Contacts of the helix formed by residues 1972 - 1989 (chain B) in PDB entry 4JKE
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 THR1972 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1971B LEU* 1.3 77.1 - - - +
1973B ASP* 1.3 60.6 + - - +
1974B GLU* 3.7 8.8 + - - +
1975B GLU* 2.6 46.6 + - - +
1976B TRP* 2.9 26.7 + - - -
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Residues in contact with ASP1973 (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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1926B THR* 4.8 8.4 + - - +
1927B ILE* 3.9 19.3 - - - +
1935B ARG* 3.4 23.7 + - - -
1971B LEU 3.9 0.4 + - - -
1972B THR* 1.3 74.3 - - - +
1974B GLU* 1.3 60.6 + - - +
1976B TRP* 3.3 7.8 + - - +
1977B ILE* 3.2 33.0 + - - +
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Residues in contact with GLU1974 (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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1972B THR* 3.1 8.7 - - - +
1973B ASP* 1.3 76.2 - - - +
1975B GLU* 1.3 65.9 + - + +
1977B ILE* 3.2 32.4 + - - +
1978B LYS* 3.3 13.8 + - - +
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Residues in contact with GLU1975 (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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1956B PRO* 5.2 13.3 - - + +
1957B ASP* 5.1 10.6 - - - +
1960B THR* 5.2 1.2 + - - -
1970B THR 4.7 0.3 - - - +
1971B LEU* 3.3 26.8 - - + +
1972B THR* 2.6 57.1 + - - +
1974B GLU* 1.3 76.8 - - + +
1976B TRP* 1.3 57.5 + - - +
1978B LYS* 3.3 9.5 + - - +
1979B VAL* 2.9 33.0 + - - +
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Residues in contact with TRP1976 (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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1923B TRP* 3.8 23.7 - + - +
1935B ARG* 3.4 57.2 - - + +
1939B ILE* 4.0 23.6 - - + -
1954B LEU* 4.1 14.8 - - + -
1968B TRP* 4.4 3.4 - - + -
1969B PRO* 3.7 25.1 + - + -
1971B LEU* 3.6 38.7 + - + +
1972B THR 2.9 22.3 + - - -
1973B ASP* 3.5 10.8 - - - +
1974B GLU 3.2 0.2 - - - -
1975B GLU* 1.3 74.6 - - - +
1977B ILE* 1.3 60.1 + - + +
1979B VAL* 3.2 25.4 + - + +
1980B GLU* 2.8 40.5 + - + +
1983B LEU* 5.5 0.2 - - + -
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Residues in contact with ILE1977 (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 ASP* 3.2 23.2 + - - +
1974B GLU* 3.2 27.3 + - - +
1976B TRP* 1.3 74.6 - - + +
1978B LYS* 1.3 58.8 + - - +
1980B GLU* 3.4 11.6 + - - +
1981B VAL* 3.1 42.1 + - + +
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Residues in contact with LYS1978 (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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1974B GLU 3.3 8.1 + - - +
1975B GLU* 3.5 11.2 - - - +
1976B TRP 3.2 0.2 - - - -
1977B ILE* 1.3 78.9 - - - +
1979B VAL* 1.3 65.5 + - + +
1981B VAL* 3.4 8.3 + - - +
1982B GLN* 3.2 40.0 + - + +
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Residues in contact with VAL1979 (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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1953B ILE* 3.6 28.7 - - + +
1954B LEU* 4.0 10.3 - - + -
1956B PRO* 3.9 11.9 - - + -
1971B LEU* 3.9 20.0 - - + -
1975B GLU 2.9 20.2 + - - +
1976B TRP* 3.7 24.9 - - + +
1978B LYS* 1.3 74.4 - - + +
1980B GLU* 1.3 57.9 + - - +
1982B GLN* 3.1 13.7 + - - +
1983B LEU* 2.9 45.1 + - + +
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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
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1931B THR* 5.7 5.1 - - - +
1935B ARG* 2.9 51.8 + - + +
1938B LEU* 3.8 24.7 - - + +
1976B TRP* 2.8 26.9 + - + +
1977B ILE* 3.7 9.9 - - - +
1979B VAL* 1.3 73.7 - - - +
1981B VAL* 1.3 65.2 + - + +
1983B LEU* 4.4 7.2 - - + -
1984B LYS* 3.0 34.2 + - - +
