Contacts of the strand formed by residues 1948 - 1959 (chain A) in PDB entry 6AJ4
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 ARG1948 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1816A PHE* 4.7 4.6 - - - -
1824A LEU* 4.2 13.9 - - - +
1829A PHE* 3.2 46.2 - - + -
1830A VAL 3.2 9.6 - - - +
1831A TYR* 2.9 48.1 + - + +
1850A TYR* 5.7 1.6 + - - -
1942A PHE* 4.3 0.2 - - - -
1944A TYR* 3.9 3.6 - - - -
1946A LYS* 3.6 23.9 - - + +
1947A THR* 1.3 83.4 + - - +
1949A VAL* 1.3 65.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1949 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1829A PHE* 4.3 2.7 - - - -
1830A VAL* 2.8 26.6 + - - +
1938A THR* 3.8 20.4 - - + +
1939A SER* 4.4 2.9 - - - +
1940A HIS* 3.7 48.0 - - + +
1942A PHE* 3.4 34.5 - - + -
1944A TYR* 4.1 10.5 - - + +
1948A ARG* 1.3 79.7 - - - +
1950A ASN* 1.3 64.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1950 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1827A GLN* 4.7 18.9 - - + +
1828A GLU 3.3 17.0 - - - +
1829A PHE* 3.8 22.1 - - + +
1938A THR* 4.6 0.7 - - - -
1939A SER* 3.1 42.6 + - - -
1949A VAL* 1.3 77.3 - - - +
1951A VAL* 1.3 67.0 + - - +
1952A THR* 5.8 0.4 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
1813A ARG* 5.2 0.2 - - + -
1828A GLU* 2.8 46.3 + - + +
1829A PHE 4.2 1.3 - - - +
1830A VAL* 4.2 14.8 - - + -
1936A LEU* 4.1 35.9 - - + -
1937A THR 3.5 11.4 - - - +
1938A THR* 4.4 2.2 - - + +
1950A ASN* 1.3 80.8 + - - +
1952A THR* 1.3 67.8 + - - +
1953A HIS 3.3 20.6 - - - +
1954A LYS* 5.2 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1952 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1908A ARG* 5.7 0.5 + - - -
1937A THR* 2.9 20.8 + - - +
1938A THR 4.1 4.0 + - - -
1939A SER* 3.6 31.4 - - - +
1950A ASN* 3.7 3.1 - - - +
1951A VAL* 1.3 83.3 - - - +
1953A HIS* 1.3 79.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1953 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1937A THR* 3.5 27.7 + - - +
1951A VAL* 3.3 19.4 - - - +
1952A THR* 1.3 92.8 + - - +
1954A LYS* 1.3 68.4 + - - +
1955A GLU* 5.8 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1954 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1813A ARG* 3.9 3.0 - - - +
1828A GLU* 3.7 28.5 + - - -
1867A PRO* 5.8 7.1 - - - +
1912A TYR* 3.7 17.3 + - - -
1934A THR* 4.1 13.2 - - + -
1935A ILE 3.2 13.0 - - - +
1936A LEU* 3.4 22.0 - - + -
1937A THR* 4.7 0.2 + - - -
1951A VAL* 5.2 2.5 - - + -
1953A HIS* 1.3 83.0 - - - +
1955A GLU* 1.3 68.8 + - - +
1956A GLU* 4.5 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1955 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1909A ARG* 2.4 34.1 + - - -
1933A LYS 3.7 0.9 - - - +
1934A THR* 3.3 5.2 - - - -
1935A ILE* 2.7 63.7 + - + +
1937A THR* 4.7 6.0 + - - +
1953A HIS* 5.8 1.6 - - + -
1954A LYS* 1.3 82.8 - - - +
1956A GLU* 1.3 64.8 + - - +
1957A ILE* 5.0 4.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1956 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1867A PRO* 6.0 2.1 - - - +
1932A ARG* 3.6 30.0 - - + +
1933A LYS 3.7 2.9 - - - -
1934A THR* 4.5 7.7 - - + +
1954A LYS* 4.5 18.3 - - - +
1955A GLU* 1.3 74.9 - - - +
1957A ILE* 1.3 65.6 + - - +
1958A ILE* 5.1 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1957 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1888A TYR* 4.9 4.0 - - - +
1932A ARG* 3.3 6.8 - - - +
1933A LYS* 2.6 68.3 + - + +
1935A ILE* 4.4 21.1 - - + -
1955A GLU* 5.0 5.2 - - + +
1956A GLU* 1.3 78.6 - - - +
1958A ILE* 1.3 70.7 + - - +
1959A LEU* 3.9 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1958 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1916A PHE* 4.0 27.6 - - + -
1930A PHE* 4.7 7.6 - - + -
1931A LYS 3.6 3.1 - - - +
1932A ARG* 5.3 4.7 - - + +
1956A GLU* 5.1 8.7 - - + +
1957A ILE* 1.3 86.1 - - - +
1959A LEU* 1.3 74.1 + - - +
1960A THR* 3.9 1.3 + - + +
1963A GLU* 3.8 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1959 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1930A PHE* 3.6 11.0 - - - -
1931A LYS* 2.8 52.4 + - + +
1933A LYS* 4.1 22.4 - - + -
1957A ILE* 3.9 18.6 - - + -
1958A ILE* 1.3 81.5 - - - +
1960A THR* 1.3 63.2 + - - +
1963A GLU* 3.4 22.4 - - + +
1964A VAL* 3.9 11.8 - - + +
1967A GLU* 3.4 40.8 - - + +
----------------------------------------------------------
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