Contacts of the helix formed by residues 1978 - 1999 (chain C) in PDB entry 5Y3R
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 PHE1978 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1977C ILE* 1.3 109.4 - - + +
1979C GLU* 1.3 54.2 - - + +
1980C ASN 3.2 0.2 - - - -
1981C LEU* 2.9 6.3 + - - +
1982C ILE* 2.2 46.0 + - + +
2031C LEU* 3.4 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1979 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1931C ASN 4.0 4.2 - - - +
1932C GLN* 2.8 30.6 - - - +
1933C LEU 2.7 27.9 - - - +
1934C LEU* 5.5 1.6 - - - -
1977C ILE* 4.7 1.2 - - - +
1978C PHE* 1.3 77.4 - - + +
1980C ASN* 1.3 64.1 + - - +
1981C LEU 3.1 0.2 - - - -
1982C ILE* 3.4 22.3 - - + +
1983C ASP* 2.8 31.6 + - + +
1987C ARG* 5.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1980 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1974C ASN* 3.4 16.2 - - - +
1976C LEU 3.8 2.0 - - - +
1977C ILE* 3.2 51.4 - - + +
1979C GLU* 1.3 81.0 - - - +
1981C LEU* 1.3 49.6 + - - +
1984C LEU* 2.5 35.1 + - - +
1987C ARG* 4.2 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1981 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1974C ASN 3.4 21.5 - - - +
1975C LEU* 4.4 4.7 - - + -
1976C LEU* 3.2 30.3 + - + +
1977C ILE 3.3 17.3 - - - +
1978C PHE* 2.9 12.2 + - + +
1980C ASN* 1.3 78.9 - - - +
1982C ILE* 1.3 66.0 + - - +
1984C LEU* 3.0 15.0 - - + +
1985C LYS* 3.0 25.9 + - + +
2028C LEU* 6.0 2.5 - - + -
2031C LEU* 5.5 3.4 - - + -
2033C ASP* 3.2 40.2 - - - +
2037C SER* 4.4 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1982 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1934C LEU* 4.6 3.1 - - + -
1935C GLU* 3.7 46.9 - - + +
1978C PHE* 2.2 36.3 + - + +
1979C GLU* 3.3 24.9 + - + +
1981C LEU* 1.3 72.2 - - - +
1983C ASP* 1.3 76.0 + - - +
1985C LYS* 2.9 16.3 - - - +
1986C ARG* 2.8 28.0 + - + +
2036C LEU* 6.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1983 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1931C ASN 4.8 3.2 - - - +
1933C LEU* 2.7 36.3 + - - +
1934C LEU 3.7 6.2 - - - +
1938C ARG* 2.9 31.7 + - - +
1979C GLU* 2.8 17.7 + - + +
1982C ILE* 1.3 80.1 - - - +
1984C LEU* 1.3 70.3 + - - +
1986C ARG* 3.2 23.0 - - - +
1987C ARG* 2.8 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1984 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1972C GLU* 3.4 23.6 - - + +
1973C LYS* 4.9 1.1 - - - -
1974C ASN* 3.0 59.7 - - + +
1975C LEU* 4.9 3.4 - - + -
1980C ASN 2.5 28.2 + - - +
1981C LEU* 3.0 21.5 - - + +
1982C ILE 3.0 0.6 - - - -
1983C ASP* 1.3 80.9 - - - +
1985C LYS* 1.3 65.5 + - + +
1987C ARG* 3.2 13.1 + - - +
1988C TYR* 2.9 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1985 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1981C LEU* 3.1 15.0 - - + +
1982C ILE* 2.9 24.2 - - - +
1984C LEU* 1.3 78.4 - - + +
1986C ARG* 1.3 68.3 + - + +
1987C ARG 3.1 1.0 + - - -
1988C TYR* 3.2 23.6 + - + +
1989C ASN* 3.5 29.6 + - - +
2031C LEU 4.6 1.4 + - - -
2032C ALA 3.6 3.8 + - - -
2033C ASP* 3.3 16.0 + - - +
2036C LEU* 3.1 31.8 - - + +
2037C SER* 2.8 56.3 + - - +
