Contacts of the helix formed by residues 1773 - 1784 (chain C) in PDB entry 5JCZ
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 THR1773 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1771C ALA 5.7 0.7 - - - +
1772C LEU* 1.3 76.4 - - - +
1774C THR* 1.3 64.6 + - - +
1775C ALA 3.6 1.9 + - - -
1776C GLN* 3.1 26.9 + - - +
1777C ILE* 3.1 21.5 + - - +
1809C ARG* 4.1 1.1 - - - -
1811C ASP* 3.7 9.4 - - + -
1812C SER* 3.3 42.0 - - - +
1814C GLN* 2.6 33.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1774 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1773C THR* 1.3 72.7 - - - +
1775C ALA* 1.3 64.1 + - - +
1777C ILE* 3.4 1.7 + - - +
1778C VAL* 3.0 35.0 + - + +
1803C GLN* 5.4 6.3 - - + +
1806C LEU* 3.8 49.9 + - + +
1809C ARG* 4.0 2.6 - - - +
1811C ASP* 2.8 31.1 + - - -
1812C SER 4.8 0.2 + - - -
1524E ASP* 5.9 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1775 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1773C THR* 3.2 1.4 + - - +
1774C THR* 1.3 80.0 - - - +
1776C GLN* 1.3 57.1 + - - +
1778C VAL* 4.2 4.1 - - - +
1779C LYS* 3.1 29.6 + - - +
1812C SER 5.3 0.6 + - - -
1813C PRO* 3.9 5.8 - - + +
1814C GLN 3.6 18.2 - - - +
1815C LEU* 3.6 9.9 - - + +
1524E ASP* 3.5 30.8 - - + +
1528E ARG* 3.7 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1776 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1699C LEU* 4.7 2.0 - - + +
1703C LEU* 3.6 22.4 - - + +
1771C ALA 4.5 1.9 - - - +
1772C LEU* 3.6 25.6 - - + +
1773C THR* 3.1 35.8 + - - +
1774C THR 3.2 0.4 - - - -
1775C ALA* 1.3 75.8 - - - +
1777C ILE* 1.3 64.7 + - - +
1779C LYS* 3.4 1.7 + - - +
1780C VAL* 3.1 30.4 + - + +
1814C GLN* 3.1 31.5 + - - +
1815C LEU* 2.8 31.6 + - - +
1817C MET* 4.1 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1777 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1751C LEU* 3.9 17.2 - - + +
1765C ILE* 4.3 13.0 - - + +
1766C CYS* 5.6 0.4 - - - -
1769C CYS* 3.6 34.1 - - + +
1772C LEU* 3.7 17.7 - - + +
1773C THR 3.1 17.5 + - - +
1774C THR 3.4 3.8 + - - +
1776C GLN* 1.3 76.4 - - - +
1778C VAL* 1.3 62.1 + - - +
1780C VAL* 3.3 4.9 + - - +
1781C LEU* 3.1 37.5 + - + +
1802C ILE* 4.2 14.8 - - + -
1806C LEU* 3.9 20.0 - - + -
1809C ARG* 3.9 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1778 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1774C THR* 3.0 30.0 + - + +
1775C ALA* 4.2 3.6 - - - +
1777C ILE* 1.3 77.4 - - + +
1779C LYS* 1.3 57.5 + - - +
1781C LEU* 3.4 8.0 + - - +
1782C ASN* 2.9 45.8 + - - +
1799C ILE* 3.9 15.3 - - + -
1802C ILE* 4.6 14.1 - - + -
1803C GLN* 3.9 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1779 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1703C LEU* 3.5 33.9 - - + +
1704C LEU* 5.6 2.7 - - - +
1775C ALA 3.1 21.1 + - - +
1776C GLN 3.6 5.6 - - - +
1777C ILE 3.2 0.2 - - - -
1778C VAL* 1.3 77.7 - - - +
1780C VAL* 1.3 57.3 + - - +
1782C ASN* 3.3 9.7 + - + +
1783C LEU* 2.9 52.5 + - + +
1815C LEU* 3.7 29.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1780 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1699C LEU* 5.6 0.7 - - + -
1702C LEU* 5.0 11.0 - - + +
1703C LEU* 3.7 17.5 - - + -
1709C CYS* 4.4 5.6 - - - -
1748C ALA* 4.8 15.0 - - + +
1751C LEU* 3.7 27.6 - - + -
1752C LEU* 3.7 30.3 - - + -
1756C LYS* 6.4 0.7 - - - -
1772C LEU* 5.7 2.5 - - + -
1776C GLN 3.1 17.1 + - - +
1777C ILE 3.7 4.0 - - - +
1779C LYS* 1.3 75.4 - - - +
1781C LEU* 1.3 60.2 + - + +
1783C LEU* 3.3 6.7 + - - +
1784C TYR* 2.9 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1781 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1751C LEU* 4.1 19.5 - - + -
1756C LYS* 4.0 31.4 - - + -
1765C ILE* 4.6 2.2 - - + -
1777C ILE* 3.1 34.2 + - + +
1778C VAL* 3.7 7.2 - - - +
1780C VAL* 1.3 77.6 - - + +
1782C ASN* 1.3 61.8 + - - +
1784C TYR* 3.5 17.2 + - - +
1793C ARG* 5.5 1.0 + - - -
1794C VAL* 3.8 21.1 - - + +
1798C PHE* 4.5 7.9 - - + -
1799C ILE* 3.9 22.3 - - + +
1802C ILE* 3.8 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1782 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1706C LYS* 4.9 2.6 - - - -
1778C VAL* 2.9 41.9 + - - +
1779C LYS* 3.6 11.6 - - + +
1781C LEU* 1.3 76.9 - - - +
1783C LEU* 1.3 64.8 + - + +
1784C TYR 3.5 0.5 + - - -
1793C ARG* 3.5 22.3 + - - +
1796C VAL* 5.9 2.8 - - - +
1799C ILE* 3.2 22.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1783 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1702C LEU 3.7 10.3 - - - +
1703C LEU* 3.4 37.2 - - - +
1704C LEU 3.8 7.0 - - - +
1705C ARG 4.0 9.2 - - - +
1706C LYS* 3.6 42.8 - - + +
1709C CYS* 3.7 15.3 - - - +
1779C LYS* 2.9 38.4 + - + +
1781C LEU 3.3 0.2 - - - -
1782C ASN* 1.3 79.6 - - + +
1784C TYR* 1.3 65.9 + - - +
1785C THR* 2.9 14.8 + - - -
1793C ARG* 4.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1784 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1709C CYS* 3.5 11.0 - - - -
1710C SER* 3.6 18.1 - - - -
1711C TRP* 3.5 30.8 + - - +
1752C LEU* 3.4 37.8 + - + -
1756C LYS* 3.8 20.0 + - + -
1780C VAL* 2.9 15.4 + - + +
1781C LEU* 3.5 13.2 - - - +
1782C ASN 3.3 2.5 - - - +
1783C LEU* 1.3 74.4 - - - +
1785C THR* 1.3 57.4 + - - +
1786C PRO* 4.1 25.0 - - + +
1791C GLU* 4.9 1.7 + - - -
1792C GLU 4.7 7.0 - - - -
1793C ARG* 3.3 30.5 + - - +
1794C VAL* 3.9 24.4 + - + -
73D TYR* 5.6 3.5 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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