Contacts of the helix formed by residues 1856 - 1868 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1809F ARG* 4.6 4.6 - - - +
1854F ILE 3.3 6.5 + - - -
1855F PHE* 1.3 75.6 - - - +
1857F ASP* 1.3 66.5 + - - -
1858F GLU 3.4 2.7 - - - -
1859F ASP* 3.6 9.0 - - - +
1860F VAL* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1857 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1765F GLY 5.6 0.7 - - - -
1766F VAL* 5.6 9.2 - - + +
1856F GLY* 1.3 69.0 - - - -
1858F GLU* 1.3 61.4 + - - +
1860F VAL* 3.2 11.8 - - - +
1861F LYS* 2.9 45.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1858 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1856F GLY* 4.5 0.2 - - - -
1857F ASP* 1.3 78.4 - - - +
1859F ASP* 1.3 57.7 + - - +
1861F LYS* 3.4 10.9 + - - +
1862F GLN* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1859 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1809F ARG* 4.1 13.8 - - - +
1813F LEU* 4.7 16.3 - - + +
1855F PHE* 3.6 24.0 - - + -
1856F GLY* 3.4 24.0 + - - +
1857F ASP 3.2 0.6 - - - -
1858F GLU* 1.3 79.8 - - - +
1860F VAL* 1.3 59.3 + - - +
1862F GLN* 3.3 5.8 + - - +
1863F ILE* 2.9 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1860 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1764F PRO 4.8 8.2 - - - +
1765F GLY* 3.5 27.4 - - - +
1766F VAL* 4.0 16.2 - - + -
1850F LEU* 3.9 26.9 - - + -
1855F PHE* 3.9 11.4 - - + +
1856F GLY 3.1 16.3 + - - +
1857F ASP* 3.2 15.0 - - - +
1859F ASP* 1.3 74.9 - - - +
1861F LYS* 1.3 60.6 + - - +
1863F ILE* 3.6 9.0 - - - +
1864F LEU* 2.9 30.3 + - - +
1947F PHE* 6.3 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1861 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1763F LEU* 3.9 26.8 - - + +
1766F VAL* 4.1 21.7 - - + +
1857F ASP* 2.9 31.8 + - - +
1858F GLU* 3.6 9.0 - - - +
1859F ASP 3.2 0.2 - - - -
1860F VAL* 1.3 77.5 - - - +
1862F GLN* 1.3 56.8 + - - +
1864F LEU* 3.3 5.5 + - - +
1865F LYS* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1862 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1813F LEU* 5.1 13.2 - - + -
1858F GLU 2.9 17.8 + - - +
1859F ASP* 3.7 5.8 - - - +
1861F LYS* 1.3 75.0 - - - +
1863F ILE* 1.3 58.4 + - - +
1865F LYS* 3.3 6.8 + - - +
1866F MET* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1863 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1813F LEU* 4.6 13.2 - - + -
1846F VAL* 4.1 17.5 - - + -
1850F LEU* 4.2 13.0 - - + -
1855F PHE* 3.6 38.1 - - + -
1859F ASP 2.9 21.2 + - - +
1860F VAL* 3.6 7.0 - - + +
1861F LYS 3.2 0.2 - - - -
1862F GLN* 1.3 76.4 - - - +
1864F LEU* 1.3 57.7 + - - +
1866F MET* 3.2 7.6 + - - +
1867F ILE* 2.9 43.2 + - + +
1943F LEU* 5.8 4.0 - - + -
1947F PHE* 4.0 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1864 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1763F LEU* 5.6 7.2 - - + -
1764F PRO* 5.3 17.3 - - + +
1860F VAL 2.9 17.4 + - - +
1861F LYS* 3.8 5.8 - - - +
1863F ILE* 1.3 78.8 - - - +
1865F LYS* 1.3 60.0 + - - +
1867F ILE* 3.6 5.8 + - - +
1868F GLU 2.9 26.3 + - - +
1871F VAL* 3.8 25.9 - - + +
1947F PHE* 5.9 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1865 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1861F LYS 2.9 17.6 + - - +
1862F GLN* 3.7 7.4 - - - +
1863F ILE 3.2 0.2 - - - -
1864F LEU* 1.3 76.2 - - - +
1866F MET* 1.3 61.4 + - - +
1868F GLU 3.4 17.6 - - - +
1869F PRO* 4.1 6.3 - - - +
1871F VAL 5.3 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1866 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1816F LEU* 3.7 45.3 - - + +
1817F GLY* 4.8 1.6 - - - -
1819F ALA* 5.9 1.1 - - + -
1820F VAL* 4.1 29.5 - - + +
1843F LEU* 5.4 8.3 - - + -
1862F GLN 2.9 18.5 + - - +
1863F ILE* 3.7 7.9 - - - +
1865F LYS* 1.3 75.2 - - - +
1867F ILE* 1.3 72.0 + - + +
1868F GLU* 4.6 0.2 - - - -
1925F GLU 4.8 7.1 - - - +
1926F GLY* 5.7 0.2 - - - -
1927F LEU* 4.4 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1867 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1843F LEU* 6.1 1.1 - - + -
1863F ILE* 2.9 33.1 + - + +
1864F LEU* 4.0 7.0 - - - +
1865F LYS 3.4 0.2 - - - -
1866F MET* 1.3 85.6 - - + +
1868F GLU* 1.3 65.8 + - + +
1869F PRO* 4.9 0.3 - - - +
1871F VAL* 6.0 2.5 - - + -
1926F GLY* 5.5 1.4 - - - -
1927F LEU* 4.5 14.6 + - + -
1928F LEU* 3.4 35.5 + - + +
1929F GLN* 5.2 1.6 - - - +
1940F MET* 3.6 29.2 - - + -
1943F LEU* 4.8 8.5 - - + -
1944F LEU* 5.4 12.6 - - + -
1947F PHE* 4.8 12.3 - - + -
2098F LEU* 6.0 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1868 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1864F LEU 2.9 17.4 + - - +
1865F LYS* 3.4 8.4 - - - +
1866F MET 3.4 0.4 - - - -
1867F ILE* 1.3 86.6 - - + +
1869F PRO* 1.3 75.0 - - + +
1870F GLU* 3.5 3.3 + - + +
1871F VAL* 3.5 28.3 + - + +
1928F LEU* 5.8 2.0 - - + -
1929F GLN* 6.1 0.7 - - - +
2098F LEU* 5.3 11.2 - - + -
----------------------------------------------------------
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