Contacts of the helix formed by residues 1935 - 1952 (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 TRP1935 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1838D ALA* 5.5 12.1 - - - +
1930D LEU* 3.2 15.5 + - - +
1931D SER* 4.8 3.4 + - - +
1933D ASN 3.8 0.6 - - - -
1934D GLY* 1.3 76.9 - - - +
1936D LEU* 1.3 65.4 + - - +
1937D SER 3.7 1.3 - - - -
1938D PRO 4.2 3.1 - - - -
1939D ALA* 3.6 15.6 + - - -
2074D ASN 3.7 6.3 - - - -
2076D LEU* 4.2 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1936 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1935D TRP* 1.3 69.6 - - - +
1937D SER* 1.3 66.5 + - - +
1939D ALA* 3.2 1.9 + - - -
1940D LEU* 3.0 22.3 + - - -
2074D ASN* 3.3 19.1 + - - +
2075D SER 4.7 1.8 - - - -
2076D LEU* 4.0 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1937 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1840D THR 4.9 1.3 - - - -
1935D TRP 3.7 0.2 - - - -
1936D LEU* 1.3 74.6 - - - +
1938D PRO* 1.4 63.7 - - - +
1940D LEU* 4.0 0.6 - - - +
1941D ALA* 2.9 21.5 + - - -
2074D ASN* 5.2 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1938 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1837D ASN 5.7 2.5 - - - +
1838D ALA 4.7 9.3 - - - +
1840D THR 3.5 23.7 - - - +
1841D LYS* 5.5 1.6 - - - -
1930D LEU* 6.2 0.7 - - - -
1935D TRP 4.2 3.6 - - - +
1936D LEU 3.4 0.4 - - - -
1937D SER* 1.4 74.9 - - - +
1939D ALA* 1.3 58.0 + - - +
1941D ALA* 3.3 2.3 + - - -
1942D ALA* 2.9 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1939 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1926D CYS 5.8 0.2 - - - -
1927D VAL* 5.1 19.5 - - - +
1930D LEU* 5.5 4.3 - - - +
1931D SER* 5.4 5.6 - - - +
1935D TRP 3.6 12.6 + - - -
1936D LEU 3.2 5.2 + - - -
1937D SER 3.2 0.4 - - - -
1938D PRO* 1.3 75.3 - - - +
1940D LEU* 1.3 62.3 + - - +
1942D ALA* 2.9 12.9 + - - +
1943D MET* 3.0 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1940 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1936D LEU 3.0 15.3 + - - -
1937D SER 4.0 0.7 - - - -
1939D ALA* 1.3 73.7 - - - +
1941D ALA* 1.3 56.8 + - - +
1943D MET* 3.2 3.4 + - - +
1944D GLU* 2.9 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1941 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1841D LYS* 6.4 1.3 - - - +
1842D VAL* 5.7 9.2 - - - +
1937D SER 2.9 15.6 + - - -
1938D PRO* 3.6 4.5 - - - -
1940D LEU* 1.3 78.1 - - - +
1942D ALA* 1.3 55.1 + - - +
1944D GLU* 3.4 3.5 + - - +
1945D LEU* 2.9 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1942 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1923D ILE* 5.2 13.1 - - - +
1926D CYS 6.3 0.2 - - - -
1927D VAL* 5.8 6.5 - - - +
1938D PRO 2.9 10.4 + - - -
1939D ALA* 2.9 8.8 + - - +
1941D ALA* 1.3 73.3 - - - +
1943D MET* 1.3 65.4 + - - +
1945D LEU* 3.0 3.8 + - - +
1946D ALA* 2.9 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1943 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1927D VAL* 5.9 1.4 - - - +
1939D ALA 3.0 11.6 + - - -
1940D LEU* 3.2 4.0 + - - +
1942D ALA* 1.3 75.6 - - - +
1944D GLU* 1.3 62.1 + - - +
1946D ALA* 3.0 12.9 + - - +
1947D GLN* 3.0 10.0 + - - -
