Contacts of the helix formed by residues 1878 - 1893 (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 GLU1878 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1867A CYS* 4.7 15.9 - - - -
1877A LEU* 1.3 77.5 - - - +
1879A GLU* 1.3 56.3 + - - +
1880A SER* 3.7 16.3 + - - +
1881A GLN* 2.9 23.6 + - + +
1882A LEU* 2.7 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1879 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1877A LEU 4.4 0.4 + - - -
1878A GLU* 1.3 71.7 - - - +
1880A SER* 1.3 62.6 + - - +
1882A LEU* 3.3 33.4 - - + +
1883A SER* 4.0 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1880 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1878A GLU* 3.7 18.0 + - - +
1879A GLU* 1.3 76.0 - - - +
1881A GLN* 1.3 72.7 + - - +
1882A LEU 3.5 0.3 + - - -
1883A SER* 3.8 13.7 + - - -
1884A MET* 4.5 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1881 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1859A TRP* 4.1 19.5 - - + +
1864A GLY* 4.5 4.6 + - - -
1867A CYS* 3.2 37.5 + - + +
1868A VAL* 3.8 3.8 - - - +
1877A LEU* 2.9 34.7 - - - +
1878A GLU* 2.9 39.8 + - + +
1880A SER* 1.3 80.6 + - - +
1882A LEU* 1.3 64.9 + - - +
1884A MET* 3.1 9.2 + - - +
1885A LEU* 3.0 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1882 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807A TYR* 2.9 46.4 + - + +
811A PRO* 4.1 11.8 - - + +
812A THR* 4.2 28.0 - - + +
814A VAL 4.9 10.5 - - - -
1877A LEU* 5.6 4.0 - - + -
1878A GLU 2.7 20.7 + - - +
1879A GLU* 3.3 21.3 - - + +
1880A SER 3.3 0.4 - - - -
1881A GLN* 1.3 72.5 - - - +
1883A SER* 1.3 78.8 + - - +
1885A LEU* 3.5 3.3 + - - -
1886A ALA* 3.2 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1883 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811A PRO* 4.4 2.5 - - - -
1803A ARG 4.4 11.1 + - - -
1805A MET 5.2 0.3 + - - -
1806A SER* 2.9 39.3 + - - -
1808A THR* 4.9 0.3 - - - +
1879A GLU 5.0 0.9 - - - -
1880A SER 3.8 10.7 + - - -
1881A GLN 3.2 0.4 + - - -
1882A LEU* 1.3 91.4 - - - +
1884A MET* 1.3 69.4 + - - +
1886A ALA* 3.5 11.4 - - - +
1887A CYS* 3.8 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1884 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1800A LEU* 5.2 6.7 - - - +
1803A ARG* 3.8 33.2 - - + +
1855A THR* 6.3 2.0 - - - -
1856A LEU* 5.7 5.3 - - + +
1859A TRP* 3.7 51.7 - - + +
1880A SER 5.1 7.6 - - - +
1881A GLN* 3.1 9.6 + - - +
1883A SER* 1.3 84.7 - - - +
1885A LEU* 1.3 67.2 + - - +
1887A CYS* 3.0 32.0 - - - -
1888A PHE* 3.3 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1885 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807A TYR* 3.7 11.4 - - + +
1859A TRP* 4.1 10.4 - - + -
1867A CYS 4.9 0.2 - - - +
1868A VAL* 4.7 11.2 - - + -
1871A TYR* 3.9 26.9 - - + -
1877A LEU* 2.9 41.1 - - + -
1881A GLN* 3.0 36.2 + - - +
1882A LEU* 3.7 5.6 - - - +
1884A MET* 1.3 74.3 - - - +
1886A ALA* 1.3 69.5 + - - +
1888A PHE* 3.0 7.1 + - + +
1889A LEU* 2.8 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1886 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807A TYR* 4.0 18.4 + - - +
808A ARG* 3.9 17.2 - - - +
811A PRO* 4.0 18.6 - - + -
1808A THR* 4.5 6.7 - - + -
1882A LEU 3.2 10.9 + - - +
1883A SER 3.5 11.7 - - - +
1884A MET 3.3 0.2 - - - -
