Contacts of the helix formed by residues 1964 - 1987 (chain B) in PDB entry 5NUG
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 GLU1964 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1934B GLU* 3.0 48.5 - - + +
1936B PHE 5.2 2.0 - - - -
1962B ARG* 3.4 4.4 - - - +
1963B LEU* 1.3 90.9 - - - +
1965B GLU* 1.3 67.3 + - - +
1966B ARG* 3.4 32.0 + - + +
1967B MET* 4.0 17.5 - - - +
1968B LEU* 2.8 16.6 + - - +
2026B SER* 4.1 10.4 + - - -
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Residues in contact with GLU1965 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1964B GLU* 1.3 71.1 - - - +
1966B ARG* 1.3 67.5 + - - +
1968B LEU* 3.3 9.1 + - - +
1969B SER* 3.2 14.0 + - - -
2026B SER* 3.7 26.5 + - - +
2027B ASN* 3.7 34.7 + - - +
2029B PRO* 4.5 3.3 - - + +
4100B HIS* 5.4 1.1 + - - -
4101B LEU* 3.6 37.7 - - + +
4133B LYS* 4.8 10.4 + - - -
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Residues in contact with ARG1966 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1964B GLU* 3.2 30.9 + - + +
1965B GLU* 1.3 83.0 - - - +
1967B MET* 1.3 66.8 + - - +
1969B SER* 3.2 10.4 + - - -
1970B ALA 3.8 0.2 + - - -
4072B GLY* 3.1 45.7 + - - +
4073B SER* 5.6 2.2 - - - +
4077B PHE* 5.6 5.2 - - - -
4101B LEU* 3.9 29.1 - - + +
4102B ALA* 5.4 4.3 - - - +
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Residues in contact with MET1967 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1936B PHE 2.9 29.8 - - - +
1937B ASP* 3.1 27.6 - - - +
1938B PHE* 3.0 27.8 - - + +
1941B MET* 3.5 21.8 - - + -
1963B LEU* 3.7 28.9 - - + +
1964B GLU* 3.3 18.6 + - - +
1966B ARG* 1.3 82.2 - - - +
1968B LEU* 1.3 63.0 + - - +
1970B ALA* 3.2 12.9 + - - +
1971B VAL* 3.3 11.4 + - + +
4072B GLY 3.2 11.6 + - - +
4073B SER* 5.7 0.2 - - - -
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Residues in contact with LEU1968 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1960B PHE* 3.4 44.2 - - + +
1961B ASN 4.6 8.3 - - - +
1963B LEU* 3.6 17.2 + - + +
1964B GLU 2.8 23.3 + - - +
1965B GLU* 3.4 6.5 - - - +
1966B ARG 3.2 0.2 + - - -
1967B MET* 1.3 70.0 - - - +
1969B SER* 1.3 66.4 + - - +
1971B VAL* 3.2 17.0 + - + +
1972B SER* 3.3 10.6 + - - -
2026B SER* 5.3 0.9 - - - -
2027B ASN 4.0 9.0 - - - +
2028B LEU* 3.6 23.6 - - + -
2029B PRO* 3.6 22.0 - - + -
2032B LEU* 3.6 13.9 - - + +
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Residues in contact with SER1969 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1965B GLU 3.2 7.1 + - - -
1966B ARG 3.2 8.7 + - - -
1968B LEU* 1.3 80.7 - - - +
1970B ALA* 1.3 56.8 + - - +
1972B SER* 2.2 32.1 + - - -
2029B PRO* 4.0 10.7 - - - +
4070B ALA* 3.4 8.9 - - - +
4071B ILE 2.8 21.9 + - - -
4098B ASN* 2.5 38.4 + - - +
4101B LEU* 4.0 5.8 - - - -
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Residues in contact with ALA1970 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1938B PHE* 3.2 25.0 - - + -
1966B ARG 3.8 2.0 + - - -
1967B MET 3.2 11.1 + - - +
1969B SER* 1.3 76.7 - - - +
1971B VAL* 1.3 63.5 + - - +
1973B GLN* 3.1 22.8 + - - +
1974B GLN 3.7 0.3 + - - -
4070B ALA* 4.2 12.8 - - - +
4071B ILE 3.9 2.8 + - - -
4072B GLY 4.2 0.9 - - - -
4073B SER* 3.2 39.9 - - - +
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Residues in contact with VAL1971 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1938B PHE* 3.8 17.9 - - + -
1941B MET* 3.8 39.0 - - + -
1945B PHE* 4.1 4.9 - - + -
1960B PHE* 4.0 25.6 - - + -
1963B LEU* 5.0 2.2 - - + -
1967B MET* 3.7 17.7 - - + +
1968B LEU* 3.2 13.7 + - - +