2040C MET* 5.0 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1986 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1935C GLU* 3.0 62.9 + - - +
1936C ARG* 4.3 1.2 - - - +
1938C ARG* 3.1 25.1 - - - +
1939C LEU* 4.2 19.2 - - - +
1982C ILE* 2.8 28.1 + - + +
1983C ASP* 3.2 16.2 - - - +
1985C LYS* 1.3 75.1 - - + +
1987C ARG* 1.3 49.1 + - - +
1989C ASN* 5.6 0.2 - - - -
1990C PHE* 2.4 41.2 + - - +
2036C LEU* 5.1 6.7 - - - +
2040C MET* 4.2 31.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1987 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1928C ALA* 3.7 16.1 - - + +
1929C GLY* 5.0 4.3 - - - -
1930C GLU* 5.7 8.5 - - - +
1938C ARG* 3.3 29.8 - - - +
1969C GLU* 3.7 26.2 + - - +
1972C GLU* 2.1 38.4 + - - -
1974C ASN* 2.9 16.4 - - - +
1979C GLU 5.0 0.8 + - - -
1980C ASN* 4.2 5.7 + - - +
1983C ASP* 2.8 51.3 + - - +
1984C LEU* 3.2 10.8 - - - +
1985C LYS 3.1 0.4 + - - -
1986C ARG* 1.3 78.1 - - - +
1988C TYR* 1.3 60.6 + - + +
1990C PHE* 3.0 9.7 - - - +
1991C PRO* 2.7 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1988 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1969C GLU* 4.2 9.4 - - + +
1970C LYS* 3.5 67.5 + - + +
1972C GLU* 4.2 11.9 - - + +
1984C LEU* 2.9 42.2 - - + +
1985C LYS* 3.2 20.6 - - + +
1987C ARG* 1.3 74.9 - - - +
1989C ASN* 1.3 99.5 + - - +
1991C PRO* 2.9 20.7 - - - +
1992C VAL* 4.2 9.2 - - - +
2021C GLY* 5.3 3.3 + - - -
2025C MET* 6.1 0.7 - - - +
2037C SER 4.8 1.0 + - - -
2041C SER* 4.5 12.6 - - - -
2044C ASP* 4.4 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1989 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1985C LYS 3.5 11.9 + - - +
1986C ARG* 4.8 0.4 - - - +
1988C TYR* 1.3 116.7 + - - +
1990C PHE* 1.3 66.0 + - - +
1992C VAL* 3.1 12.0 - - - +
1993C GLU* 2.9 24.6 + - - +
2040C MET* 3.1 37.9 + - + +
2041C SER* 3.9 2.4 - - - +
2043C PHE* 3.3 25.9 - - + +
2044C ASP* 3.0 20.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1990 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1924C THR* 4.9 3.4 - - - -
1925C GLU* 5.3 1.6 - - - -
1928C ALA* 3.7 24.9 - - + -
1938C ARG* 2.8 50.9 - - + -
1941C HIS* 3.0 32.3 - + - -
1942C CYS* 2.9 57.1 - - + -
1945C TYR* 5.9 2.5 - + - -
1986C ARG 2.4 27.0 + - - +
1987C ARG* 3.0 13.5 - - - +
1989C ASN* 1.3 76.4 - - - +
1991C PRO* 1.3 62.8 - - + +
1993C GLU* 2.9 18.0 - - - +
1994C VAL* 5.8 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1991 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1963C GLN* 3.9 32.3 - - + +
1966C LEU* 5.4 7.0 - - + +
1969C GLU* 5.2 5.6 - - - +
1970C LYS* 6.5 0.2 - - + -
1987C ARG 2.7 27.1 - - - +
1988C TYR* 2.9 24.9 - - - +
1989C ASN 3.3 0.4 - - - -
1990C PHE* 1.3 78.6 - - + +
1992C VAL* 1.3 66.5 + - + +
1993C GLU 3.0 2.1 + - - -
1994C VAL* 3.1 11.7 - - + +
1995C GLU* 2.7 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1992 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1967C PHE* 6.2 3.1 - - + -
1970C LYS* 5.4 11.9 - - + +
1988C TYR 4.2 8.1 - - - +
1989C ASN* 3.1 31.4 - - + +
1991C PRO* 1.3 78.6 - - + +
1993C GLU* 1.3 64.3 + - - +
1995C GLU* 3.0 33.0 + - - +
