Contacts of the helix formed by residues 1905 - 1934 (chain D) in PDB entry 6AH0
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 SER1905 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1904D LEU* 1.3 75.4 - - - +
1906D ALA* 1.3 61.4 + - - +
1907D GLU 3.1 4.3 + - - +
1908D LEU* 3.2 5.4 + - - +
1909D GLN* 2.8 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1906 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1623D GLY* 6.2 4.5 - - - -
1904D LEU 3.8 2.3 + - - -
1905D SER* 1.3 70.6 - - - +
1907D GLU* 1.3 56.7 + - - +
1909D GLN* 3.6 4.7 - - - +
1910D SER* 2.9 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1907 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1905D SER* 3.1 2.0 - - - +
1906D ALA* 1.3 79.5 - - - +
1908D LEU* 1.3 58.3 + - - +
1910D SER* 3.7 5.9 + - - -
1911D ASP* 3.7 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1908 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1905D SER* 3.2 6.1 + - - +
1907D GLU* 1.3 73.2 - - - +
1909D GLN* 1.3 59.5 + - - +
1910D SER 3.4 0.2 - - - -
1911D ASP* 3.3 4.2 + - - +
1912D THR* 2.9 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1909 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1904D LEU* 5.7 2.2 - - - +
1905D SER 2.8 16.7 + - - -
1906D ALA* 3.7 4.5 - - - +
1907D GLU 3.3 0.2 - - - -
1908D LEU* 1.3 75.3 - - - +
1910D SER* 1.3 65.3 + - - +
1912D THR* 3.2 3.3 + - - +
1913D GLU* 3.0 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1910 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1906D ALA 2.9 15.0 + - - -
1907D GLU 4.2 2.2 - - - -
1909D GLN* 1.3 74.0 - - - +
1911D ASP* 1.3 63.1 + - - +
1913D GLU* 3.1 4.8 + - - +
1914D GLU* 3.0 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1911 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1907D GLU 3.7 6.0 + - - -
1908D LEU* 3.3 10.0 + - - +
1909D GLN 3.2 0.6 - - - -
1910D SER* 1.3 75.0 - - - +
1912D THR* 1.3 62.7 + - - +
1914D GLU* 3.0 4.6 + - - +
1915D ILE* 2.9 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1912 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1894D LEU* 5.5 11.4 - - - +
1908D LEU 2.9 14.6 + - - -
1909D GLN* 3.2 5.1 + - - +
1911D ASP* 1.3 72.8 - - - +
1913D GLU* 1.3 64.2 + - - +
1915D ILE* 3.1 3.5 + - - +
1916D LEU* 2.9 20.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1913 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1909D GLN 3.0 13.4 + - - -
1910D SER* 3.5 4.5 - - - +
1912D THR* 1.3 74.9 - - - +
1914D GLU* 1.3 62.4 + - - +
1916D LEU* 3.4 3.0 + - - +
1917D SER* 3.0 20.1 + - - -
2057D PRO* 6.0 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1914 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1910D SER 3.0 13.1 + - - -
1911D ASP* 3.0 4.4 + - - +
1913D GLU* 1.3 72.9 - - - +
1915D ILE* 1.3 63.9 + - - +
1917D SER* 3.2 12.8 + - - +
1918D LYS 3.7 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1915 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1911D ASP 2.9 13.7 + - - -
1912D THR 3.6 2.9 - - - -
1914D GLU* 1.3 74.8 - - - +
1916D LEU* 1.3 62.8 + - - +
1917D SER 3.2 0.7 + - - -
1918D LYS 3.2 4.9 + - - -
1919D ALA* 3.0 19.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1916 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1912D THR 2.9 13.0 + - - -
1913D GLU* 3.7 4.0 - - - +
1915D ILE* 1.3 75.6 - - - +
1917D SER* 1.3 64.0 + - - +
1919D ALA* 3.2 13.6 + - - +
1920D ILE 4.4 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1917 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1913D GLU 3.0 14.1 + - - -
1914D GLU* 3.2 6.2 + - - +
1915D ILE 3.2 1.4 - - - -
1916D LEU* 1.3 77.8 - - - +
1918D LYS* 1.3 56.1 - - - +
1920D ILE 5.1 1.2 + - - -
2057D PRO 6.6 0.2 - - - -
2058D GLN* 6.2 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1918 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1914D GLU 3.7 4.8 + - - -
1915D ILE 3.2 6.6 + - - -
1917D SER* 1.3 74.4 - - - +
1919D ALA* 1.3 65.0 + - - +
1920D ILE 3.5 2.0 + - - -
1921D ARG* 3.6 10.2 + - - -
1922D LEU* 3.8 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1919 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1915D ILE 3.0 14.0 + - - -
1916D LEU* 3.2 9.3 + - - +
1918D LYS* 1.3 76.7 - - - +
1920D ILE* 1.3 63.1 + - - +
1922D LEU* 3.0 6.4 + - - -
1923D ILE* 3.0 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1920 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1916D LEU 4.4 4.6 + - - -
