Contacts of the helix formed by residues 1866 - 1883 (chain D) in PDB entry 4JQ0
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 GLY1866 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1865D SER* 1.3 72.5 + - - -
1867D GLU* 1.3 64.6 + - - -
1868D MET 3.2 3.4 + - - -
1869D ASP* 3.4 13.2 + - - +
1870D ALA* 3.9 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1867 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1866D GLY* 1.3 69.0 - - - -
1868D MET* 1.3 70.9 + - - +
1869D ASP 3.1 2.7 - - - -
1870D ALA* 3.2 10.1 + - + +
1871D LEU* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1868 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1862D LEU* 3.8 53.1 - - + +
1865D SER* 3.1 18.6 - - - +
1866D GLY 3.2 0.8 - - - -
1867D GLU* 1.3 89.4 - - - +
1869D ASP* 1.3 57.8 + - - +
1871D LEU* 3.8 19.6 - - + +
1872D LYS* 2.9 26.1 + - - +
1875D MET* 5.1 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1869 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1859D LYS* 6.2 0.3 - - - +
1864D GLU* 4.8 6.8 - - - +
1865D SER* 3.1 40.4 + - - +
1866D GLY 3.8 9.2 - - - +
1867D GLU 3.1 1.0 - - - -
1868D MET* 1.3 78.1 - - - +
1870D ALA* 1.3 59.8 + - - +
1872D LYS* 3.1 9.5 + - - +
1873D ILE* 2.9 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1870 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1866D GLY 3.9 3.0 + - - +
1867D GLU* 3.2 14.8 + - - +
1869D ASP* 1.3 77.9 - - - +
1871D LEU* 1.3 58.7 + - - +
1873D ILE* 3.2 9.1 + - - +
1874D GLN* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1871 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1862D LEU* 6.4 0.9 - - + -
1867D GLU 2.9 16.2 + - - +
1868D MET* 4.0 23.1 - - + +
1870D ALA* 1.3 76.8 - - - +
1872D LYS* 1.3 58.4 + - - +
1874D GLN* 4.2 10.8 - - + -
1875D MET* 2.9 66.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1872 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1855D PHE* 6.2 4.5 - - + -
1862D LEU* 5.9 2.0 - - + -
1868D MET 2.9 21.6 + - - +
1869D ASP* 3.1 14.4 - - - +
1870D ALA 3.1 0.4 - - - -
1871D LEU* 1.3 77.0 - - - +
1873D ILE* 1.3 60.5 + - + +
1875D MET* 3.4 13.6 + - + +
1876D GLU* 2.9 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1873 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1869D ASP* 2.9 21.2 + - + +
1870D ALA* 3.2 8.5 + - - +
1872D LYS* 1.3 76.9 - - + +
1874D GLN* 1.3 58.6 + - - +
1876D GLU* 3.2 23.8 + - - +
1877D GLU* 2.9 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1874 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1870D ALA 2.9 16.6 + - - +
1871D LEU* 3.6 15.7 - - + +
1872D LYS 3.3 0.2 - - - -
1873D ILE* 1.3 76.9 - - - +
1875D MET* 1.3 57.8 + - + +
1877D GLU* 3.2 9.5 + - - +
1878D LYS* 2.9 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1875 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1791D PHE* 4.9 21.3 - - + -
1858D THR* 6.1 2.7 - - + +
1862D LEU* 5.5 9.2 - - + -
1868D MET 5.1 1.3 - - - +
1871D LEU* 2.9 58.7 + - + +
1872D LYS* 3.7 11.4 - - + +
1874D GLN* 1.3 72.2 - - - +
1876D GLU* 1.3 60.2 + - - +
1878D LYS* 3.3 10.3 + - + +
1879D PHE* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1876 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1851D MET* 5.4 12.3 - - + +
1855D PHE* 4.5 19.9 - - + +
1872D LYS* 2.9 22.4 + - + +
1873D ILE* 3.3 36.6 - - + +
1875D MET* 1.3 74.5 - - - +
1877D GLU* 1.3 59.1 + - - +
1879D PHE* 3.2 8.5 + - - +
1880D MET* 2.9 33.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1877 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1873D ILE* 2.9 13.8 + - + +
1874D GLN* 3.4 11.2 - - - +
1876D GLU* 1.3 75.2 - - - +
1878D LYS* 1.3 57.8 + - - +
1880D MET* 3.1 13.6 + - - +
1881D ALA* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1878 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1874D GLN 2.9 14.2 + - - +
1875D MET* 3.4 13.9 - - + +
1877D GLU* 1.3 76.8 - - - +
1879D PHE* 1.3 57.2 + - - +
1881D ALA* 3.5 5.8 + - - +
1882D ALA* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1879 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1794D PHE* 5.3 10.8 - + - -
1798D TRP* 6.0 1.1 - + - -
1807D GLN* 6.1 0.2 - - + -
1849D HIS* 3.9 9.6 - + - -
1850D CYS* 3.5 35.0 - - + -
1851D MET* 4.3 18.2 - - + -
1875D MET 2.9 13.0 + - - +
1876D GLU* 3.2 10.7 + - - +
1878D LYS* 1.3 73.6 - - - +
1880D MET* 1.3 68.2 + - + +
1882D ALA* 3.3 8.5 + - + +
1883D ASN* 3.0 52.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1880 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLY* 5.9 1.3 - - - -
56A LEU* 3.9 30.3 - - + +
1876D GLU* 2.9 17.2 + - + +
1877D GLU* 3.1 14.1 + - - +
1879D PHE* 1.3 80.7 - - + +
1881D ALA* 1.3 63.9 + - - +
1883D ASN* 3.1 24.9 + - - +
1889D TYR* 3.8 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1881 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1877D GLU 2.9 15.4 + - - +
1878D LYS* 3.8 6.5 - - - +
1880D MET* 1.3 76.7 - - - +
1882D ALA* 1.3 63.8 + - - +
1883D ASN 3.2 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1882 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1878D LYS 2.9 17.9 + - - +
1879D PHE* 3.7 11.4 - - + +
1880D MET 3.2 0.2 - - - -
1881D ALA* 1.3 76.9 - - - +
1883D ASN* 1.3 60.6 + - - +
1884D PRO* 3.4 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1883 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1807D GLN* 2.7 45.6 + - - +
1849D HIS* 4.4 3.2 + - - -
1879D PHE* 3.0 46.4 + - - +
1880D MET* 3.1 16.3 + - - +
1881D ALA 3.8 4.7 - - - +
1882D ALA* 1.3 77.6 - - - +
1884D PRO* 1.3 68.5 - - - +
1885D SER 4.0 5.1 + - - +
1886D LYS* 5.5 2.4 + - - -
1888D SER* 4.8 0.4 + - - +
1889D TYR* 4.9 12.9 + - + +
----------------------------------------------------------
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