Contacts of the helix formed by residues 1974 - 1984 (chain B) in PDB entry 3NBN
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 ALA1974 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1937B ALA 3.5 23.8 - - - +
1940B SER* 3.3 29.6 - - - +
1969B ALA* 3.2 16.3 + - - +
1972B ALA* 3.7 6.3 - - + +
1973B ASP* 1.3 73.5 - - - +
1975B GLN* 1.3 64.5 + - - +
1976B GLY 2.8 4.3 + - - -
1977B VAL* 3.1 5.6 + - + -
1978B PHE* 3.0 21.5 + - - +
2011B MET* 3.7 1.4 - - - +
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Residues in contact with GLN1975 (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 3.5 6.3 + - - -
1974B ALA* 1.3 71.2 - - - +
1976B GLY* 1.3 66.9 + - - +
1978B PHE* 3.2 32.0 - - - +
1979B GLN* 2.9 40.6 + - + +
2009B GLU 4.0 9.0 - - - +
2010B GLY* 4.7 3.6 - - - -
2011B MET* 4.6 5.8 + - - +
2014B ASP* 3.2 25.3 + - - +
22C ARG* 3.7 35.0 + - - +
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Residues in contact with GLY1976 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1940B SER* 5.1 3.0 + - - -
1942B SER* 3.6 22.0 - - - -
1974B ALA 2.8 2.6 + - - -
1975B GLN* 1.3 82.1 - - - +
1977B VAL* 1.3 61.4 + - - +
1979B GLN* 3.4 3.3 + - - +
1980B ILE* 3.3 22.7 + - - +
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Residues in contact with VAL1977 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1933B LEU* 5.4 1.6 - - + -
1936B ALA 3.4 20.9 - - - +
1937B ALA* 3.7 25.6 - - + +
1940B SER* 3.8 13.0 - - - +
1941B ARG 3.7 4.3 - - - +
1942B SER* 3.6 23.8 - - - +
1945B ALA* 3.7 21.5 - - + -
1969B ALA* 4.6 0.7 - - + -
1974B ALA* 3.1 6.3 + - + +
1976B GLY* 1.3 70.1 - - - +
1978B PHE* 1.3 71.8 + - - +
1980B ILE* 2.9 17.8 + - - +
1981B LEU* 2.9 30.4 + - + +
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Residues in contact with PHE1978 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1966B LEU* 3.7 26.2 - - + -
1969B ALA* 4.0 8.1 - - + +
1970B VAL* 4.1 13.2 - - + -
1974B ALA 3.0 13.6 + - - +
1975B GLN* 3.2 38.8 - - - +
1977B VAL* 1.3 72.8 - - - +
1979B GLN* 1.3 63.0 + - - +
1981B LEU* 2.8 36.2 + - - +
1982B ILE* 2.9 20.6 + - + +
2011B MET* 3.6 55.0 - - + -
2014B ASP* 3.9 14.1 - - + -
2015B LEU* 3.9 21.1 - - + -
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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
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1975B GLN* 2.9 34.3 + - + +
1976B GLY* 3.5 6.1 - - - +
1978B PHE* 1.3 82.8 - - - +
1980B ILE* 1.3 69.2 + - + +
1982B ILE* 3.7 9.2 - - - +
1983B ARG* 3.0 67.7 + - - +
2014B ASP* 3.0 30.6 - - - +
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Residues in contact with ILE1980 (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 SER* 3.8 22.9 - - - +
1945B ALA* 5.0 7.0 - - + -
1946B LYS* 4.4 29.8 - - + -
1949B LEU* 4.8 19.7 - - + -
1976B GLY* 3.3 15.5 - - - +
1977B VAL* 2.9 18.1 + - + +
1979B GLN* 1.3 78.2 - - + +
1981B LEU* 1.3 69.5 + - + +
1983B ARG* 3.0 31.0 + - - +
1984B ASN* 3.0 13.5 + - + +
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Residues in contact with LEU1981 (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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1933B LEU* 3.6 31.0 - - + -
1949B LEU* 5.5 4.3 - - + -
1955B ALA* 4.7 11.7 - - + +
1965B PRO* 4.0 3.1 - - + -
1966B LEU* 3.9 28.9 - - + +
1969B ALA* 3.8 13.2 - - + -
1977B VAL* 2.9 44.0 - - + +
1978B PHE* 2.8 19.1 + - - +
1980B ILE* 1.3 77.2 - - + +
1982B ILE* 1.3 55.9 + - - +
1984B ASN* 3.1 25.9 + - - +
1987B THR* 3.1 29.0 + - + +
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Residues in contact with ILE1982 (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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1966B LEU* 5.0 2.0 - - + -
1978B PHE* 2.9 44.4 + - + +
1979B GLN* 3.7 15.3 - - - +
1981B LEU* 1.3 71.2 - - - +
1983B ARG* 1.3 62.3 + - + +
1984B ASN 3.1 0.2 - - - -
1989B LEU* 4.2 20.0 - - + -
2014B ASP* 3.4 36.3 - - + +
2015B LEU* 4.1 6.5 - - + +
2018B SER* 3.3 30.9 + - - +
1985E ARG* 2.9 30.3 + - - -
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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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1979B GLN* 3.0 56.2 + - - +
1980B ILE* 3.0 26.4 + - - +
1982B ILE* 1.3 78.5 - - + +
1984B ASN* 1.3 52.2 + - - +
1949E LEU* 4.4 14.2 + - - -
1950E GLU* 4.4 33.9 + - - +
1952E SER* 5.0 8.9 + - - +
1984E ASN* 3.5 21.0 - - - +
1985E ARG* 2.8 30.7 + - - +
1986E ALA 4.6 0.8 + - - +
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Residues in contact with ASN1984 (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 LEU* 3.3 30.8 - - + +
1955B ALA* 5.2 0.6 - - - +
1980B ILE* 3.0 12.9 + - + +
1981B LEU* 3.1 20.4 - - - +
1982B ILE 3.1 0.2 - - - -
1983B ARG* 1.3 76.3 - - - +
1985B ARG* 1.3 62.3 + - - +
1986B ALA* 2.9 25.1 + - - +
1987B THR* 2.5 28.8 + - - +
1983E ARG* 3.5 20.2 - - - +
1984E ASN* 4.8 0.2 - - - +
1985E ARG* 3.3 16.0 + - - -
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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