 3.1 0.6 - - - -
2011D ALA* 1.3 79.3 - - - +
2013D ALA* 1.3 56.8 + - - +
2015D GLY* 4.0 1.1 - - - -
2016D GLN* 3.1 26.7 + - - +
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Residues in contact with ALA2013 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131D ALA* 4.4 11.0 - - + +
1132D LEU* 4.9 6.5 - - + -
1135D SER* 3.7 23.1 - - - +
2009D ALA 3.1 12.7 + - - +
2010D LEU* 2.9 9.6 + - - +
2012D ALA* 1.3 75.7 - - - +
2014D LEU* 1.3 54.1 + - - +
2016D GLN* 3.2 9.3 + - + +
2017D ILE* 2.8 47.6 + - + +
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Residues in contact with LEU2014 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115D LEU* 3.7 32.1 - - + -
1132D LEU* 4.5 12.3 - - + -
2010D LEU* 2.9 52.0 + - + +
2011D ALA* 3.9 7.9 - - - +
2013D ALA* 1.3 76.2 - - - +
2015D GLY* 1.3 56.5 + - - +
2017D ILE* 3.4 7.2 + - - +
2018D GLU* 3.0 37.9 + - + +
2026D ILE* 4.4 17.3 - - + +
2027D MET* 5.9 1.6 - - - -
2028D ARG* 5.4 8.5 - - - +
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Residues in contact with GLY2015 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2011D ALA 2.9 17.1 + - - -
2012D ALA 4.0 0.9 - - - -
2014D LEU* 1.3 77.0 - - - +
2016D GLN* 1.3 55.7 - - - +
2018D GLU* 3.4 4.9 + - - +
2019D LYS* 3.0 32.3 + - - +
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Residues in contact with GLN2016 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131D ALA* 5.2 8.8 - - + +
1134D ARG* 5.1 9.6 - - - +
2012D ALA 3.1 19.1 + - - +
2013D ALA* 3.2 9.6 + - - +
2015D GLY* 1.3 76.7 - - - +
2017D ILE* 1.3 66.3 + - + +
2019D LYS* 3.5 11.5 + - - +
2020D GLN* 3.1 50.9 + - - +
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Residues in contact with ILE2017 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128D ILE* 3.9 33.0 - - + -
1131D ALA* 4.0 25.8 - - + -
1132D LEU* 3.9 30.5 - - + -
2013D ALA* 2.8 26.3 + - + +
2014D LEU* 3.7 8.5 - - - +
2015D GLY 3.3 0.2 - - - -
2016D GLN* 1.3 75.0 - - + +
2018D GLU* 1.3 53.3 + - - +
2020D GLN* 3.1 4.5 + - - -
2021D PHE* 2.7 43.6 + - + +
2025D SER* 4.0 8.3 - - - +
2026D ILE* 3.7 23.8 - - + -
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Residues in contact with GLU2018 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2014D LEU* 3.0 22.2 + - + +
2015D GLY* 4.0 5.1 - - - +
2017D ILE* 1.3 75.6 - - - +
2019D LYS* 1.3 58.1 + - - +
2022D GLY* 2.9 39.2 + - - +
2023D LYS 2.9 22.3 - - - +
2024D GLY* 3.6 7.8 - - - -
2025D SER* 3.7 4.2 + - - +
2026D ILE* 2.9 34.9 - - + +
2027D MET* 5.1 0.9 - - - +
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Residues in contact with LYS2019 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2015D GLY 3.0 18.6 + - - +
2016D GLN* 3.8 12.8 - - - +
2018D GLU* 1.3 77.1 - - - +
2020D GLN* 1.3 62.5 + - - +
2022D GLY 4.8 0.7 + - - -
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Residues in contact with GLN2020 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D GLU* 3.8 23.0 + - - +
1127D GLU* 4.6 4.0 - - - +
2016D GLN* 3.1 45.1 + - - +
2017D ILE* 3.1 5.0 + - - +
2019D LYS* 1.3 83.0 - - - +
2021D PHE* 1.3 92.8 + - + +
2022D GLY 3.6 0.7 - - - -
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Residues in contact with PHE2021 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D GLU* 4.4 4.5 - - - -
1120D ASP* 5.2 3.8 - - - +
1124D GLN* 3.5 39.7 + - + +
1127D GLU* 3.8 34.3 - - + -
1128D ILE* 4.3 14.6 - - + -
2017D ILE* 2.7 37.1 + - + +
2020D GLN* 1.3 106.0 - - + +
2022D GLY* 1.3 59.9 + - - +
2025D SER* 3.3 25.5 - - - +
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Residues in contact with GLY2022 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2018D GLU* 2.9 21.6 + - - +
2019D LYS 4.6 1.0 + - - -
2020D GLN 3.6 2.4 + - - -
2021D PHE* 1.3 78.1 - - - +
2023D LYS* 1.3 71.5 + - - +
2024D GLY 3.7 0.9 - - - -
2025D SER* 3.1 13.4 + - - -
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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