1885A LEU* 1.3 82.5 - - - +
1887A CYS* 1.3 61.5 + - - +
1889A LEU* 3.3 4.2 + - - +
1890A VAL* 3.1 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1887 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1800A LEU* 4.0 24.5 - - + -
1808A THR* 3.8 19.2 - - + +
1811A LEU* 3.4 30.4 - - + +
1856A LEU* 4.6 11.4 - - - -
1883A SER 3.8 3.2 + - - +
1884A MET* 3.0 35.6 + - - -
1885A LEU 3.3 0.6 - - - -
1886A ALA* 1.3 76.1 - - - +
1888A PHE* 1.3 60.5 + - - +
1890A VAL* 3.3 2.5 + - - -
1891A TYR* 3.0 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1888 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1856A LEU* 4.3 18.2 - - + -
1859A TRP* 4.1 20.4 - + + -
1860A LEU* 3.7 32.3 - - + -
1868A VAL* 4.8 19.5 - - + -
1884A MET 3.3 11.8 + - - +
1885A LEU* 3.0 14.4 + - + +
1887A CYS* 1.3 76.7 - - - +
1889A LEU* 1.3 63.2 + - - +
1891A TYR 3.2 0.9 + - - -
1892A HIS* 2.8 75.2 + + + +
1894A VAL* 4.2 12.3 - - + -
1914A GLU* 5.0 12.3 - - + -
1917A PHE* 4.9 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1889 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807A TYR* 5.9 0.4 - - + -
808A ARG* 3.5 29.6 + - - +
1871A TYR* 4.2 6.3 - - + +
1885A LEU* 2.8 34.4 + - + +
1886A ALA* 3.7 5.6 - - - +
1888A PHE* 1.3 74.2 - - - +
1890A VAL* 1.3 56.6 + - - +
1893A SER* 2.9 27.9 + - - -
1894A VAL* 3.4 23.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1890 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808A ARG* 3.7 31.6 - - + +
1808A THR* 4.9 4.7 - - - +
1811A LEU* 4.0 15.7 - - + -
1812A TRP* 3.5 58.4 - - + +
1815A LYS* 3.5 20.6 + - + +
1886A ALA 3.1 17.5 + - - +
1887A CYS* 3.5 9.9 - - - +
1888A PHE 3.1 0.2 - - - -
1889A LEU* 1.3 76.5 - - - +
1891A TYR* 1.3 67.0 + - - +
1892A HIS 3.4 0.2 + - - -
1893A SER* 3.4 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1891 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1811A LEU* 4.1 18.8 - - + -
1814A ILE* 5.0 2.0 - - + -
1815A LYS* 4.0 34.7 - - + +
1818A LEU* 3.6 20.7 - - + +
1849A LYS* 3.3 36.9 + - - +
1852A ILE* 3.9 24.5 - - + -
1853A ASP* 3.1 24.5 + - - -
1856A LEU* 4.7 4.0 - - + -
1887A CYS 3.0 16.4 + - - +
1888A PHE* 4.0 1.8 - - - +
1890A VAL* 1.3 78.9 - - - +
1892A HIS* 1.3 86.0 + + + +
1893A SER* 3.7 5.9 + - - -
1921A GLN* 5.4 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1892 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1853A ASP* 4.3 10.3 - - - -
1856A LEU* 3.5 16.5 - - + +
1888A PHE* 2.8 72.9 + + + +
1891A TYR* 1.3 103.9 - + - +
1893A SER* 1.3 74.3 + - - +
1894A VAL* 3.7 9.3 - - + +
1914A GLU 5.9 0.4 - - - -
1917A PHE* 4.3 26.2 + - + +
1918A LYS* 4.3 18.7 + - + -
1921A GLN* 4.1 12.8 - - - -
1922A LEU 4.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1893 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808A ARG* 4.1 4.7 - - - +
846A GLN* 5.5 6.7 - - - +
853A LYS* 5.2 0.3 + - - -
1815A LYS* 2.9 31.8 + - - -
1889A LEU 2.9 13.3 + - - -
1890A VAL 3.4 3.6 + - - -
1891A TYR 3.7 1.6 + - - -
1892A HIS* 1.3 81.6 - - - +
1894A VAL* 1.3 57.4 + - - +
1895A PRO* 3.8 1.9 - - - +
1921A GLN* 3.5 21.9 - - - +
1922A LEU* 3.4 34.5 + - - +
----------------------------------------------------------
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