1970B ALA* 1.3 76.3 - - - +
1972B SER* 1.3 56.3 + - - +
1974B GLN* 3.2 5.6 + - - +
1975B VAL* 2.9 39.1 + - + +
2032B LEU* 5.1 2.0 - - + -
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Residues in contact with SER1972 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1968B LEU 3.3 3.2 + - - -
1969B SER* 2.2 28.0 + - - -
1971B VAL* 1.3 78.1 - - - +
1973B GLN* 1.3 67.9 + - - +
1975B VAL* 3.2 1.3 + - - -
1976B GLN* 2.9 22.1 + - - +
2031B ASN* 2.7 34.9 + - - -
2032B LEU* 3.5 28.9 - - - +
2035B LEU* 3.2 16.7 - - - +
4070B ALA* 3.9 2.3 - - - +
4097B LYS* 5.9 0.4 - - - -
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Residues in contact with GLN1973 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1938B PHE* 3.8 26.7 - - - -
1970B ALA* 3.1 9.4 + - - +
1972B SER* 1.3 82.7 + - - +
1974B GLN* 1.3 59.2 + - - +
1976B GLN* 3.2 10.9 + - - +
1977B CYS* 2.9 44.7 + - - -
4068B SER 4.3 10.7 - - - +
4069B ILE* 4.3 14.0 - - - +
4070B ALA* 4.1 23.2 + - + +
4075B GLU* 4.7 5.1 + - - +
4076B GLY* 5.9 2.0 - - - +
4079B GLN* 3.3 26.3 + - - +
4097B LYS* 5.5 5.4 - - - +
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Residues in contact with GLN1974 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1938B PHE* 3.1 48.3 + - + +
1941B MET* 4.1 4.2 - - - +
1942B GLY* 3.3 32.2 + - - -
1945B PHE* 4.1 10.2 - - + -
1970B ALA 3.7 0.6 + - - -
1971B VAL* 3.2 10.1 + - - +
1973B GLN* 1.3 81.9 - - - +
1975B VAL* 1.3 58.4 + - - +
1977B CYS* 3.2 10.1 + - - +
1978B ILE* 2.9 33.5 + - - +
2001B LEU* 3.6 24.0 - - + +
2002B LEU* 4.0 23.0 - - - +
4075B GLU* 5.1 0.6 + - - -
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Residues in contact with VAL1975 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1945B PHE* 4.3 17.9 - - + -
1971B VAL* 2.9 30.8 + - + +
1972B SER* 3.5 8.1 - - - +
1974B GLN* 1.3 75.7 - - - +
1976B GLN* 1.3 56.1 + - - +
1978B ILE* 3.2 9.1 + - + +
1979B GLN* 2.9 48.7 + - + +
2014B ILE* 4.7 9.0 - - + -
2035B LEU* 3.7 28.3 - - + -
2036B PHE* 4.0 27.8 - - + -
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Residues in contact with GLN1976 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1972B SER 2.9 12.0 + - - +
1973B GLN* 3.3 11.7 - - - +
1975B VAL* 1.3 75.9 - - - +
1977B CYS* 1.3 64.0 + - - +
1979B GLN* 3.3 4.1 + - - +
1980B GLU* 3.1 46.9 + - + +
2031B ASN* 5.1 4.6 + - - +
2035B LEU* 3.8 30.2 - - + +
4056B GLU* 5.1 9.8 - - - +
4068B SER* 4.5 12.0 + - - -
4097B LYS* 3.6 28.8 + - - +
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Residues in contact with CYS1977 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1973B GLN* 2.9 39.0 + - - -
1974B GLN* 3.2 10.7 + - - +
1976B GLN* 1.3 77.6 - - - +
1978B ILE* 1.3 62.1 + - - +
1980B GLU* 3.7 16.4 + - - +
1981B ALA 3.7 0.2 + - - -
1999B CYS* 3.3 30.5 - - + -
2000B GLU* 3.8 27.8 - - - +
2001B LEU* 5.2 2.0 - - + -
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Residues in contact with ILE1978 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1945B PHE* 3.7 45.8 - - + -
1949B CYS* 4.0 10.1 - - - -
1974B GLN 2.9 17.6 + - - +
1975B VAL* 3.2 10.7 + - - +
1977B CYS* 1.3 76.7 - - - +
1979B GLN* 1.3 63.8 + - - +
1981B ALA* 3.2 23.1 + - - +
1982B LEU* 3.5 9.3 + - + +
1999B CYS* 4.9 3.6 - - + -
2001B LEU* 3.7 23.3 - - + -
2008B VAL* 4.6 2.6 - - + +
2012B MET* 3.2 27.1 - - + -
2014B ILE* 3.7 19.5 - - + -
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Residues in contact with GLN1979 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1899B ARG* 3.0 29.7 - - - +
