Contacts of the helix formed by residues 1949 - 1969 (chain A) in PDB entry 2HC2
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 THR1949 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A NA 3.1 23.1 - - - -
1707A TYR* 3.2 12.4 + - - -
1947A VAL* 4.1 1.2 - - - +
1948A GLN* 1.3 95.8 - - + +
1950A GLU* 1.3 64.5 + - - +
1951A CYS 3.5 4.1 + - - -
1952A GLN* 3.0 34.6 + - - +
1953A TYR 3.2 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1950 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1700A ASN* 2.9 30.1 + - - +
1703A LEU* 3.5 21.0 - - + +
1704A SER* 2.7 33.4 + - - -
1707A TYR* 3.5 32.2 - - + -
1708A GLU* 6.2 0.2 - - - +
1949A THR* 1.3 74.2 - - - +
1951A CYS 1.3 50.0 + - - +
1953A TYR* 3.0 3.0 + - - +
1954A VAL* 2.8 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1951 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1873A VAL* 3.9 11.8 - - - -
1949A THR* 3.1 6.4 + - - -
1950A GLU* 1.3 77.2 + - - +
1952A GLN* 1.3 56.3 - - - +
1954A VAL* 3.4 7.1 - - - +
1955A TYR* 2.9 28.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1952 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A NA 3.8 14.0 - - - -
1868A TRP* 4.7 5.3 - - + +
1872A GLY 5.7 0.6 + - - -
1873A VAL* 3.9 15.2 - - + +
1909A GLY* 3.4 26.1 + - - -
1910A ARG* 3.6 12.7 - - - +
1913A THR* 3.4 25.0 + - + +
1947A VAL* 3.6 8.4 - - + -
1948A GLN* 2.8 33.5 + - - +
1949A THR* 3.0 27.8 + - - +
1951A CYS 1.3 77.3 - - - +
1953A TYR* 1.3 61.4 + - - +
1955A TYR* 3.2 3.4 + - - +
1956A LEU* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1953 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1695A LEU* 5.5 0.2 - - + -
1703A LEU* 4.2 17.5 - - + -
1706A GLU* 2.6 32.2 + - + -
1707A TYR* 3.6 47.3 - + + -
1710A LEU* 3.8 21.1 - - + -
1932A ILE* 4.0 11.0 - - + -
1933A TYR* 3.5 21.9 + - - +
1936A VAL* 4.0 24.7 - - + -
1947A VAL* 3.9 6.2 - - + +
1949A THR 3.2 5.9 + - - +
1950A GLU* 3.0 8.4 + - - +
1952A GLN* 1.3 74.5 - - - +
1954A VAL* 1.3 61.1 + - - +
1956A LEU* 3.3 7.0 + - + +
1957A HIS* 2.9 48.7 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1954 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1692A PHE* 4.0 11.4 - - + -
1696A GLN* 4.7 5.4 - - - +
1700A ASN* 3.9 14.8 - - - +
1703A LEU* 3.6 35.7 - - + -
1950A GLU* 2.8 21.2 + - + +
1951A CYS 3.6 5.2 - - - -
1953A TYR* 1.3 75.0 - - - +
1955A TYR* 1.3 58.0 + - - +
1957A HIS* 3.0 7.7 + - - +
1958A GLN* 2.8 49.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1955 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1873A VAL* 4.0 24.2 - - + -
1874A PRO* 3.6 30.2 - - + +
1876A THR 2.8 29.3 + - - -
1877A THR* 3.5 16.3 - - + -
1880A LEU* 3.4 39.4 - - + +
1913A THR* 4.2 16.4 - - + -
1951A CYS 2.9 17.7 - - - -
1952A GLN 3.2 4.9 + - - +
1954A VAL* 1.3 78.0 - - - +
1956A LEU* 1.3 59.6 + - + +
1958A GLN* 3.1 19.5 + - - +
1959A CYS* 2.9 46.8 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
1913A THR* 3.7 33.9 - - + +
1916A ALA* 3.8 20.4 - - + -
1917A LEU* 3.8 29.0 - - + +
1920A ILE* 4.5 3.1 - - + -
1932A ILE* 4.1 18.4 - - + -
1936A VAL* 4.0 18.8 - - + -
1947A VAL* 4.2 13.9 - - + -
1952A GLN 3.0 17.8 + - - +
1953A TYR* 3.5 9.0 - - - +
1954A VAL 3.2 0.2 - - - -
1955A TYR* 1.3 77.1 - - + +
1957A HIS* 1.3 61.8 + - - +
1959A CYS* 3.3 6.1 + - - +
1960A VAL* 3.2 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1957 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1683A ILE* 5.0 1.8 - - - +
1688A PHE* 3.4 27.7 - + + -
1691A HIS* 4.4 5.8 + + - -
1692A PHE* 3.4 35.0 - + + -
1695A LEU* 3.9 19.0 - - + +
1703A LEU* 5.1 1.5 - - + +
1706A GLU* 4.2 4.9 + - - -
1932A ILE* 3.7 27.6 - - + +
1953A TYR* 2.9 56.7 + + - -
1954A VAL* 3.0 9.0 + - - +
1956A LEU* 1.3 79.1 - - - +
1958A GLN* 1.3 57.5 + - - +
1960A VAL 3.4 0.3 + - - -
1961A ARG* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1958 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1692A PHE* 3.7 19.1 - - + -
1696A GLN* 4.7 7.9 - - - +
1873A VAL* 5.6 1.7 - - - +
1877A THR* 3.8 13.7 - - + +
1954A VAL* 2.8 30.5 + - - +
1955A TYR* 3.5 29.9 + - - +
