Contacts of the helix formed by residues 1886 - 1900 (chain r) in PDB entry 6FF7
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 ASP1886 (chain r).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1883r LYS* 3.5 22.5 + - + +
1884r PHE 3.4 3.1 - - - -
1885r ASN* 1.3 77.7 - - - +
1887r PRO* 1.3 64.7 - - - +
1888r HIS* 4.5 5.8 - - + +
1889r VAL* 3.2 12.0 + - + +
1890r LYS* 3.1 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1887 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1855r TYR 3.7 17.0 - - - +
1856r GLU* 4.3 9.6 - - + +
1858r ILE* 3.2 33.5 - - + +
1859r PRO 5.3 3.6 - - - +
1885r ASN 3.8 3.8 - - - +
1886r ASP* 1.3 67.9 - - - +
1888r HIS* 1.3 59.6 + - - +
1890r LYS* 3.6 11.5 - - + +
1891r THR* 2.9 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1888 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1850r SER* 3.7 29.8 - - - +
1851r ASN* 4.2 15.9 - - + +
1855r TYR* 4.7 2.4 + - - -
1856r GLU* 5.8 0.2 - - - +
1886r ASP* 3.2 5.0 - - + +
1887r PRO* 1.3 74.7 - - - +
1889r VAL* 1.3 65.9 + - - +
1891r THR* 3.3 1.4 + - - -
1892r ASN* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1889 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1882r PRO* 4.8 14.1 - - + -
1883r LYS 3.7 19.7 - - - +
1884r PHE* 5.4 2.7 - - - -
1886r ASP* 3.2 14.3 + - + +
1888r HIS* 1.3 79.5 - - - +
1890r LYS* 1.3 62.2 + - - +
1892r ASN* 3.2 9.1 + - - +
1893r LEU* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1890 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1858r ILE* 5.9 3.4 - - + -
1859r PRO 5.7 4.7 - - - +
1868r LEU* 5.7 11.4 - - + -
1884r PHE 5.8 3.4 - - - +
1886r ASP 3.1 10.0 + - - +
1887r PRO* 3.6 13.7 - - + +
1888r HIS 3.3 0.2 - - - -
1889r VAL* 1.3 81.0 - - - +
1891r THR* 1.3 56.4 + - - +
1893r LEU* 3.4 5.9 + - - +
1894r LEU* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1891 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1850r SER* 4.7 7.6 - - - -
1855r TYR* 4.5 20.6 - - - -
1858r ILE* 5.6 5.1 - - - +
1887r PRO 2.9 17.8 + - - -
1888r HIS* 3.9 4.3 - - - -
1890r LYS* 1.3 72.8 - - - +
1892r ASN* 1.3 59.6 + - - +
1894r LEU* 4.0 6.4 - - - +
1895r LEU* 2.9 32.4 + - - +
1915r ILE* 5.3 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1892 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1846r ILE* 5.2 9.6 - - + +
1847r GLU* 5.2 7.4 - - + -
1850r SER* 4.1 15.7 - - - -
1888r HIS 3.0 13.6 + - - +
1889r VAL* 3.3 12.6 - - - +
1891r THR* 1.3 74.6 - - - +
1893r LEU* 1.3 57.4 + - - +
1895r LEU* 3.2 7.1 + - - +
1896r GLN* 2.9 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1893 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1868r LEU* 5.3 8.5 - - + +
1871r LEU* 5.5 7.2 - - + +
1872r ALA* 5.1 20.0 - - + +
1875r VAL* 5.3 7.6 - - + +
1889r VAL 3.0 14.8 + - - +
1890r LYS* 3.8 6.5 - - - +
1892r ASN* 1.3 73.4 - - - +
1894r LEU* 1.3 59.9 + - - +
1896r GLN* 3.6 6.4 + - - +
1897r ALA* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1894 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1890r LYS 2.9 19.4 + - - +
1891r THR* 4.0 7.2 - - - +
1893r LEU* 1.3 76.1 - - - +
1895r LEU* 1.3 57.8 + - - +
1897r ALA* 3.4 8.2 - - - +
1898r HIS* 2.9 27.0 + - - +
1908r LEU* 5.5 4.3 - - + +
1911r ASP* 6.1 2.2 - - + -
1912r THR* 4.8 25.9 - - - +
1915r ILE* 6.0 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1895 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1846r ILE* 6.2 3.8 - - + -
1891r THR 2.9 20.1 + - - +
1892r ASN* 3.4 7.0 - - - +
1894r LEU* 1.3 73.8 - - - +
1896r GLN* 1.3 60.5 + - - +
1898r HIS* 3.0 9.1 + - - +
1899r LEU* 2.9 27.6 + - - +
1915r ILE* 6.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1896 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1875r VAL* 4.4 19.5 - - + -
1876r PRO* 5.2 9.9 - - + -
1877r HIS* 5.5 6.3 - - + +
1892r ASN 2.9 15.6 + - - +
1893r LEU* 3.9 5.6 - - - +
1895r LEU* 1.3 75.1 - - - +
1897r ALA* 1.3 58.7 + - - +
1899r LEU* 3.1 9.6 + - - +
1900r SER* 2.8 31.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1897 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1871r LEU* 6.5 0.9 - - + -
1875r VAL* 5.5 2.3 - - - +
1893r LEU 2.9 19.8 + - - +
1894r LEU* 3.4 10.8 - - - +
1896r GLN* 1.3 75.6 - - - +
1898r HIS* 1.3 60.1 + - - +
1900r SER* 3.3 3.7 + - - +
1901r ARG 3.1 3.6 + - - -
1902r MET* 3.0 46.5 + - + +
1904r LEU* 6.0 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1898 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1894r LEU 2.9 14.2 + - - +
1895r LEU* 3.0 11.2 + - - +
1897r ALA* 1.3 76.6 - - - +
1899r LEU* 1.3 63.0 + - - +
1901r ARG* 3.1 13.8 + - - +
1902r MET 5.5 0.9 - - - -
1912r THR* 5.4 9.2 - - - -
1952r ALA* 3.7 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1899 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1895r LEU 2.9 12.7 + - - +
1896r GLN* 3.1 12.5 + - - +
1898r HIS* 1.3 77.2 - - - +
1900r SER* 1.3 58.5 + - - +
1901r ARG* 3.2 0.9 + - - +
1948r MET* 5.4 2.9 - - + +
1952r ALA* 3.8 3.1 - - - +
1953r MET* 3.3 44.2 + - - +
1954r TRP* 3.6 10.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1900 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1876r PRO* 6.2 4.9 - - - -
1896r GLN 2.8 15.7 + - - -
1897r ALA* 3.3 6.3 + - - -
1898r HIS 3.2 0.2 - - - -
1899r LEU* 1.3 74.8 - - - +
1901r ARG* 1.3 70.3 + - - +
1902r MET* 3.1 7.8 + - - +
1954r TRP* 6.2 0.9 - - - -
----------------------------------------------------------
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