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Residues in contact with VAL1981 (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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1977B ILE* 3.1 28.8 + - + +
1978B LYS* 3.6 10.3 - - + +
1980B GLU* 1.3 76.0 - - - +
1982B GLN* 1.3 67.1 + - + +
1984B LYS* 3.4 12.0 + - + +
1985B ASP* 3.2 29.4 + - - +
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Residues in contact with GLN1982 (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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1949B ARG* 3.8 12.8 + - - +
1953B ILE* 3.7 40.5 + - + +
1956B PRO* 6.0 3.4 - - - +
1978B LYS* 3.2 35.5 + - + +
1979B VAL* 3.1 12.9 + - - +
1981B VAL* 1.3 80.0 - - + +
1983B LEU* 1.3 60.1 + - - +
1985B ASP* 3.2 8.7 + - - +
1986B LEU* 2.9 27.7 + - - +
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Residues in contact with LEU1983 (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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1935B ARG* 6.3 0.2 - - + -
1938B LEU* 4.2 14.6 - - + +
1939B ILE* 4.0 35.9 - - + +
1942B ALA* 3.7 24.5 - - + -
1950B ALA* 4.6 9.0 - - + +
1953B ILE* 3.6 30.1 - - + -
1954B LEU* 4.9 6.5 - - + -
1976B TRP* 5.5 0.2 - - + -
1979B VAL* 2.9 35.8 + - + +
1980B GLU* 3.9 9.6 - - + +
1982B GLN* 1.3 72.3 - - - +
1984B LYS* 1.3 66.8 + - - +
1986B LEU* 3.2 5.4 + - - +
1987B ILE* 3.0 30.6 + - - +
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Residues in contact with LYS1984 (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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1938B LEU* 3.9 32.5 - - + -
1980B GLU* 3.0 23.2 + - - +
1981B VAL* 3.5 12.3 - - + +
1983B LEU* 1.3 76.8 - - - +
1985B ASP* 1.3 58.8 + - - +
1987B ILE* 3.3 9.6 + - - +
1988B LEU* 3.0 38.4 + - + +
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Residues in contact with ASP1985 (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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1981B VAL* 3.2 23.4 + - - +
1982B GLN* 3.5 11.9 - - - +
1983B LEU 3.2 0.4 - - - -
1984B LYS* 1.3 77.3 - - - +
1986B LEU* 1.3 65.0 + - - +
1988B LEU* 3.4 11.1 + - - +
1989B ALA* 3.0 24.8 + - - +
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Residues in contact with LEU1986 (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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1942B ALA* 3.7 18.8 - - + +
1945B VAL* 3.4 31.3 - - + +
1946B ASN* 3.8 19.1 - - + +
1949B ARG* 3.7 19.3 - - + -
1950B ALA* 3.6 37.0 - - + +
1953B ILE* 4.0 8.7 - - + -
1982B GLN 2.9 12.3 + - - +
1983B LEU* 3.5 8.1 - - + +
1985B ASP* 1.3 75.5 - - - +
1987B ILE* 1.3 63.8 + - - +
1989B ALA* 3.2 24.0 + - - +
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Residues in contact with ILE1987 (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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1938B LEU* 3.7 44.6 - - + +
1941B ARG* 3.7 30.1 - - + +
1942B ALA* 4.0 18.2 - - + +
1945B VAL* 4.5 9.5 - - + +
1983B LEU 3.0 22.2 + - - +
1984B LYS* 3.6 5.8 - - - +
1986B LEU* 1.3 80.9 - - + +
1988B LEU* 1.3 62.8 + - + +
1989B ALA 3.5 4.2 + - - -
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Residues in contact with LEU1988 (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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1984B LYS* 3.0 26.5 + - + +
1985B ASP* 3.7 11.4 - - - +
1986B LEU 3.4 0.2 - - - -
1987B ILE* 1.3 79.6 - - + +
1989B ALA* 1.3 59.6 + - - +
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Residues in contact with ALA1989 (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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1945B VAL* 6.5 0.2 - - - -
1985B ASP 3.0 17.2 + - - +
1986B LEU* 3.2 16.9 + - - +
1987B ILE 4.0 3.8 - - - -
1988B LEU* 1.3 80.3 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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