Contacts of the helix formed by residues 1931 - 1940 (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 THR1931 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1924B GLN 4.8 10.5 + - - +
1929B GLY 3.8 0.8 + - - -
1930B GLU* 1.3 74.3 - - - +
1932B ALA* 1.3 76.3 + - - +
1933B LEU* 3.5 13.8 + - + +
1934B HIS* 2.9 51.9 + - + +
1935B LEU* 3.1 25.8 + - - +
1954B ASP 5.5 0.4 - - - +
1957B ILE* 4.3 23.7 - - + +
1965B PRO* 4.0 4.5 - - + -
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Residues in contact with ALA1932 (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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1924B GLN 5.8 0.2 - - - +
1931B THR* 1.3 81.2 + - - +
1933B LEU* 1.3 62.3 + - - +
1935B LEU* 3.6 12.2 + - - +
1936B ALA* 3.3 18.7 + - - +
1948B LEU* 3.4 24.7 - - + +
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Residues in contact with LEU1933 (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* 3.1 8.7 + - + +
1932B ALA* 1.3 74.1 - - - +
1934B HIS* 1.3 67.4 + - - +
1935B LEU 2.9 2.6 + - - -
1936B ALA* 2.9 6.8 + - + +
1937B ALA* 2.9 22.8 + - + +
1945B ALA* 3.9 18.4 - - + +
1948B LEU* 3.4 35.2 - - + +
1949B LEU* 3.9 22.7 - - + -
1953B ALA* 6.0 4.5 - - + -
1954B ASP 5.1 5.8 - - - +
1955B ALA* 4.7 8.5 - - + -
1965B PRO* 3.3 35.2 - - + -
1977B VAL* 5.4 0.4 - - + -
1981B LEU* 3.6 21.3 - - + -
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Residues in contact with HIS1934 (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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1929B GLY 4.8 0.4 - - - -
1930B GLU* 3.3 24.3 - - + +
1931B THR* 2.9 34.9 + - + +
1933B LEU* 1.3 75.3 - - - +
1935B LEU* 1.3 62.6 + - - +
1937B ALA* 3.1 4.7 - - - +
1938B ARG* 3.0 22.9 + - - +
1957B ILE* 3.0 27.4 + - + -
1958B GLN 3.9 1.1 - - - -
1959B ASP* 3.5 26.4 + - + -
1963B ARG* 2.3 28.8 + - + -
1964B THR 3.6 1.3 - - - -
1965B PRO* 3.2 34.4 - - + +
1968B ALA* 3.7 10.6 - - + +
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Residues in contact with LEU1935 (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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434A PRO* 4.0 40.6 - - + +
1925B THR* 4.7 11.9 - - - +
1930B GLU* 3.6 28.0 - - + +
1931B THR 3.1 14.8 + - - +
1932B ALA* 3.6 13.7 - - - +
1933B LEU 2.9 1.4 + - - -
1934B HIS* 1.3 75.2 - - - +
1936B ALA* 1.3 57.4 + - - +
1937B ALA 3.0 1.3 - - - -
1938B ARG* 2.9 22.8 + - - +
1939B TYR* 2.7 43.0 + - + +
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Residues in contact with ALA1936 (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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1932B ALA 3.3 9.4 + - - +
1933B LEU* 2.9 11.8 + - + +
1935B LEU* 1.3 77.0 - - - +
1937B ALA* 1.3 61.5 + - - +
1940B SER 3.1 1.6 + - - -
1941B ARG* 3.0 49.8 + - + +
1944B ALA* 4.2 10.8 - - + -
1945B ALA* 4.1 20.4 - - + +
1948B LEU* 5.7 1.6 - - + -
1977B VAL* 3.4 6.5 - - - +
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Residues in contact with ALA1937 (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* 2.9 11.0 + - + +
1934B HIS* 3.1 11.4 - - - +
1936B ALA* 1.3 76.7 - - - +
1938B ARG* 1.3 63.0 + - - +
1940B SER* 3.2 9.4 + - - -
1965B PRO* 3.3 31.9 - - + +
1968B ALA* 3.7 1.1 - - + -
1969B ALA* 3.6 15.3 - - + +
1972B ALA* 4.1 1.4 - - - +
1974B ALA* 3.5 20.4 - - - +
1977B VAL* 3.7 17.4 - - + +
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Residues in contact with ARG1938 (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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348A LEU* 3.4 34.7 - - - +
350A GLY* 2.9 45.4 + - - +
351A GLY* 4.1 3.2 + - - -
434A PRO* 5.6 3.0 - - - +
1928B THR* 5.8 1.4 - - - +
1930B GLU* 2.6 49.4 + - - +
1934B HIS 3.0 8.0 + - - +
1935B LEU* 2.9 22.1 + - - +
1937B ALA* 1.3 77.3 - - - +
1939B TYR* 1.3 90.2 + - + +
1940B SER* 3.2 2.7 + - - -
1963B ARG* 5.6 2.2 - - - +
1968B ALA* 4.2 12.7 - - + +
1972B ALA* 3.5 20.0 - - + +
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Residues in contact with TYR1939 (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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351A GLY* 3.7 20.4 - - - -
352A GLY* 4.1 9.8 + - - -
433A GLU* 3.2 37.7 - - + +
434A PRO* 4.1 15.7 - - + +
1935B LEU* 2.7 27.2 + - + +
1936B ALA* 4.6 0.2 - - - -
1938B ARG* 1.3 107.9 + - - +
1940B SER* 1.3 69.6 + - - +
1941B ARG* 3.2 47.8 + - + +
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Residues in contact with SER1940 (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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1936B ALA 3.1 8.2 + - - -
1937B ALA 3.2 5.6 + - - -
1938B ARG 3.2 6.4 - - - -
1939B TYR* 1.3 79.5 - - - +
1941B ARG* 1.3 60.7 + - - +
1942B SER* 3.1 11.1 + - - -
1972B ALA 5.4 2.5 - - - -
1973B ASP 5.0 0.2 + - - -
1974B ALA* 3.3 27.9 - - - +
1976B GLY* 5.1 3.1 + - - -
1977B VAL* 3.8 7.2 - - - +
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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