Contacts of the helix formed by residues 1911 - 1920 (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 SER1911 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1865A ASP* 4.5 20.0 - - - -
1869A HIS* 5.6 0.2 - - - -
1910A THR* 1.3 76.3 - - - +
1912A PHE* 1.3 63.0 + - - +
1913A ALA 3.2 0.9 - - - -
1914A GLU* 3.3 23.6 + - - +
1915A LEU* 3.7 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1912 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1910A THR 4.0 8.3 - - - +
1911A SER* 1.3 78.1 - - - +
1913A ALA* 1.3 56.0 + - - +
1914A GLU 3.2 0.2 - - - -
1915A LEU* 3.2 11.6 + - - +
1916A LEU* 2.9 26.7 + - - +
1934A PRO* 4.6 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1913 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1869A HIS* 6.0 1.6 - - + -
1872A LEU* 6.1 5.2 - - + -
1894A VAL* 5.8 0.3 - - - +
1910A THR* 3.2 22.3 + - - +
1911A SER 3.2 1.0 - - - -
1912A PHE* 1.3 74.3 - - - +
1914A GLU* 1.3 58.8 + - - +
1916A LEU* 3.7 11.0 - - + +
1917A PHE* 2.8 27.5 + - - +
1934A PRO* 5.3 5.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1914 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1860A LEU* 4.7 21.3 - - + +
1865A ASP* 5.0 9.4 - - - +
1868A VAL* 6.0 5.2 - - + -
1888A PHE* 5.0 11.7 - - + -
1892A HIS* 5.7 0.7 + - - -
1910A THR 4.0 1.8 + - - +
1911A SER* 3.3 16.9 + - - +
1912A PHE 3.2 0.4 - - - -
1913A ALA* 1.3 76.6 - - - +
1915A LEU* 1.3 59.3 + - - +
1916A LEU 3.3 0.2 - - - -
1917A PHE* 3.6 6.8 - - - +
1918A LYS* 3.2 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1915 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1911A SER 3.7 3.1 + - - +
1912A PHE* 3.2 14.9 + - - +
1914A GLU* 1.3 78.3 - - - +
1916A LEU* 1.3 57.8 - - - +
1918A LYS* 3.6 7.7 + - - +
1919A PHE* 3.2 24.6 + - - +
78N VAL* 4.7 2.3 - - - +
79N LEU* 6.0 5.6 - - + -
82N ASP* 5.4 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1916 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1912A PHE 2.9 16.0 + - - +
1913A ALA* 3.8 11.2 - - + +
1915A LEU* 1.3 74.1 - - - +
1917A PHE* 1.3 55.7 + - - +
1919A PHE* 3.3 7.3 + - - +
1920A LYS* 2.7 37.6 + - - +
1930A LEU* 4.8 21.2 - - + +
1931A ARG* 6.3 0.2 - - - -
1933A ALA 6.4 0.4 - - - -
1934A PRO* 5.4 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1917 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1888A PHE* 4.9 5.4 - - + -
1892A HIS* 4.3 30.5 + - + +
1894A VAL* 4.5 16.8 - - + -
1913A ALA 2.8 20.5 + - - +
1914A GLU* 3.6 10.1 - - - +
1915A LEU 3.4 0.2 - - - -
1916A LEU* 1.3 73.6 - - - +
1918A LYS* 1.3 64.7 + - - +
1920A LYS 2.8 23.9 - - - +
1921A GLN* 4.0 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1918 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1849A LYS* 5.0 4.9 + - - -
1853A ASP* 6.2 3.8 - - - -
1892A HIS* 4.3 18.7 + - + -
1914A GLU 3.2 12.1 + - - +
1915A LEU* 3.6 11.7 - - - +
1916A LEU 3.3 0.2 - - - -
1917A PHE* 1.3 79.9 - - - +
1919A PHE* 1.3 61.1 + - - +
1920A LYS 5.0 0.2 - - - -
78N VAL* 3.4 28.9 - - + +
82N ASP* 5.2 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1919 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1915A LEU 3.2 13.6 + - - +
1916A LEU* 3.5 10.3 - - - +
1917A PHE 3.2 0.2 - - - -
1918A LYS* 1.3 82.6 - - - +
1920A LYS* 1.3 60.9 + - + +
74N TRP* 4.6 13.6 + - - +
75N PHE* 4.0 28.8 - - + -
78N VAL* 3.6 18.6 - - + +
79N LEU* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1920 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1916A LEU 2.7 19.7 + - - +
1917A PHE* 2.8 23.7 - - - +
1918A LYS 5.0 0.2 - - - -
1919A PHE* 1.3 77.9 - - + +
1921A GLN* 1.3 65.2 + - - +
1922A LEU 4.0 1.0 + - - -
1926A VAL 5.9 0.2 - - - +
1930A LEU* 4.6 19.3 - - + -
74N TRP 5.9 1.6 - - - +
----------------------------------------------------------
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