Contacts of the helix formed by residues 1776 - 1787 (chain X) in PDB entry 3COJ
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 PRO1776 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1701X LEU* 4.7 7.4 - - + -
1772X PHE 6.0 0.2 - - - +
1773X THR 4.9 1.1 - - - +
1774X ASN 4.5 2.0 - - - +
1775X MET* 1.3 85.5 - - + +
1777X THR* 1.3 67.7 + - - +
1778X ASP* 3.2 16.8 - - - +
1779X GLN* 2.8 34.9 + - + +
1780X LEU* 3.1 9.4 + - - +
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Residues in contact with THR1777 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1768X CYS* 3.8 19.3 - - + +
1770X GLY 4.4 5.9 + - - +
1771X PRO* 5.9 0.2 - - - +
1772X PHE* 3.7 39.0 + - + +
1775X MET 3.5 2.6 + - - -
1776X PRO* 1.3 69.8 - - - +
1778X ASP* 1.3 57.8 + - - +
1780X LEU* 3.3 6.6 + - - +
1781X GLU* 3.0 37.7 + - - +
1793X LYS* 6.1 1.6 - - - -
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Residues in contact with ASP1778 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1776X PRO* 3.4 17.7 - - - +
1777X THR* 1.3 74.5 - - - +
1779X GLN* 1.3 84.6 + - - +
1781X GLU* 3.3 18.1 + - - +
1782X TRP* 3.0 28.4 + - - +
1793X LYS* 5.7 1.1 - - - +
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Residues in contact with GLN1779 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1679X LEU* 5.3 8.7 - - - +
1680X ILE* 5.0 7.9 + - - +
1701X LEU* 3.7 31.0 - - + +
1705X LEU* 4.0 20.0 - - + +
1775X MET* 4.6 0.9 - - + -
1776X PRO* 2.8 33.1 + - + +
1778X ASP* 1.3 95.5 + - - +
1780X LEU* 1.3 60.5 + - - +
1782X TRP* 3.3 22.7 + - - +
1783X MET* 3.1 19.4 + - - +
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Residues in contact with LEU1780 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1768X CYS* 3.3 26.5 - - - -
1772X PHE* 3.5 42.6 - - + -
1775X MET* 3.6 30.4 - - + +
1776X PRO 3.1 4.3 + - - +
1777X THR* 3.6 6.3 - - - +
1779X GLN* 1.3 75.6 - - - +
1781X GLU* 1.3 63.4 + - - +
1783X MET* 2.9 20.1 + - + +
1784X VAL* 3.0 14.2 + - + +
1809X VAL* 5.0 2.2 - - + -
1835X ARG* 4.4 13.0 - - + -
1838X VAL* 3.9 34.8 - - + -
1839X LEU* 6.1 0.2 - - + -
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Residues in contact with GLU1781 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1768X CYS* 3.7 32.3 + - + +
1777X THR* 3.0 21.6 + - - +
1778X ASP* 3.3 25.1 + - - +
1780X LEU* 1.3 75.9 - - - +
1782X TRP* 1.3 57.2 + - - +
1784X VAL* 3.5 2.4 + - - +
1785X GLN* 2.9 25.8 + - - +
1791X VAL* 3.4 39.5 - - + +
1792X VAL 4.2 2.1 - - - +
1793X LYS* 3.1 48.4 + - - +
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Residues in contact with TRP1782 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1680X ILE* 4.2 16.6 - - + -
1681X THR* 3.8 25.8 - - - -
1682X GLU* 4.1 33.0 + - + -
1705X LEU* 3.6 34.3 - - + -
1711X LYS* 5.6 3.6 - - - -
1778X ASP 3.0 13.0 + - - +
1779X GLN* 3.4 24.7 - - - +
1780X LEU 3.1 0.2 - - - -
1781X GLU* 1.3 75.0 - - - +
1783X MET* 1.3 64.6 + - - +
1785X GLN* 3.2 16.7 + - + +
1786X LEU* 3.0 58.0 + - + +
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Residues in contact with MET1783 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1701X LEU* 4.7 7.0 - - + -
1704X PHE* 3.4 45.8 - - + +
1705X LEU* 3.7 18.1 - - + +
1708X ALA* 3.9 6.0 - - + +
1775X MET* 3.8 33.7 - - + -
1779X GLN 3.1 7.4 + - - +
1780X LEU* 2.9 12.2 + - + +
1782X TRP* 1.3 75.1 - - - +
1784X VAL* 1.3 61.8 + - - +
1786X LEU* 3.5 5.9 + - - +
1787X CYS* 3.4 28.4 + - - -
1838X VAL* 4.2 14.6 - - + -
1839X LEU* 4.0 7.4 - - + -
1842X VAL* 3.6 24.5 - - + -
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Residues in contact with VAL1784 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1761X PHE* 3.8 17.7 - - + -
1766X ILE* 3.5 36.1 - - + -
1768X CYS* 5.6 0.2 - - - -
1780X LEU* 3.0 12.9 + - + +
1781X GLU* 3.6 11.4 - - - +
1783X MET* 1.3 75.3 - - - +
1785X GLN* 1.3 67.6 + - - +
1787X CYS* 3.0 15.2 + - - +
1789X ALA* 3.3 34.2 + - + +
1791X VAL* 3.6 18.8 - - + -
1838X VAL* 3.9 24.0 - - + -
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Residues in contact with GLN1785 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1781X GLU* 2.9 21.3 + - - +
1782X TRP* 3.2 21.5 + - + +
1784X VAL* 1.3 76.0 - - - +
1786X LEU* 1.3 62.9 - - + +
1788X GLY* 3.4 10.4 + - - -
1789X ALA 3.3 20.5 + - - +
1790X SER* 5.1 1.2 - - - -
1791X VAL* 3.5 27.1 + - + +
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Residues in contact with LEU1786 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1682X GLU* 5.2 6.5 - - + +
1705X LEU* 4.5 8.1 - - + +
1708X ALA* 3.9 33.0 - - + +
1709X GLY* 4.5 11.7 - - - +
1711X LYS* 6.1 1.1 - - - +
1759X LYS* 2.9 29.7 + - - +
1782X TRP* 3.0 68.0 + - + +
1783X MET* 3.6 7.4 - - - +
1784X VAL 3.2 0.2 - - - -
1785X GLN* 1.3 78.8 - - + +
1787X CYS* 1.3 58.0 + - - +
1788X GLY 3.1 2.5 + - - -
1845X TYR* 4.9 0.5 + - - -
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Residues in contact with CYS1787 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1708X ALA* 3.7 20.4 - - - -
1759X LYS* 3.7 6.5 - - - -
1760X ILE* 3.5 17.9 + - + -
1761X PHE* 2.8 38.0 + - + +
1783X MET 3.4 14.6 + - - -
1784X VAL 3.0 4.1 + - - +
1786X LEU* 1.3 75.6 - - - +
1788X GLY* 1.3 53.8 + - - -
1789X ALA 3.2 7.7 + - - -
1842X VAL* 3.4 27.6 - - - -
1845X TYR* 3.9 20.0 - - + -
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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