1957A HIS* 1.3 74.5 - - - +
1959A CYS* 1.3 59.4 + - - +
1961A ARG* 3.5 21.7 + - - +
1962A ASP* 2.9 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1959 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1877A THR* 3.8 21.5 - - - -
1881A ILE* 3.7 20.5 - - + +
1917A LEU* 3.7 29.2 - - + -
1921A LEU* 5.6 0.4 - - - -
1955A TYR* 2.9 46.1 + - - -
1956A LEU* 3.6 8.5 - - - +
1957A HIS 3.3 0.2 - - - -
1958A GLN* 1.3 77.4 - - - +
1960A VAL* 1.3 63.4 + - - +
1962A ASP 3.2 0.9 + - - -
1963A VAL* 3.0 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1960 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1688A PHE* 3.6 31.2 - - + -
1917A LEU* 5.2 2.0 - - + -
1920A ILE* 3.1 35.4 - - + -
1921A LEU* 5.1 2.9 - - + -
1924A LEU* 4.1 23.6 - - + -
1930A VAL* 4.4 2.9 - - + -
1932A ILE* 4.0 8.1 - - + -
1956A LEU 3.2 14.6 + - - +
1957A HIS 3.8 3.8 - - - +
1959A CYS* 1.3 73.2 - - + +
1961A ARG* 1.3 68.4 + - - +
1963A VAL* 3.2 3.3 + - - +
1964A LEU* 3.0 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1961 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1688A PHE* 3.7 14.3 - - + -
1689A GLU* 3.7 22.4 - - - +
1692A PHE* 3.9 25.5 - - + -
1693A MET* 6.5 0.2 - - - -
1696A GLN* 4.7 7.9 + - - +
1877A THR* 5.5 0.2 - - - +
1957A HIS 2.9 17.2 + - - +
1958A GLN* 3.6 28.4 - - - +
1960A VAL* 1.3 78.5 - - - +
1962A ASP* 1.3 84.0 + - - +
1964A LEU* 3.3 4.1 + - - +
1965A ARG* 2.9 73.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1962 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1877A THR* 2.6 37.1 + - - +
1881A ILE* 4.8 3.8 - - + -
1958A GLN 2.9 16.5 + - - +
1959A CYS 3.2 3.8 + - - +
1961A ARG* 1.3 107.2 + - - +
1963A VAL* 1.3 66.2 + - - +
1965A ARG* 3.7 14.6 + - - +
1966A ALA* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1963 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1881A ILE* 3.8 21.8 - - + -
1885A ARG* 3.6 31.2 - - - +
1921A LEU* 3.9 15.0 - - + -
1924A LEU* 3.7 22.9 - - + -
1959A CYS 3.0 16.8 + - - +
1960A VAL 3.6 6.3 - - - +
1962A ASP* 1.3 76.8 - - - +
1964A LEU* 1.3 58.0 + - - +
1966A ALA* 3.3 6.4 + - - +
1967A ARG* 3.0 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1964 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1685A ILE* 3.3 49.6 - - + +
1688A PHE* 3.9 20.2 - - + -
1689A GLU* 5.4 2.5 - - + +
1924A LEU* 4.2 12.6 - - + -
1930A VAL* 5.7 0.2 - - + -
1960A VAL* 3.0 31.5 + - + +
1961A ARG* 3.8 4.0 - - - +
1963A VAL* 1.3 72.4 - - - +
1965A ARG* 1.3 65.2 - - + +
1967A ARG* 3.3 36.5 - - - +
1968A LYS* 3.3 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1965 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1689A GLU* 2.9 41.1 + - - +
1961A ARG* 2.9 54.8 + - - +
1962A ASP* 3.7 14.2 + - - +
1964A LEU* 1.3 76.9 - - - +
1966A ALA* 1.3 62.2 + - - +
1968A LYS* 3.2 22.2 + - - +
1969A LEU* 3.4 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1966 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1962A ASP 3.0 18.2 + - - +
1963A VAL* 3.6 6.5 - - - +
1964A LEU 3.2 0.2 - - - -
1965A ARG* 1.3 72.8 - - - +
1967A ARG* 1.3 67.7 + - - +
1968A LYS 3.1 1.6 - - - -
1969A LEU* 2.9 30.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1967 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1685A ILE* 4.2 12.7 - - - +
1924A LEU* 2.5 42.0 + - - +
1925A ASP* 3.6 14.3 + - - +
1963A VAL* 3.0 21.7 + - + +
1964A LEU* 3.3 42.3 - - - +
1966A ALA* 1.3 75.9 - - - +
1968A LYS* 1.3 58.5 + - + +
1969A LEU* 2.9 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1968 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1686A ASN* 5.8 7.0 + - - +
1689A GLU* 5.0 16.0 + - - +
1964A LEU* 3.3 21.5 - - - +
1965A ARG* 3.2 16.9 + - - +
1966A ALA 3.1 1.2 - - - -
1967A ARG* 1.3 78.7 - - + +
1969A LEU* 1.3 67.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1969 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1965A ARG 3.4 7.2 + - - -
1966A ALA* 2.9 19.0 + - - +
1967A ARG* 2.9 22.0 - - - +
1968A LYS* 1.3 82.7 - - - +
----------------------------------------------------------
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