Contacts of the helix formed by residues 1844 - 1863 (chain A) in PDB entry 5G04
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 PHE1844 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1770A LEU* 5.4 7.0 - - + -
1773A SER* 6.2 4.0 - - - -
1774A VAL* 4.0 15.9 - - + -
1777A GLU* 3.2 32.1 - - - +
1790A TYR* 3.7 37.9 - + - -
1793A MET* 3.9 21.5 - - + -
1794A ASP* 3.0 28.9 - - - -
1797A ILE* 5.5 2.0 - - + -
1840A MET* 5.3 0.9 - - + -
1842A SER* 3.0 2.3 + - - +
1843A GLU* 1.3 77.3 - - - +
1845A LEU* 1.3 61.2 + - + +
1846A PRO* 3.5 0.7 - - - -
1847A VAL* 3.3 9.1 + - + +
1848A VAL* 3.0 44.4 + - + +
163N PHE* 5.4 13.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1845 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1793A MET* 3.7 25.4 - - + -
1817A VAL* 3.9 17.7 - - + -
1818A LEU* 4.5 11.3 - - + +
1821A PHE* 3.4 43.5 - - + -
1840A MET* 3.5 49.6 - - + +
1842A SER 3.6 4.9 + - - +
1844A PHE* 1.3 78.5 - - + +
1846A PRO* 1.3 72.8 - - + +
1848A VAL* 3.3 5.8 + - - +
1849A LYS* 3.3 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1846 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1821A PHE* 4.8 15.4 - - + -
1842A SER 4.1 1.6 - - - +
1843A GLU* 3.7 29.4 - - + +
1844A PHE 3.7 0.2 - - - -
1845A LEU* 1.3 93.8 - - + +
1847A VAL* 1.3 59.3 + - + +
1849A LYS* 3.2 11.9 + - + +
1850A CYS* 3.1 32.8 + - - -
155N THR* 3.8 19.3 - - + +
156N MET* 3.8 31.9 - - + +
159N GLY* 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1847 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1843A GLU 3.4 22.9 - - - +
1844A PHE* 3.3 9.4 + - + +
1845A LEU 3.3 0.6 - - - -
1846A PRO* 1.3 75.6 - - + +
1848A VAL* 1.3 59.8 + - + +
1850A CYS* 3.3 11.2 + - + +
1851A THR* 3.0 37.6 + - + +
155N THR 5.3 0.2 - - - +
159N GLY* 3.8 36.3 - - - +
162N PHE 5.9 0.4 - - - +
163N PHE* 4.0 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1848 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1793A MET* 3.9 26.7 - - + -
1797A ILE* 3.9 27.4 - - + -
1814A ILE* 4.7 11.4 - - + -
1818A LEU* 4.6 12.1 - - + -
1844A PHE* 3.0 48.1 + - + +
1845A LEU 3.3 6.5 + - - +
1847A VAL* 1.3 71.5 - - + +
1849A LYS* 1.3 57.5 + - - +
1851A THR* 2.7 20.3 + - - -
1852A ILE* 2.8 29.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1849 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1818A LEU* 3.6 29.7 - - + +
1821A PHE* 5.8 8.3 - - + -
1845A LEU 3.3 7.5 + - - +
1846A PRO* 3.2 13.8 + - + +
1848A VAL* 1.3 76.4 - - - +
1850A CYS* 1.3 58.6 - - - +
1852A ILE* 3.1 24.4 - - - +
1853A ASP* 3.2 30.7 + - - +
1891A TYR* 3.3 20.4 + - - +
1918A LYS 5.0 4.0 + - - -
77N GLU* 4.3 13.5 - - - -
78N VAL* 4.4 18.2 - - - +
81N ASN* 5.6 1.8 - - - +
156N MET* 4.9 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1850 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1846A PRO 3.1 26.4 + - - -
1847A VAL* 3.4 14.8 - - + +
1849A LYS* 1.3 73.8 - - - +
1851A THR* 1.3 55.0 + - + +
1853A ASP* 3.2 2.6 + - - +
1854A ASN* 2.6 39.1 + - + +
81N ASN* 3.4 37.6 + - - +
156N MET* 3.7 15.7 - - - -
159N GLY* 6.0 1.1 - - - -
160N VAL* 4.4 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1851 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1797A ILE* 3.8 29.5 - - + +
1800A LEU* 5.9 0.2 - - - -
1847A VAL* 3.0 24.3 + - + +
1848A VAL* 2.7 27.0 + - - -
1850A CYS* 1.3 72.0 - - + +
1852A ILE* 1.3 49.5 + - - +
1854A ASN* 3.4 9.1 + - + +
1855A THR* 2.5 39.5 + - - -
163N PHE* 6.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1852 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1797A ILE* 3.5 26.7 - - + -
1800A LEU* 3.5 26.7 - - + -
1811A LEU* 5.1 5.2 - - + -
1814A ILE* 4.9 15.7 - - + -
1848A VAL* 2.8 29.4 - - + +
1849A LYS* 3.1 11.4 - - - +
1851A THR* 1.3 71.8 - - - +
1853A ASP* 1.3 63.1 + - - +
1855A THR* 3.3 4.9 + - - -
1856A LEU* 3.1 40.9 + - + +