1917D SER 5.1 1.2 + - - -
1918D LYS 3.5 0.8 - - - -
1919D ALA* 1.3 73.3 - - - +
1921D ARG* 1.3 61.2 + - - +
1923D ILE* 3.2 3.3 + - - +
1924D GLN* 2.9 21.5 + - - -
1946D ALA* 6.2 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1921 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1822D TYR* 5.7 9.1 - - - +
1918D LYS 3.6 6.7 + - - -
1919D ALA 3.2 0.8 + - - -
1920D ILE* 1.3 74.5 - - - +
1922D LEU* 1.3 57.8 + - - +
1924D GLN* 3.2 1.6 + - - -
1925D ALA* 2.9 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1922 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1849D ILE* 6.5 0.4 - - - -
1918D LYS 3.8 7.1 + - - -
1919D ALA* 3.0 7.3 + - - +
1921D ARG* 1.3 74.7 - - - +
1923D ILE* 1.3 61.4 + - - +
1925D ALA* 3.0 4.5 + - - +
1926D CYS* 2.9 18.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1923 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1919D ALA 3.0 13.1 + - - -
1920D ILE* 3.6 4.3 - - - +
1922D LEU* 1.3 73.7 - - - +
1924D GLN* 1.3 61.5 + - - +
1926D CYS* 3.0 5.5 + - - +
1927D VAL* 2.9 17.7 + - - -
1942D ALA* 5.2 12.0 - - - +
1946D ALA* 6.3 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1924 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1920D ILE 2.9 14.0 + - - -
1921D ARG* 3.6 3.8 - - - +
1923D ILE* 1.3 74.4 - - - +
1925D ALA* 1.3 62.9 + - - +
1927D VAL* 3.0 5.3 + - - +
1928D ASP* 2.9 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1925 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1921D ARG 2.9 13.7 + - - -
1922D LEU* 3.0 5.8 + - - +
1924D GLN* 1.3 76.0 - - - +
1926D CYS* 1.3 58.2 + - - +
1928D ASP* 3.1 2.9 + - - +
1929D VAL* 2.9 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1926 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1922D LEU 2.9 12.9 + - - -
1923D ILE 3.0 4.7 + - - -
1925D ALA* 1.3 75.1 - - - +
1927D VAL* 1.3 65.0 + - - +
1929D VAL* 3.3 1.8 + - - +
1930D LEU* 2.9 23.2 + - - -
1939D ALA* 5.8 0.2 - - - -
1942D ALA* 6.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1927 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1923D ILE 2.9 12.7 + - - -
1924D GLN* 3.0 7.0 + - - +
1926D CYS* 1.3 74.9 - - - +
1928D ASP* 1.3 56.6 + - - +
1930D LEU* 3.9 0.3 - - - -
1931D SER* 2.9 27.9 + - - -
1939D ALA* 5.1 17.8 - - - +
1942D ALA* 5.8 5.7 - - - +
1943D MET 5.9 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1928 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1924D GLN 2.9 12.9 + - - -
1925D ALA* 3.1 4.4 + - - +
1927D VAL* 1.3 73.9 - - - +
1929D VAL* 1.3 58.0 + - - +
1931D SER* 4.0 0.4 - - - +
1932D SER* 2.9 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1929 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1925D ALA 2.9 17.2 + - - -
1926D CYS* 3.3 3.3 + - - +
1928D ASP* 1.3 72.3 - - - +
1930D LEU* 1.3 57.3 + - - +
1932D SER* 3.9 0.9 - - - +
1933D ASN* 2.9 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1930 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1926D CYS 2.9 15.5 + - - -
1927D VAL* 3.9 0.7 - - - +
1929D VAL* 1.3 77.1 - - - +
1931D SER* 1.3 59.7 + - - +
1933D ASN* 3.3 2.6 + - - +
1934D GLY 2.8 22.9 + - - -
1935D TRP* 3.2 17.0 + - - +
1938D PRO 6.2 0.4 - - - -
1939D ALA* 5.5 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1931 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1927D VAL 2.9 16.7 + - - -
1928D ASP* 4.0 0.7 - - - +
1930D LEU* 1.3 75.3 - - - +
1932D SER* 1.3 63.1 + - - +
1934D GLY* 3.1 14.0 + - - -
1935D TRP 4.8 4.3 - - - +
1939D ALA* 5.4 3.6 - - - +
2076D LEU* 5.0 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1932 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1928D ASP 2.9 17.0 + - - -
1929D VAL 3.9 0.9 - - - -
1931D SER* 1.3 78.2 - - - +
1933D ASN* 1.3 60.1 + - - +
1934D GLY* 3.1 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1933 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1929D VAL 2.9 17.0 + - - -
1930D LEU* 3.3 5.6 + - - +
1932D SER* 1.3 73.7 - - - +
1934D GLY* 1.3 59.5 + - - +
1935D TRP 3.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1934 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1930D LEU 2.8 7.3 + - - -
1931D SER 3.1 11.6 + - - -
1932D SER 3.0 5.1 - - - -
1933D ASN* 1.3 79.8 - - - +
1935D TRP* 1.3 56.7 + - - -
2074D ASN 3.7 6.1 - - - +
2075D SER* 3.8 3.3 - - - -
2076D LEU* 3.3 28.4 + - - -
----------------------------------------------------------
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