1900B LEU* 3.2 12.2 - - + +
1901B GLY* 3.2 26.9 - - - +
1975B VAL* 2.9 41.8 + - + +
1976B GLN* 3.3 6.3 + - - +
1978B ILE* 1.3 74.1 - - - +
1980B GLU* 1.3 65.4 + - + +
1982B LEU* 3.2 13.0 + - - +
1983B ARG* 3.0 28.6 + - - +
2014B ILE* 4.4 15.9 - - + +
2035B LEU* 3.2 20.7 + - + +
2036B PHE* 5.8 0.2 - - - -
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Residues in contact with GLU1980 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1976B GLN* 3.1 42.7 + - + +
1977B CYS* 3.8 10.6 + - - +
1979B GLN* 1.3 77.8 - - - +
1981B ALA* 1.3 57.1 + - - +
1983B ARG* 3.2 14.3 + - - +
1984B GLU* 2.9 42.2 + - - +
1999B CYS* 5.0 3.2 - - - -
4056B GLU* 5.6 1.6 - - - +
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Residues in contact with ALA1981 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1977B CYS 3.7 1.6 + - - -
1978B ILE 3.2 11.5 + - - +
1980B GLU* 1.3 78.5 - - - +
1982B LEU* 1.3 58.0 + - - +
1984B GLU* 3.2 7.5 + - - +
1985B HIS* 2.9 28.8 + - - +
1997B ILE* 3.8 21.8 - - + +
1999B CYS* 3.0 30.4 - - - -
2008B VAL* 4.0 20.0 - - + -
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Residues in contact with LEU1982 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1899B ARG* 3.6 43.4 + - + +
1978B ILE* 3.5 13.0 - - + +
1979B GLN* 3.2 17.4 + - - +
1981B ALA* 1.3 78.3 - - - +
1983B ARG* 1.3 57.6 + - - +
1985B HIS* 3.2 8.3 + - + +
1986B SER* 2.9 24.6 + - - -
2008B VAL* 3.4 31.2 - - + -
2010B PRO* 3.4 35.9 - - + +
2012B MET* 3.7 23.1 - - + +
2014B ILE* 6.5 0.4 - - + -
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Residues in contact with ARG1983 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1898B ALA 4.5 8.7 + - - +
1899B ARG* 3.7 29.2 - - + -
1900B LEU* 5.6 7.7 - - - +
1979B GLN* 3.0 23.0 + - - +
1980B GLU* 3.2 13.9 + - - +
1982B LEU* 1.3 74.3 - - - +
1984B GLU* 1.3 63.4 + - + +
1986B SER* 3.2 6.9 + - - -
1987B ASN* 3.0 19.8 + - - +
4217B ASP* 5.0 9.5 + - - -
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Residues in contact with GLU1984 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1980B GLU* 2.9 28.1 + - - +
1981B ALA* 3.4 11.6 + - - +
1983B ARG* 1.3 76.4 - - + +
1985B HIS* 1.3 63.8 + - - +
1987B ASN* 3.2 22.1 + - - +
1997B ILE* 4.1 18.7 - - + +
1998B THR 5.3 1.6 - - - +
1999B CYS* 5.2 4.4 - - - -
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Residues in contact with HIS1985 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1899B ARG* 4.8 5.1 + - - +
1981B ALA 2.9 9.8 + - - +
1982B LEU* 3.3 12.8 - - - +
1984B GLU* 1.3 77.3 - - - +
1986B SER* 1.3 64.3 + - - +
1987B ASN* 3.4 4.7 + - - +
1997B ILE* 3.3 31.5 - - + +
2008B VAL 4.6 8.5 - - - -
2010B PRO* 3.7 47.1 - - + +
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Residues in contact with SER1986 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1897B GLU 5.0 2.1 + - - -
1899B ARG* 3.5 35.6 + - - +
1982B LEU 2.9 12.7 + - - -
1983B ARG* 3.3 12.3 - - - -
1985B HIS* 1.3 77.4 - - - +
1987B ASN* 1.3 68.4 + - - +
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Residues in contact with ASN1987 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1983B ARG 3.0 12.6 + - - +
1984B GLU* 3.2 15.3 + - - +
1985B HIS 3.9 4.3 - - - +
1986B SER* 1.3 84.7 + - - +
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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) + - + + + + + -
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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