Contacts of the helix formed by residues 1937 - 1955 (chain A) in PDB entry 4M6W
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 CYS1937 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1899A GLU* 4.1 5.6 - - - +
1902A ARG* 3.5 21.3 - - - +
1935A SER* 2.6 23.6 + - - -
1936A SER* 1.3 90.3 - - - +
1938A GLN* 1.3 61.3 + - - +
1939A GLU* 3.2 15.5 - - + +
1940A GLU* 3.2 21.9 + - - +
1941A THR* 2.9 15.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1938 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1829A SER 4.1 12.5 + - - -
1830A GLY* 3.3 10.8 - - - -
1831A LEU 4.9 0.8 - - - +
1832A GLU* 3.1 29.6 + - + +
1833A VAL* 3.1 30.6 + - + +
1865A ARG* 3.7 14.3 - - - +
1899A GLU* 3.6 24.0 + - - +
1902A ARG* 3.4 28.0 - - - +
1937A CYS* 1.3 71.5 - - - +
1939A GLU* 1.3 59.1 + - - +
1941A THR* 3.5 2.5 - - - -
1942A ALA* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1939 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1832A GLU* 4.2 16.9 - - + +
1836A SER* 3.0 25.1 + - - -
1840A ILE* 4.6 14.8 - - - +
1841A HIS* 3.9 12.5 + - - -
1902A ARG* 4.8 0.4 - - - +
1937A CYS* 3.2 13.6 - - + +
1938A GLN* 1.3 79.2 - - - +
1940A GLU* 1.3 61.8 + - - +
1942A ALA* 3.3 2.8 + - - +
1943A ASP* 3.2 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1940 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1934A PHE 3.6 8.1 - - - +
1935A SER* 3.5 13.1 - - - +
1936A SER* 2.6 41.8 + - - -
1937A CYS* 3.2 20.3 + - - +
1939A GLU* 1.3 76.5 - - - +
1941A THR* 1.3 60.0 + - - +
1943A ASP* 3.2 10.9 + - + +
1944A LEU* 3.0 35.8 + - + +
101B PHE* 5.6 2.8 - - - -
102B PRO* 4.4 26.5 - - + +
105B GLN* 5.0 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1941 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1833A VAL* 4.4 8.7 - - + -
1865A ARG* 4.3 18.4 - - - +
1897A ILE* 3.9 28.0 - - + -
1899A GLU* 2.8 26.9 + - - +
1935A SER* 2.7 27.4 + - - -
1937A CYS 2.9 4.7 + - - -
1938A GLN* 3.5 9.6 - - - -
1940A GLU* 1.3 73.7 - - - +
1942A ALA* 1.3 59.4 + - - +
1944A LEU* 3.4 7.6 + - - +
1945A LEU* 3.0 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1942 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1833A VAL* 3.8 21.7 - - + +
1836A SER* 3.6 31.0 - - - +
1837A LEU* 3.6 17.7 - - + +
1841A HIS* 4.2 4.7 - - + -
1938A GLN 3.0 10.7 + - - +
1939A GLU 3.5 9.4 - - - +
1940A GLU 3.2 0.4 - - - -
1941A THR* 1.3 72.9 - - - +
1943A ASP* 1.3 60.6 + - - +
1945A LEU* 3.2 1.7 + - - +
1946A LYS* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1943 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1841A HIS* 3.9 19.6 + - + +
1939A GLU* 3.2 11.2 + - - +
1940A GLU* 3.2 15.1 + - + +
1942A ALA* 1.3 78.5 - - - +
1944A LEU* 1.3 59.5 + - + +
1946A LYS* 3.4 18.0 + - - +
1947A GLU* 3.0 54.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1944 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1897A ILE* 4.2 20.0 - - + -
1933A LEU* 4.2 23.6 - - + -
1934A PHE 3.9 12.6 - - - +
1935A SER* 3.9 28.7 - - - -
1940A GLU* 3.0 22.0 + - + +
1941A THR* 3.4 8.7 - - - +
1943A ASP* 1.3 80.2 - - + +
1945A LEU* 1.3 57.0 + - - +
1947A GLU* 3.3 17.5 + - - +
1948A LEU* 2.9 35.9 + - + +
102B PRO* 6.0 3.4 - - + +
105B GLN* 4.3 13.9 - - + +
110B LEU* 4.6 6.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
1820A ILE* 4.3 9.0 - - + -
1833A VAL* 3.6 30.7 - - + -
1837A LEU* 3.9 22.4 - - + -
1855A TYR* 3.9 29.2 - - + -
1857A VAL* 3.7 2.5 - - + +
1863A VAL* 3.8 40.4 - - + -
1897A ILE* 3.9 9.2 - - + -
1941A THR* 3.0 19.7 + - + +
1942A ALA 3.2 4.5 + - - +
1944A LEU* 1.3 72.9 - - - +
1946A LYS* 1.3 59.1 + - - +
1948A LEU* 3.4 6.4 + - + +
1949A SER* 2.6 34.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1946 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1815A GLY* 4.6 11.9 + - - +
1816A LYS* 5.4 7.9 - - - +
1837A LEU* 4.1 2.1 - - + +
