Contacts of the strand formed by residues 1930 - 1938 (chain A) in PDB entry 2AAV
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 GLY1930 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1905A PRO* 4.0 13.2 - - - -
1928A LEU 3.6 2.0 + - - -
1929A PRO* 1.3 74.8 - - - +
1931A ASP* 1.3 65.5 + - - -
1932A TYR* 3.5 6.2 + - - -
1950A ALA 3.4 2.3 - - - +
1951A ARG* 3.7 3.3 - - - +
1952A VAL* 3.0 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1931 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1904A GLY* 3.9 12.6 - - - -
1905A PRO* 4.3 4.9 - - - +
1930A GLY* 1.3 71.6 - - - -
1932A TYR* 1.3 60.4 + - - +
1933A SER* 3.2 13.3 + - - -
1949A THR* 3.9 20.4 - - + +
1950A ALA 3.8 3.6 - - - -
1951A ARG* 3.8 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1932 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1902A ILE* 3.8 23.1 - - + -
1903A GLU 3.2 9.6 - - - +
1904A GLY* 4.9 0.2 - - - -
1905A PRO* 4.1 10.8 - - + -
1906A SER* 3.5 32.3 + - - -
1907A LYS 4.2 11.1 + - - -
1908A ALA* 4.9 1.1 - - + -
1924A TYR* 4.5 10.3 - + + -
1926A PRO* 3.5 22.4 - - + -
1927A VAL 3.5 6.8 + - - -
1928A LEU 2.8 37.6 + - - -
1930A GLY* 3.7 15.7 - - - -
1931A ASP* 1.3 69.5 - - - +
1933A SER* 1.3 57.5 + - - +
1934A ILE* 3.3 10.9 - - + +
1949A THR* 4.3 0.4 - - - -
1950A ALA* 2.8 46.7 + - + +
1952A VAL* 3.3 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1933 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1902A ILE* 3.5 4.0 - - - -
1903A GLU* 2.9 43.5 + - - -
1931A ASP 3.2 9.1 + - - -
1932A TYR* 1.3 69.4 - - - +
1934A ILE* 1.3 61.3 + - - +
1935A LEU* 3.5 9.8 - - - +
1947A PRO* 5.3 5.8 - - - -
1948A PHE 3.2 11.7 - - - -
1949A THR* 4.0 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1934 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1874A GLY 3.9 7.6 - - - +
1875A LEU* 4.0 11.7 - - + -
1886A PHE* 4.0 30.7 - - + -
1900A LEU* 4.4 4.7 - - + -
1901A ALA 3.7 5.6 - - - +
1902A ILE* 4.1 17.9 - - + -
1924A TYR* 4.4 5.2 - - + +
1932A TYR* 3.3 18.4 - - + +
1933A SER* 1.3 71.1 - - - +
1935A LEU* 1.3 62.8 + - - +
1936A VAL* 3.6 28.6 + - + -
1947A PRO* 3.5 8.8 - - - +
1948A PHE* 2.9 42.3 + - + +
1950A ALA* 3.9 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1935 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1900A LEU* 3.4 6.1 - - - -
1901A ALA* 2.8 49.2 + - + +
1903A GLU* 4.0 22.9 - - + -
1933A SER* 3.5 21.1 - - - +
1934A ILE* 1.3 71.9 - - - +
1936A VAL* 1.3 61.3 + - - +
1937A LYS* 3.8 2.7 + - + +
1942A HIS* 4.0 27.6 - - + +
1946A SER* 4.8 1.3 - - - -
1947A PRO* 4.0 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1936 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1870A ALA* 4.5 18.2 - - + -
1875A LEU* 5.2 0.2 - - + -
1886A PHE* 5.2 2.0 - - + -
1888A VAL* 5.3 1.6 - - + -
1898A LEU* 4.4 9.9 - - + -
1899A SER 4.3 0.4 - - - +
1900A LEU* 3.6 20.2 - - + -
1934A ILE* 3.6 23.3 - - + -
1935A LEU* 1.3 70.0 - - - +
1937A LYS* 1.3 67.9 + - - +
1942A HIS* 3.3 8.7 + - - -
1943A VAL* 3.0 36.3 + - + -
1946A SER* 3.0 24.8 + - - +
1948A PHE* 3.7 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1937 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1898A LEU* 3.6 8.0 - - - +
1899A SER* 2.9 44.2 + - - +
1900A LEU* 6.3 0.2 - - - -
1935A LEU 3.8 2.4 + - - +
1936A VAL* 1.3 74.8 - - - +
1938A TYR* 1.3 60.4 + - - +
1939A ASN 4.3 0.4 - - - -
1940A GLU* 2.9 34.8 + - - +
1941A GLN* 3.2 12.5 - - - +
1942A HIS* 3.4 45.5 - - + +
1943A VAL* 4.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1938 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1868A VAL* 3.9 21.3 - - + -
1890A THR* 4.9 0.4 - - + -
1893A ALA* 3.3 44.6 + - + +
1896A GLY 4.8 9.8 + - - -
1897A GLY 5.4 0.9 - - - -
1898A LEU* 3.7 25.6 - - + +
1936A VAL* 6.0 0.2 - - + -
1937A LYS* 1.3 72.2 - - - +
1939A ASN* 1.3 87.1 + - + +
1941A GLN* 2.9 21.2 + - - +
1943A VAL* 4.3 21.5 - - + +
----------------------------------------------------------
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