Contacts of the helix formed by residues 1931 - 1940 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1924E GLN 4.8 10.1 + - - +
1925E THR* 5.8 0.2 - - - -
1929E GLY 3.9 1.0 + - - -
1930E GLU* 1.3 74.6 - - - +
1932E ALA* 1.3 76.2 + - - +
1933E LEU* 3.3 13.8 + - + +
1934E HIS* 2.8 52.4 + - + +
1935E LEU* 3.1 25.8 + - - +
1954E ASP 5.5 0.4 - - - +
1957E ILE* 4.3 24.2 - - + +
1965E PRO* 4.1 3.4 - - + -
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Residues in contact with ALA1932 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1931E THR* 1.3 81.6 + - - +
1933E LEU* 1.3 62.3 + - - +
1935E LEU* 3.6 12.4 + - - +
1936E ALA* 3.3 19.4 + - - +
1948E LEU* 3.4 24.9 - - + +
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Residues in contact with LEU1933 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1931E THR* 3.1 8.7 + - + +
1932E ALA* 1.3 75.9 - - - +
1934E HIS* 1.3 66.7 + - - +
1935E LEU 2.9 2.1 + - - -
1936E ALA* 3.0 6.6 + - + +
1937E ALA* 2.9 21.5 + - + +
1945E ALA* 3.8 18.6 - - + +
1948E LEU* 3.4 36.6 - - + +
1949E LEU* 3.8 23.6 - - + -
1953E ALA* 6.0 4.3 - - + +
1954E ASP 5.2 6.1 - - - +
1955E ALA* 4.8 7.9 - - + -
1965E PRO* 3.3 34.1 - - + -
1977E VAL* 5.4 0.2 - - + -
1981E LEU* 3.5 21.5 - - + -
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Residues in contact with HIS1934 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1929E GLY 4.9 0.2 - - - -
1930E GLU* 3.3 24.2 - - + +
1931E THR* 2.8 33.8 + - + +
1933E LEU* 1.3 76.3 - - - +
1935E LEU* 1.3 57.8 + - - +
1937E ALA* 3.2 3.8 - - - +
1938E ARG* 3.0 29.1 + - - +
1957E ILE* 3.0 27.6 - - + -
1958E GLN 3.9 1.6 - - - -
1959E ASP* 3.6 21.8 - - + -
1963E ARG* 2.3 28.3 + - + -
1964E THR 3.5 1.8 - - - -
1965E PRO* 3.1 40.4 - - + +
1968E ALA* 3.7 9.9 - - + +
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Residues in contact with LEU1935 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434D PRO* 4.0 42.2 - - + +
1925E THR* 4.8 11.4 - - - +
1930E GLU* 3.6 29.2 - - + +
1931E THR 3.1 15.0 + - - +
1932E ALA* 3.6 14.6 - - - +
1933E LEU 2.9 4.0 + - - -
1934E HIS* 1.3 72.5 - - - +
1936E ALA* 1.3 56.2 + - - +
1938E ARG* 2.9 22.5 + - - +
1939E TYR* 2.7 43.4 + - + +
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Residues in contact with ALA1936 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1932E ALA 3.3 9.4 + - - +
1933E LEU* 3.0 10.5 + - + +
1935E LEU* 1.3 75.2 - - - +
1937E ALA* 1.3 57.8 + - - +
1939E TYR* 3.9 0.4 - - - -
1940E SER 3.1 4.9 + - - -
1941E ARG* 3.0 50.3 + - + +
1944E ALA* 4.1 11.4 - - + -
1945E ALA* 4.1 19.3 - - + +
1948E LEU* 5.7 1.8 - - + -
1977E VAL* 3.5 7.4 - - - +
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Residues in contact with ALA1937 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1933E LEU* 2.9 11.0 + - + +
1934E HIS 3.2 10.5 - - - +
1936E ALA* 1.3 76.7 - - - +
1938E ARG* 1.3 63.0 + - - +
1940E SER* 3.2 9.0 + - - -
1965E PRO* 3.5 31.0 - - + +
1968E ALA* 3.8 0.7 - - + -
1969E ALA* 3.6 16.9 - - + +
1974E ALA* 3.5 21.0 - - - +
1977E VAL* 3.7 17.4 - - + +
1981E LEU* 5.3 0.2 - - + -
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Residues in contact with ARG1938 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348D LEU* 3.4 33.1 - - - +
349D ASN* 5.3 0.2 - - - -
350D GLY* 3.0 46.2 + - - +
351D GLY* 4.1 3.4 + - - -
434D PRO* 5.6 3.2 - - - +
1928E THR* 5.8 1.8 - - - +
1930E GLU* 2.6 43.3 + - - -
1934E HIS 3.0 8.2 + - - +
1935E LEU* 2.9 21.0 + - - +
1937E ALA* 1.3 76.6 - - - +
1939E TYR* 1.3 90.4 + - + +
1940E SER* 3.2 2.0 + - - -
1963E ARG* 5.5 2.0 - - - +
1968E ALA* 4.2 12.5 - - + +
1972E ALA* 3.4 23.3 - - + +
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Residues in contact with TYR1939 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351D GLY* 3.5 20.9 - - - -
352D GLY* 3.9 11.2 + - - -
433D GLU* 3.2 37.6 + - + +
434D PRO* 4.3 13.2 - - + +
1935E LEU* 2.7 26.3 + - + +
1938E ARG* 1.3 108.4 + - - +
1940E SER* 1.3 70.1 + - - +
1941E ARG* 3.2 48.0 + - + +
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Residues in contact with SER1940 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1936E ALA 3.1 8.4 + - - -
1937E ALA 3.2 8.7 + - - -
1938E ARG 3.2 2.4 - - - -
1939E TYR* 1.3 80.2 - - - +
1941E ARG* 1.3 63.7 + - - +
1942E SER* 3.1 10.0 + - - -
1972E ALA 5.4 2.2 - - - -
1974E ALA* 3.3 28.3 - - - +
1976E GLY* 5.1 2.8 + - - -
1977E VAL* 3.9 7.4 - - - +
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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