Contacts of the helix formed by residues 1925 - 1937 (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 GLN1925 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1772A THR* 4.0 8.3 - - - +
1773A PRO* 3.2 46.2 - - - +
1774A LEU* 3.8 8.7 - - + +
1923A SER* 2.8 20.4 + - - +
1924A PRO* 1.3 78.6 - - - +
1926A SER* 1.3 66.5 + - - +
1927A GLY* 2.9 5.3 + - - -
1928A THR* 3.1 34.6 + - + +
1929A ILE* 3.1 11.1 - - - +
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Residues in contact with SER1926 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1924A PRO* 3.3 8.8 - - - +
1925A GLN* 1.3 75.5 - - - +
1927A GLY* 1.3 62.4 + - - +
1929A ILE* 3.4 4.9 + - - +
1930A ALA* 3.0 24.3 + - - +
1950A VAL* 3.8 19.5 - - - -
1969A GLY 5.6 0.2 - - - -
1970A LEU* 4.0 29.3 + - - +
1973A LEU* 3.7 19.9 - - - +
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Residues in contact with GLY1927 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1925A GLN 2.9 2.6 + - - -
1926A SER* 1.3 78.4 - - - +
1928A THR* 1.3 60.6 + - - -
1930A ALA* 3.2 3.6 + - - +
1931A GLU* 3.0 24.7 + - - +
1946A ALA* 3.8 7.7 - - - +
1947A SER* 5.8 0.9 - - - -
1950A VAL* 3.7 20.8 - - - +
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Residues in contact with THR1928 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1770A ILE* 3.9 2.2 - - - +
1771A TYR 5.1 4.9 - - - -
1772A THR* 3.4 14.5 - - - +
1773A PRO* 5.7 2.0 - - + -
1925A GLN* 3.1 37.1 + - + +
1927A GLY* 1.3 71.4 - - - +
1929A ILE* 1.3 67.5 + - - +
1931A GLU* 3.5 14.4 + - - +
1932A MET* 3.3 31.7 + - + +
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Residues in contact with ILE1929 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1770A ILE* 3.8 21.7 - - + +
1772A THR* 3.5 21.1 - - + -
1924A PRO 3.1 28.5 - - - +
1925A GLN 3.1 16.8 - - - +
1926A SER* 3.4 5.8 + - - +
1927A GLY 3.3 0.6 - - - -
1928A THR* 1.3 81.0 + - - +
1930A ALA* 1.3 63.6 + - - +
1932A MET 3.3 0.2 + - - -
1933A ILE* 3.1 44.6 + - + +
1970A LEU* 4.1 32.3 - - + -
1974A LYS* 4.6 9.4 - - + -
1977A LEU* 4.9 2.7 - - + -
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Residues in contact with ALA1930 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1926A SER 3.0 14.7 + - - +
1927A GLY 3.6 3.8 - - - +
1929A ILE* 1.3 80.0 - - - +
1931A GLU* 1.3 58.7 + - - +
1933A ILE* 3.9 0.5 - - - +
1934A LEU* 2.9 36.7 + - + +
1946A ALA* 4.0 16.2 - - + +
1949A ILE* 5.8 0.9 - - + -
1950A VAL* 4.5 4.5 - - + -
1973A LEU* 4.2 17.3 - - + -
1977A LEU* 3.6 24.7 - - + -
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Residues in contact with GLU1931 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1927A GLY 3.0 15.6 + - - +
1928A THR* 3.7 17.3 - - - +
1929A ILE 3.3 0.2 - - - -
1930A ALA* 1.3 78.4 - - - +
1932A MET* 1.3 68.9 + - - +
1934A LEU* 3.7 0.2 - - - +
1935A GLN* 2.7 39.2 + - - +
1942A SER* 3.5 23.7 + - - +
1943A LYS* 3.1 47.5 - - + +
1946A ALA* 3.6 15.0 - - + +
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Residues in contact with MET1932 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1706A LEU* 3.7 36.3 - - + +
1707A HIS* 6.4 0.2 - - - -
1710A ASN* 5.1 19.5 - - + +
1770A ILE* 3.7 31.6 - - + -
1771A TYR 5.6 3.4 - - - +
1928A THR* 3.3 20.9 - - + +
1929A ILE 3.3 2.2 + - - -
1931A GLU* 1.3 90.1 - - - +
1933A ILE* 1.3 61.3 + - - +
1935A GLN* 3.2 17.7 + - - +
1936A ILE* 2.8 32.7 + - - +
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Residues in contact with ILE1933 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1770A ILE* 3.7 18.6 - - + -
1929A ILE* 3.1 37.6 + - + +
1932A MET* 1.3 73.8 - - - +
1934A LEU* 1.3 63.9 + - - +
1935A GLN 3.0 1.1 - - - -
1936A ILE* 3.1 7.2 + - - +
1937A MET* 3.0 44.8 + - + +
1974A LYS* 3.8 23.1 - - + +
1977A LEU* 3.6 29.8 - - + +
1978A ARG* 4.4 26.0 + - - +
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Residues in contact with LEU1934 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1930A ALA* 2.9 25.1 + - + +
1931A GLU 3.7 3.8 - - - +
1933A ILE* 1.3 77.5 - - - +
1935A GLN* 1.3 56.3 + - - +
1937A MET* 3.5 11.5 + - + +
1938A GLY 3.0 17.8 + - - -
1939A PHE* 3.3 45.5 + - + +
1942A SER* 4.0 13.9 - - - +
1945A LEU* 3.7 29.6 - - + -
1946A ALA* 3.7 15.9 - - - +
1949A ILE* 3.8 15.0 - - + -
1977A LEU* 3.5 26.0 - - + -
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Residues in contact with GLN1935 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1680A ILE* 6.1 1.0 - - - +
1684A LEU* 3.8 19.0 - - + +
1706A LEU* 4.2 25.6 - - + +
1931A GLU* 2.7 23.0 + - - +
1932A MET* 3.2 24.8 - - - +
1933A ILE 3.0 0.2 - - - -
1934A LEU* 1.3 72.5 - - - +
1936A ILE* 1.3 55.3 + - + +
1938A GLY* 2.9 28.2 + - - +
1942A SER* 3.7 22.5 + - - -
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Residues in contact with ILE1936 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1684A LEU* 3.7 7.3 - - - +
1687A LEU* 3.3 17.8 - - - +
1699A GLU* 3.4 46.0 - - + +
1702A LEU* 3.5 28.0 - - + -
1703A VAL* 3.4 36.1 - - + +
1706A LEU* 4.0 11.2 - - + -
1770A ILE* 5.2 3.1 - - + -
1932A MET 2.8 23.1 + - - +
1933A ILE* 3.1 6.2 + - - +
1935A GLN* 1.3 71.8 - - - +
1937A MET* 1.3 60.9 + - - +
1938A GLY* 2.9 5.1 + - - -
1978A ARG* 6.1 3.1 - - - +
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Residues in contact with MET1937 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1684A LEU* 5.3 0.2 - - - -
1699A GLU* 5.5 6.1 - - - +
1933A ILE* 3.0 47.7 + - + +
1934A LEU* 3.7 19.1 - - + +
1936A ILE* 1.3 76.6 - - - +
1938A GLY* 1.3 55.9 + - - +
1939A PHE* 3.0 39.0 + - + +
1977A LEU 3.3 26.9 - - - +
1978A ARG* 5.4 9.2 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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