1841A HIS* 3.4 42.6 + - + +
1843A LEU* 4.3 16.8 - - + -
1942A ALA 2.9 14.0 + - - +
1943A ASP* 3.5 25.7 + - - +
1944A LEU 3.4 0.2 - - - -
1945A LEU* 1.3 75.5 - - - +
1947A GLU* 1.3 75.0 + - + +
1949A SER* 3.2 9.8 + - - -
1950A LEU* 3.2 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1947 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1943A ASP* 3.0 40.9 + - - +
1944A LEU* 3.7 15.8 - - - +
1945A LEU 3.3 0.2 - - - -
1946A LYS* 1.3 87.5 - - + +
1948A LEU* 1.3 62.4 + - - +
1950A LEU* 3.4 8.4 + - + +
1951A VAL* 3.2 27.5 + - - +
106B LYS* 3.8 40.8 - - - +
110B LEU* 3.2 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1948 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1857A VAL* 4.2 11.2 - - + -
1861A MET* 4.2 17.0 - - + -
1863A VAL* 4.0 23.8 - - + -
1895A CYS* 3.9 26.2 - - + -
1897A ILE* 5.1 2.5 - - + -
1933A LEU* 4.3 12.6 - - + -
1944A LEU* 2.9 20.5 + - + +
1945A LEU* 3.7 8.1 - - + +
1946A LYS 3.4 0.2 - - - -
1947A GLU* 1.3 75.3 - - - +
1949A SER* 1.3 62.2 + - - +
1951A VAL* 3.6 6.6 + - + +
1952A GLU* 3.2 28.5 + - - +
109B VAL* 6.0 0.7 - - + -
110B LEU* 3.9 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1949 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1818A THR* 3.7 23.4 - - - +
1819A CYS 4.9 1.6 + - - -
1820A ILE* 4.2 7.6 - - - +
1843A LEU* 4.4 6.2 - - - +
1857A VAL* 3.3 26.7 + - - +
1945A LEU 2.6 22.4 + - - -
1946A LYS* 3.2 11.9 + - - -
1948A LEU* 1.3 76.4 - - - +
1950A LEU* 1.3 60.1 + - - +
1952A GLU* 3.4 3.6 + - - +
1953A GLN* 2.8 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1950 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1815A GLY* 3.5 42.0 - - - +
1818A THR* 4.4 11.0 - - - +
1843A LEU* 5.7 0.7 - - + -
1946A LYS* 3.2 32.1 + - + +
1947A GLU* 3.8 10.1 - - + +
1949A SER* 1.3 79.5 - - - +
1951A VAL* 1.3 56.9 + - - +
1953A GLN* 3.0 8.0 + - + +
1954A ARG* 2.7 64.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1951 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1947A GLU 3.2 16.7 + - - +
1948A LEU* 3.8 9.4 - - + +
1950A LEU* 1.3 75.8 - - - +
1952A GLU* 1.3 62.1 + - + +
1954A ARG* 3.3 21.3 + - - +
1955A LYS* 3.0 47.7 + - + +
106B LYS* 6.2 1.6 - - - +
110B LEU* 4.2 37.9 - - + +
111B ASP* 5.7 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1952 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1857A VAL* 4.3 9.9 - - + +
1858A SER* 2.9 38.9 + - - +
1860A ARG* 3.1 36.3 + - - -
1861A MET* 3.4 24.4 - - + +
1893A ARG* 5.4 0.2 + - - -
1948A LEU 3.2 17.5 + - - +
1949A SER* 3.8 4.7 - - - +
1951A VAL* 1.3 78.6 - - + +
1953A GLN* 1.3 63.9 + - - +
1955A LYS* 3.4 14.4 + - - +
1957A VAL* 3.2 34.9 + - + +
1958A GLY* 3.3 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1953 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1818A THR* 3.4 44.7 + - + +
1819A CYS 4.5 2.2 - - - +
1949A SER 2.8 20.6 + - - +
1950A LEU* 3.0 11.9 + - + +
1952A GLU* 1.3 75.4 - - - +
1954A ARG* 1.3 64.6 + - + +
1956A ASN* 3.0 15.1 + - - -
1958A GLY* 3.7 12.0 - - - -
1959A ILE* 4.4 6.2 - - + +
1960A HIS* 3.1 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1954 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1950A LEU* 2.7 48.9 + - + +
1951A VAL* 3.6 18.1 - - - +
1953A GLN* 1.3 73.5 - - + +
1955A LYS* 1.3 57.5 + - + +
1956A ASN* 3.1 5.1 + - - +
106B LYS* 4.8 14.5 - - - +
111B ASP* 5.7 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1955 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1860A ARG* 4.0 6.2 - - - +
1893A ARG* 3.3 11.3 - - - +
1951A VAL* 3.0 32.2 + - + +
1952A GLU* 3.8 23.2 + - - +
1953A GLN 3.2 0.8 - - - -
1954A ARG* 1.3 75.4 - - + +
1956A ASN* 1.3 62.5 + - - +
1957A VAL* 3.0 17.3 + - + +
2102A SO4 2.5 46.1 + - - +
----------------------------------------------------------
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