Contacts of the helix formed by residues 1856 - 1868 (chain B) in PDB entry 6X34
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 GLY1856 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1809B ARG* 4.6 5.2 - - - +
1854B ILE 3.3 5.9 + - - -
1855B PHE* 1.3 76.5 - - - +
1857B ASP* 1.3 65.7 + - - -
1858B GLU 3.4 2.5 - - - -
1859B ASP* 3.6 8.6 - - - +
1860B VAL* 3.1 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1857 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1765B GLY 5.6 0.7 - - - -
1766B VAL* 5.6 9.4 - - + +
1856B GLY* 1.3 72.1 - - - -
1858B GLU* 1.3 58.5 + - - +
1860B VAL* 3.2 12.3 - - - +
1861B LYS* 2.9 44.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1858 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1856B GLY 3.4 0.6 - - - -
1857B ASP* 1.3 77.2 - - - +
1859B ASP* 1.3 56.6 + - - +
1861B LYS* 3.6 11.5 - - - +
1862B GLN* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1859 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1809B ARG* 4.1 14.1 - - - +
1813B LEU* 4.7 15.7 - - + +
1855B PHE* 3.6 24.5 - - + -
1856B GLY 3.4 23.3 + - - +
1857B ASP 3.2 0.8 - - - -
1858B GLU* 1.3 78.5 - - - +
1860B VAL* 1.3 57.9 + - - +
1862B GLN* 3.3 6.3 + - - +
1863B ILE* 2.9 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1860 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1764B PRO 4.8 7.8 - - - +
1765B GLY* 3.5 27.1 - - - +
1766B VAL* 4.0 15.9 - - + -
1850B LEU* 3.9 26.9 - - + -
1855B PHE* 3.9 11.9 - - + +
1856B GLY 3.1 16.2 + - - +
1857B ASP* 3.2 14.6 - - - +
1859B ASP* 1.3 75.2 - - - +
1861B LYS* 1.3 61.2 + - - +
1863B ILE* 3.6 9.2 - - + +
1864B LEU* 2.9 29.6 + - - +
1947B PHE* 6.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1861 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1763B LEU* 3.9 25.9 - - + +
1766B VAL* 4.2 22.6 - - + +
1857B ASP* 2.9 33.5 + - + +
1858B GLU* 3.6 9.2 - - - +
1859B ASP 3.2 0.2 - - - -
1860B VAL* 1.3 77.0 - - - +
1862B GLN* 1.3 57.7 + - - +
1864B LEU* 3.3 6.2 + - - +
1865B LYS* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1862 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1813B LEU* 5.1 13.7 - - + -
1858B GLU 2.9 16.9 + - - +
1859B ASP* 3.7 6.5 - - - +
1861B LYS* 1.3 76.5 - - - +
1863B ILE* 1.3 56.9 + - - +
1865B LYS* 3.3 7.5 + - - +
1866B MET* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1863 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1813B LEU* 4.6 13.9 - - + -
1846B VAL* 4.1 18.4 - - + -
1850B LEU* 4.2 13.0 - - + -
1855B PHE* 3.6 37.9 - - + -
1859B ASP 2.9 19.7 + - - +
1860B VAL* 3.6 7.4 - - - +
1861B LYS 3.2 0.2 - - - -
1862B GLN* 1.3 76.2 - - - +
1864B LEU* 1.3 58.4 + - - +
1866B MET* 3.2 8.5 + - - +
1867B ILE* 2.9 44.2 + - + +
1943B LEU* 5.8 3.8 - - + -
1947B PHE* 4.0 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1864 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1763B LEU* 5.6 7.2 - - + -
1764B PRO* 5.3 17.0 - - + +
1860B VAL 2.9 17.2 + - - +
1861B LYS* 3.8 5.6 - - - +
1863B ILE* 1.3 77.8 - - - +
1865B LYS* 1.3 59.6 + - - +
1867B ILE* 4.0 6.2 - - - +
1868B GLU 2.9 26.3 + - - +
1871B VAL* 3.8 25.6 - - + +
1947B PHE* 5.9 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1865 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1861B LYS 2.9 18.0 + - - +
1862B GLN* 3.7 7.4 - - - +
1863B ILE 3.2 0.2 - - - -
1864B LEU* 1.3 76.5 - - - +
1866B MET* 1.3 61.6 + - - +
1868B GLU 3.4 18.3 - - - +
1869B PRO* 4.1 6.0 - - - +
1871B VAL 5.3 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1866 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1816B LEU* 3.7 46.0 - - + +
1817B GLY* 4.8 1.6 - - - -
1819B ALA* 5.9 1.3 - - + -
1820B VAL* 4.1 29.1 - - + +
1843B LEU* 5.4 7.9 - - + -
1862B GLN 2.9 16.8 + - - +
1863B ILE* 3.2 8.0 + - - +
1865B LYS* 1.3 75.7 - - - +
1867B ILE* 1.3 72.0 + - + +
1868B GLU* 4.6 0.2 - - - -
1925B GLU 4.8 7.1 - - - +
1927B LEU* 4.4 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1867 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1843B LEU* 6.1 0.9 - - + -
1863B ILE* 2.9 32.9 + - + +
1864B LEU* 4.0 7.0 - - - +
1866B MET* 1.3 85.4 - - + +
1868B GLU* 1.3 65.2 + - + +
1869B PRO* 4.9 0.3 - - - +
1871B VAL* 6.0 2.7 - - + -
1926B GLY* 5.5 1.6 - - - -
1927B LEU* 4.5 14.9 + - + -
1928B LEU* 3.4 34.3 + - + +
1929B GLN* 5.2 2.1 - - - +
1940B MET* 3.6 29.4 - - + -
1943B LEU* 4.8 9.0 - - + -
1944B LEU* 5.4 12.6 - - + -
1947B PHE* 4.8 12.6 - - + -
2098B LEU* 6.0 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1868 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1864B LEU 2.9 17.5 + - - +
1865B LYS* 3.4 7.9 - - - +
1866B MET 3.4 0.4 - - - -
1867B ILE* 1.3 86.4 - - + +
1869B PRO* 1.3 74.6 - - + +
1870B GLU* 3.5 2.8 + - + +
1871B VAL* 3.5 27.3 + - + +
1928B LEU* 5.8 2.2 - - + -
1929B GLN* 6.1 1.1 - - - +
2098B LEU* 5.3 11.7 - - + -
----------------------------------------------------------
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