2110D SER 3.7 18.7 - - - +
2111D ASP* 4.6 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1944 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1940D LEU 2.9 14.3 + - - -
1941D ALA* 3.6 6.7 - - - +
1943D MET* 1.3 77.3 - - - +
1945D LEU* 1.3 54.6 + - - +
1947D GLN* 3.1 4.5 + - - +
1948D MET* 2.9 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1945 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1941D ALA 2.9 14.9 + - - -
1942D ALA* 3.0 5.9 + - - +
1944D GLU* 1.3 71.9 - - - +
1946D ALA* 1.3 66.4 + - - +
1948D MET* 3.2 3.1 + - - +
1949D VAL* 2.9 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1946 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1920D ILE* 6.2 3.8 - - - +
1923D ILE* 6.3 3.3 - - - +
1942D ALA 2.9 13.1 + - - -
1943D MET* 3.0 5.8 + - - +
1945D LEU* 1.3 75.5 - - - +
1947D GLN* 1.3 62.0 + - - +
1949D VAL* 3.2 1.2 + - - -
1950D THR* 3.0 19.6 + - - -
2111D ASP* 3.2 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1947 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1943D MET 3.0 11.6 + - - -
1944D GLU* 3.1 5.1 + - - +
1946D ALA* 1.3 76.0 - - - +
1948D MET* 1.3 55.7 + - - +
1950D THR 3.2 1.4 + - - -
1951D GLN* 3.0 26.9 + - - -
2110D SER 5.2 1.3 - - - -
2111D ASP 3.4 10.0 + - - -
2112D ALA 3.3 23.5 - - - +
2113D TYR 4.9 6.1 - - - -
2114D MET* 5.7 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1948 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1899D LEU* 5.4 1.6 - - - -
1944D GLU 2.9 14.6 + - - -
1945D LEU* 3.2 5.1 + - - +
1947D GLN* 1.3 75.7 - - - +
1949D VAL* 1.3 57.8 + - - +
1951D GLN* 4.7 0.4 - - - +
1952D ALA* 2.9 23.6 + - - -
1953D MET 3.1 27.8 + - - +
1954D TRP 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1949 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1945D LEU 2.9 13.6 + - - -
1946D ALA 3.7 2.7 - - - -
1948D MET* 1.3 75.4 - - - +
1950D THR* 1.3 66.6 + - - +
1951D GLN 3.4 0.3 + - - -
1952D ALA* 3.4 9.1 + - - +
2055D LEU 5.8 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1950 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1946D ALA 3.0 13.4 + - - -
1947D GLN 3.2 3.3 + - - -
1949D VAL* 1.3 77.8 - - - +
1951D GLN* 1.3 57.9 + - - +
2053D ALA* 4.6 17.7 - - - +
2055D LEU* 5.1 3.3 + - - -
2056D PHE* 4.8 8.5 + - - -
2111D ASP 5.1 2.9 - - - -
2112D ALA* 4.6 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1951 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1947D GLN 3.0 12.8 + - - -
1948D MET 3.8 0.4 - - - -
1950D THR* 1.3 75.1 - - - +
1952D ALA* 1.3 67.1 + - - +
1953D MET* 3.7 1.1 - - - -
1962D GLN* 5.6 7.6 - - - +
2053D ALA* 5.9 3.4 - - - +
2055D LEU* 6.4 1.8 - - - -
2112D ALA 4.3 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1952 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1898D HIS 4.1 14.7 - - - +
1899D LEU* 3.8 11.2 - - - +
1901D ARG* 5.1 4.0 + - - -
1948D MET 2.9 12.1 + - - -
1949D VAL* 3.4 8.9 + - - +
1950D THR 3.4 0.4 + - - -
1951D GLN* 1.3 80.0 - - - +
1953D MET* 1.3 56.8 + - - +
----------------------------------------------------------
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