1891A TYR* 3.9 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1853 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1849A LYS* 3.2 37.3 + - - +
1850A CYS* 3.2 7.2 + - - +
1852A ILE* 1.3 76.5 - - - +
1854A ASN* 1.3 56.6 + - - +
1856A LEU* 4.2 4.0 - - - +
1857A ASP* 2.8 40.8 + - - +
1891A TYR* 3.1 32.1 + - - -
1892A HIS* 4.3 8.6 - - + -
1918A LYS* 6.2 2.9 - - - -
81N ASN* 4.0 16.1 + - - +
82N ASP* 5.9 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1854 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1850A CYS 2.6 21.8 + - - +
1851A THR* 3.4 12.3 + - - +
1853A ASP* 1.3 72.6 - - - +
1855A THR* 1.3 65.5 + - - +
1857A ASP* 3.6 6.7 - - - +
1858A GLN* 3.4 23.5 + - - +
85N ALA* 4.5 17.6 - - + +
160N VAL* 6.0 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1855 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1797A ILE 5.1 1.9 + - - -
1800A LEU* 3.8 37.2 - - + +
1801A GLY* 4.1 10.3 + - - +
1851A THR* 2.5 24.4 + - - -
1852A ILE* 3.5 8.4 - - - -
1853A ASP 3.3 0.4 - - - -
1854A ASN* 1.3 76.1 + - - +
1856A LEU* 1.3 75.0 + - + +
1858A GLN* 3.2 27.8 + - + +
1859A TRP* 3.3 8.6 + - + +
1884A MET* 6.3 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1856 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1800A LEU* 3.9 23.6 - - + -
1811A LEU* 6.4 0.4 - - + -
1852A ILE* 3.1 32.5 + - + +
1853A ASP* 4.2 2.7 - - - +
1855A THR* 1.3 88.2 - - + +
1857A ASP* 1.3 65.8 + - - +
1859A TRP* 3.2 14.4 + - + +
1860A LEU* 3.0 31.1 + - + +
1884A MET* 5.7 5.4 - - + +
1887A CYS* 4.6 9.6 - - - +
1888A PHE* 4.3 29.8 - - + +
1891A TYR* 4.7 4.9 - - + -
1892A HIS* 3.5 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1857 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1853A ASP* 2.8 22.3 + - - +
1854A ASN* 3.6 8.7 - - - +
1856A LEU* 1.3 77.7 - - - +
1858A GLN* 1.3 62.5 + - - +
1860A LEU* 3.5 12.9 + - - +
1861A GLN* 3.3 39.7 + - - +
82N ASP* 4.2 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1858 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1854A ASN* 3.4 13.6 + - - +
1855A THR* 3.2 21.9 + - - +
1857A ASP* 1.3 77.9 - - + +
1859A TRP* 1.3 73.2 + - - +
1861A GLN* 3.4 9.6 + - - +
1862A VAL* 3.0 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1859 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1855A THR* 3.3 12.7 + - + +
1856A LEU* 3.2 19.4 + - + +
1858A GLN* 1.3 84.2 - - - +
1860A LEU* 1.3 84.9 + - + +
1862A VAL* 3.3 6.6 + - + +
1863A GLY 2.6 45.3 + - - +
1864A GLY* 4.4 9.5 - - - -
1868A VAL* 3.7 24.2 - - + -
1881A GLN* 4.1 24.4 - - + +
1884A MET* 3.7 46.4 - - + +
1885A LEU* 4.1 16.8 - - + -
1888A PHE* 4.1 20.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1860 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1856A LEU* 3.0 23.5 + - + +
1857A ASP* 3.6 12.1 - - - +
1859A TRP* 1.3 97.1 - - + +
1861A GLN* 1.3 61.9 + - + +
1863A GLY* 3.3 9.8 + - - +
1865A ASP* 3.1 47.5 - - - +
1868A VAL* 4.2 15.0 - - + -
1888A PHE* 3.7 35.4 - - + -
1914A GLU* 4.7 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1861 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1857A ASP* 3.3 28.3 + - - +
1858A GLN* 3.5 11.0 - - - +
1859A TRP 3.3 0.4 - - - -
1860A LEU* 1.3 79.4 - - + +
1862A VAL* 1.3 62.7 + - - +
1863A GLY* 3.5 0.9 + - - -
1865A ASP* 5.4 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1862 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1858A GLN* 3.0 21.4 + - - +
1859A TRP* 3.3 8.9 + - + +
1861A GLN* 1.3 75.4 - - - +
1863A GLY* 1.3 57.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1863 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1859A TRP* 2.6 36.2 + - - +
1860A LEU* 3.3 3.5 - - - +
1861A GLN 3.3 2.6 - - - -
1862A VAL* 1.3 79.5 - - - +
1864A GLY* 1.3 58.4 + - - -
1865A ASP* 3.0 12.3 + - - -
----------------------------------------------------------
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