1996C VAL* 3.0 17.9 + - + +
1997C PRO* 3.2 4.3 - - - +
2043C PHE* 5.4 0.9 - - + -
2044C ASP* 5.5 2.2 - - - +
2047C THR* 3.6 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1993 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1938C ARG 4.4 1.4 - - - +
1939C LEU* 3.8 26.3 - - - +
1942C CYS* 3.1 31.7 - - - +
1943C ALA* 4.3 3.7 + - - -
1946C ASN* 3.8 3.1 + - - -
1986C ARG 4.9 0.2 - - - +
1989C ASN* 2.9 13.2 + - + +
1990C PHE* 2.9 30.0 - - - +
1992C VAL* 1.3 75.1 - - - +
1994C VAL* 1.3 54.0 + - - +
1997C PRO* 3.0 26.0 - - - +
2043C PHE* 6.2 6.5 - - + -
2047C THR* 4.6 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1994 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1942C CYS* 3.1 21.9 - - - -
1945C TYR* 3.3 37.5 - - + -
1946C ASN* 3.2 20.6 + - + +
1949C ILE* 3.3 24.7 - - + -
1990C PHE* 4.1 2.0 - - + +
1991C PRO* 3.1 13.9 - - + +
1993C GLU* 1.3 77.9 - - - +
1995C GLU* 1.3 60.9 + - - +
1997C PRO* 3.2 1.2 - - - +
1998C MET* 2.7 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1995 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1960C LYS* 6.4 2.2 - - + -
1963C GLN* 6.2 5.2 - - + -
1991C PRO* 2.7 23.5 + - + +
1992C VAL* 3.0 26.0 + - - +
1994C VAL* 1.3 71.8 - - + +
1996C VAL* 1.3 79.4 + - - +
1998C MET* 2.9 25.3 - - - +
1999C GLU 2.5 26.6 - - - +
2000C ARG* 6.0 0.9 - - - -
2004C TYR* 4.3 23.0 - - - -
2009C LYS* 5.3 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1996 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1992C VAL* 3.0 8.7 + - + +
1995C GLU* 1.3 104.9 - - - +
1997C PRO* 1.3 63.2 - - + +
1999C GLU 2.9 6.0 - - - -
2000C ARG* 2.8 52.3 + - + +
2047C THR* 4.3 15.3 - - - +
2048C GLY* 4.9 2.9 - - - +
2050C GLN* 3.1 38.7 + - + +
2051C SER* 3.6 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1997 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1946C ASN* 3.7 11.0 - - - +
1950C SER* 4.2 3.9 + - - +
1992C VAL 3.2 5.4 - - - +
1993C GLU 3.0 25.6 - - - +
1994C VAL 3.2 2.5 - - - +
1996C VAL* 1.3 89.3 - - + +
1998C MET* 1.3 67.2 + - - +
1999C GLU* 3.3 1.4 + - - -
2000C ARG 4.7 0.2 + - - -
2047C THR* 5.0 4.5 - - + -
2050C GLN* 3.3 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1998 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1945C TYR* 4.8 4.0 - - - -
1946C ASN* 3.2 15.2 - - - +
1949C ILE* 3.4 24.9 - - + +
1950C SER* 3.1 28.0 + - - +
1956C PHE* 3.4 47.1 - - + -
1959C LEU* 4.4 5.6 - - + -
1960C LYS* 5.9 2.7 - - + -
1994C VAL* 2.7 42.0 + - - +
1995C GLU* 2.9 29.8 - - - +
1997C PRO* 1.3 74.1 - - - +
1999C GLU* 1.3 83.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1999 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1950C SER 4.4 7.3 - - - +
1954C CYS* 4.8 17.1 - - + +
1956C PHE* 4.3 22.2 - - + -
1995C GLU* 2.5 24.6 - - - +
1996C VAL* 2.9 6.0 - - - -
1997C PRO 3.9 1.3 - - - -
1998C MET* 1.3 97.2 - - + +
2000C ARG* 1.3 59.2 + - - +
2001C LYS* 2.2 54.1 + - - +
2003C LYS* 5.6 6.1 - - + -
2004C TYR* 5.7 0.5 - - - +
----------------------------------------------------------
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