Contacts of the helix formed by residues 1946 - 1954 (chain A) in PDB entry 6FF7
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 ASN1946 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1942A ALA 2.9 21.0 + - - +
1943A LEU 3.7 0.4 - - - -
1944A HIS 3.3 0.2 - - - -
1945A VAL* 1.3 82.0 - - + +
1947A ASN* 1.3 65.3 + - - +
1948A ASP* 3.2 6.4 + - + +
1949A ARG* 4.8 9.9 - - + +
1950A ALA* 3.3 14.1 + - - +
1986A LEU* 6.3 3.1 - - + -
1990A ASP* 5.8 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1947 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1898A LYS* 5.2 13.5 - - + -
1943A LEU* 3.4 22.1 + - + +
1944A HIS 5.0 1.0 + - - -
1946A ASN* 1.3 73.6 - - - +
1948A ASP* 1.3 50.8 + - - +
1951A LYS* 2.8 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1948 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5173 GLU* 4.8 16.1 - - + +
1946A ASN* 3.2 4.4 - - + -
1947A ASN* 1.3 78.0 - - - +
1949A ARG* 1.3 60.4 + - + +
1951A LYS* 3.2 6.6 + - - +
1952A VAL* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1949 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1946A ASN* 4.0 9.2 + - + +
1948A ASP* 1.3 76.9 - - + +
1950A ALA* 1.3 62.0 + - - +
1952A VAL* 3.8 6.0 - - - +
1953A ILE* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1950 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1939A ILE 5.0 1.3 - - - +
1942A ALA* 3.4 32.8 - - + +
1943A LEU* 3.7 10.5 - - + +
1946A ASN* 3.3 19.9 + - - +
1947A ASN 4.5 0.4 - - - +
1948A ASP 3.3 0.4 - - - -
1949A ARG* 1.3 76.2 - - - +
1951A LYS* 1.3 61.4 + - - +
1953A ILE* 4.0 5.7 - - - +
1954A LEU* 3.7 19.9 + - - +
1983A LEU* 6.0 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1951 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5173 GLU* 6.0 6.1 - - + -
5213 PRO 5.8 0.9 - - - +
5223 LEU* 4.3 28.0 - - + +
1947A ASN* 2.8 23.3 + - + +
1948A ASP* 3.4 5.8 - - - +
1950A ALA* 1.3 78.3 - - - +
1952A VAL* 1.3 61.7 + - - +
1953A ILE 3.5 0.2 + - - -
1954A LEU* 3.7 11.4 + - - +
1955A LYS* 4.0 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1952 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5133 ASP* 5.2 10.8 - - + +
5163 LYS* 5.3 12.8 - - + -
5173 GLU* 5.2 12.6 - - + +
1948A ASP 3.1 16.0 + - - +
1949A ARG* 3.3 6.0 + - - +
1951A LYS* 1.3 75.8 - - - +
1953A ILE* 1.3 64.7 + - - +
1954A LEU 3.4 0.2 - - - -
1955A LYS* 3.2 22.2 + - - +
1956A PRO* 4.5 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1953 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1949A ARG 2.9 18.3 + - - +
1950A ALA* 4.4 6.5 - - - +
1951A LYS 3.3 0.4 - - - -
1952A VAL* 1.3 78.1 - - - +
1954A LEU* 1.3 62.0 + - - +
1955A LYS 3.1 1.8 + - - -
1956A PRO* 3.5 18.3 - - - +
1979A VAL* 5.0 18.0 - - + +
1982A GLN* 5.7 11.0 - - + -
1983A LEU* 5.9 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1954 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5223 LEU* 4.9 9.2 - - + +
1950A ALA 3.7 16.0 + - - +
1951A LYS* 3.7 6.5 + - - +
1952A VAL 3.4 0.6 - - - -
1953A ILE* 1.3 76.9 - - - +
1955A LYS* 1.3 56.7 + - - +
1956A PRO 3.8 1.4 - - - -
1960A THR* 4.8 2.1 - - - -
1969A PRO* 4.3 19.6 - - + +
1979A VAL* 5.7 5.2 - - - -
----------------------------------------------------------
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