Contacts of the helix formed by residues 1941 - 1960 (chain A) in PDB entry 4W8F
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 ASP1941 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1939A PHE 3.9 1.6 - - - -
1940A GLU* 1.3 90.3 - - + +
1942A SER* 1.3 64.2 + - - +
1943A LYS 3.4 0.4 - - - -
1944A SER* 3.5 30.2 + - - +
1945A LEU* 3.2 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1942 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1931A GLU* 3.5 35.9 + - - +
1934A LEU* 4.0 10.3 - - - +
1935A GLN* 3.7 31.1 + - - -
1939A PHE 4.4 5.8 - - - -
1940A GLU 3.5 5.6 + - - -
1941A ASP* 1.3 70.7 - - - +
1943A LYS* 1.3 79.6 + - - +
1946A ALA* 3.1 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1943 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1931A GLU* 3.1 41.3 - - - +
1941A ASP* 3.4 0.4 - - - +
1942A SER* 1.3 86.6 + - - +
1944A SER* 1.3 62.3 + - - +
1946A ALA* 3.3 4.0 + - - +
1947A SER* 3.1 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1944 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1941A ASP* 3.5 29.7 + - - +
1942A SER 3.4 0.2 - - - -
1943A LYS* 1.3 81.5 - - - +
1945A LEU* 1.3 64.8 + - - +
1947A SER* 3.2 5.1 + - - -
1948A LYS* 3.0 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1945 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1934A LEU* 3.7 14.4 - - + -
1939A PHE* 3.4 36.6 - - + -
1940A GLU* 5.1 5.8 - - + -
1941A ASP* 3.2 22.4 + - + +
1944A SER* 1.3 81.0 + - - +
1946A ALA* 1.3 57.3 + - - +
1948A LYS* 3.9 15.0 - - + +
1949A ILE* 2.8 51.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1946 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1927A GLY* 3.8 12.8 - - - +
1930A ALA* 4.0 6.3 - - + -
1931A GLU* 3.6 30.1 - - + +
1934A LEU* 3.7 7.5 - - - +
1942A SER 3.1 21.8 + - - +
1943A LYS 3.4 5.2 - - - +
1944A SER 3.2 0.2 - - - -
1945A LEU* 1.3 75.5 - - - +
1947A SER* 1.3 64.5 + - - +
1949A ILE* 3.8 1.6 - - - +
1950A VAL* 2.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1947 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1927A GLY* 6.0 1.3 - - - -
1943A LYS 3.1 10.3 + - - -
1944A SER* 3.2 8.3 + - - -
1946A ALA* 1.3 78.1 - - - +
1948A LYS* 1.3 58.1 + - - +
1950A VAL* 4.0 4.2 - - - +
1951A HIS* 2.9 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1948 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1944A SER* 3.0 36.1 + - - +
1945A LEU* 3.9 15.2 - - + +
1947A SER* 1.3 78.9 - - - +
1949A ILE* 1.3 63.3 + - + +
1951A HIS* 4.1 4.6 - - - +
1952A PHE* 3.0 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1949 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1930A ALA* 5.8 0.4 - - + -
1934A LEU* 3.8 21.8 - - + -
1945A LEU* 2.8 46.7 + - + +
1946A ALA* 3.8 2.7 - - - +
1948A LYS* 1.3 74.4 - - + +
1950A VAL* 1.3 64.5 + - + +
1952A PHE* 3.0 11.3 + - + +
1953A LEU* 3.0 31.6 + - + +
1973A LEU* 3.8 26.2 - - + -
1976A VAL* 4.8 15.9 - - + -
1977A LEU* 4.5 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1950 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1926A SER* 3.8 25.1 - - - +
1927A GLY* 3.7 31.9 - - - +
1930A ALA* 4.5 4.3 - - + -
1946A ALA 2.9 21.1 + - - +
1947A SER* 4.0 4.3 - - - +
1949A ILE* 1.3 75.5 - - - +
1951A HIS* 1.3 63.4 - - - +
1953A LEU* 3.3 10.2 + - - +
1954A GLU* 3.1 28.3 + - + +
1973A LEU* 4.3 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1951 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1947A SER 2.9 20.2 + - - +
1948A LYS* 4.1 4.3 - - - +
1950A VAL* 1.3 76.8 - - - +
1952A PHE* 1.3 58.3 + - - +
1954A GLU* 3.2 26.0 + - - +
1955A LEU* 2.9 63.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1952 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1948A LYS 3.0 20.2 + - - +
1949A ILE* 3.0 12.7 + - + +
1951A HIS* 1.3 76.5 - - - +
1953A LEU* 1.3 69.4 + - + +
1955A LEU* 3.2 22.0 + - + +
1956A LEU* 2.9 58.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1953 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1949A ILE* 3.0 23.8 + - + +
1950A VAL* 3.9 7.0 - - - +
1952A PHE* 1.3 81.8 - - + +
1954A GLU* 1.3 57.6 + - - +
1956A LEU* 3.0 24.1 + - + +
1957A SER* 2.9 28.6 + - - -
1968A PHE* 3.7 36.3 - - + +
1969A GLY 5.3 0.2 - - - -
1972A THR* 4.9 9.6 - - + -
1973A LEU* 3.7 44.4 - - + +
1976A VAL* 5.4 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1954 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1950A VAL* 3.1 19.4 + - + +
1951A HIS* 3.2 35.7 + - - +
1953A LEU* 1.3 77.7 - - - +
1955A LEU* 1.3 63.6 + - + +
1957A SER* 3.1 7.9 + - - -
1958A SER* 3.0 23.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1955 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1951A HIS* 2.9 55.4 + - + +
1952A PHE* 3.3 24.0 - - + +
1954A GLU* 1.3 77.7 - - + +
1956A LEU* 1.3 56.0 + - - +
1958A SER* 3.0 6.1 + - - -
1959A LYS* 2.7 56.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1956 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1952A PHE* 2.9 54.0 + - + +
1953A LEU* 3.0 21.3 + - + +
1955A LEU* 1.3 77.7 - - + +
1957A SER* 1.3 60.8 + - - +
1959A LYS* 5.2 0.9 - - + -
1960A CYS* 3.2 43.7 + - - +
1968A PHE* 3.1 40.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1957 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1953A LEU 2.9 12.3 + - - -
1954A GLU* 3.5 11.7 - - - -
1955A LEU 3.1 0.4 - - - -
1956A LEU* 1.3 75.5 - - - +
1958A SER* 1.3 65.0 + - - +
1960A CYS 4.0 8.7 - - - +
1968A PHE* 3.5 19.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1958 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1954A GLU* 3.0 16.2 + - - -
1955A LEU* 3.0 7.4 + - - -
1957A SER* 1.3 81.2 - - - +
1959A LYS* 1.3 73.4 + - - +
1960A CYS 4.3 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1959 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1955A LEU* 2.7 38.4 + - + +
1956A LEU* 5.2 1.1 - - - -
1958A SER* 1.3 85.7 + - - +
1960A CYS* 1.3 65.4 + - - +
1961A SER* 3.8 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1960 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1956A LEU* 3.2 42.7 + - - +
1957A SER 4.0 12.0 - - - +
1958A SER 4.3 1.9 - - - +
1959A LYS* 1.3 83.7 - - - +
1961A SER* 1.3 71.4 + - - +
1962A SER* 3.6 1.6 + - - -
1966A TYR* 4.6 9.0 - - + -
1968A PHE* 4.4 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