Contacts of the helix formed by residues 1935 - 1948 (chain B) in PDB entry 3AU5
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 ASN1935 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1836B GLN 5.6 1.1 - - - -
1933B GLY 3.2 8.2 + - - +
1934B MET* 1.3 76.6 - - - +
1936B GLN* 1.3 64.8 + - - +
1937B GLU* 3.3 10.1 + - - +
1938B GLN* 2.8 59.4 + - - +
1939B ALA* 3.0 19.9 + - - +
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Residues in contact with GLN1936 (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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1836B GLN 5.1 2.2 - - - +
1837B TYR* 2.7 67.2 + - + +
1838B LEU* 5.0 2.0 + - - +
1840B GLY* 6.3 0.4 - - - +
1935B ASN* 1.3 74.9 - - - +
1937B GLU* 1.3 57.2 + - - +
1939B ALA* 3.3 4.5 + - - +
1940B MET* 3.0 30.2 + - - +
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Residues in contact with GLU1937 (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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1799B LYS* 5.5 10.3 - - + +
1800B ASP* 4.1 27.8 - - + +
1804B PHE* 5.7 0.3 - - - -
1935B ASN* 3.3 9.3 + - - +
1936B GLN* 1.3 78.1 - - - +
1938B GLN* 1.3 63.5 + - + +
1940B MET* 3.5 8.1 + - - +
1941B ALA* 3.0 24.7 + - + +
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Residues in contact with GLN1938 (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 GLY 4.0 4.1 + - - +
1934B MET* 3.2 37.0 - - + +
1935B ASN* 2.8 41.8 + - - +
1937B GLU* 1.3 77.4 - - + +
1939B ALA* 1.3 63.5 + - - +
1941B ALA* 3.3 6.6 + - - +
1942B LYS* 3.0 31.7 + - - +
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Residues in contact with ALA1939 (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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1808B PHE* 5.5 0.4 - - - -
1833B LEU* 4.0 17.7 - - + +
1836B GLN* 4.4 2.7 - - + -
1837B TYR* 4.0 27.1 - - + +
1934B MET* 3.5 23.9 - - + +
1935B ASN 3.0 17.0 + - - +
1936B GLN 3.7 4.0 - - - +
1938B GLN* 1.3 79.0 - - - +
1940B MET* 1.3 57.5 + - - +
1942B LYS* 3.4 1.7 + - - +
1943B TYR* 3.0 29.8 + - - +
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Residues in contact with MET1940 (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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1800B ASP* 5.7 3.6 - - - -
1804B PHE* 3.6 29.4 - - + -
1805B ALA* 4.1 25.1 - - + -
1808B PHE* 3.5 36.1 - - + -
1809B GLU* 5.5 0.2 - - - +
1837B TYR* 3.5 38.5 - - + +
1936B GLN 3.0 17.2 + - - +
1937B GLU* 3.8 8.5 - - + +
1939B ALA* 1.3 76.2 - - - +
1941B ALA* 1.3 62.2 + - - +
1943B TYR* 3.5 5.8 - - - +
1944B MET* 3.1 25.6 + - - +
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Residues in contact with ALA1941 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1799B LYS* 3.8 34.3 + - + +
1804B PHE* 4.3 6.2 - - + -
1937B GLU* 3.0 19.6 + - + +
1938B GLN* 3.6 7.9 - - - +
1939B ALA 3.2 0.2 - - - -
1940B MET* 1.3 75.4 - - - +
1942B LYS* 1.3 62.0 + - + +
1944B MET* 3.5 2.4 + - - +
1945B ALA* 2.9 29.7 + - - +
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Residues in contact with LYS1942 (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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1833B LEU* 3.8 18.7 - - + +
1931B PHE* 5.6 2.9 - - + -
1934B MET* 3.7 30.1 - - + -
1938B GLN* 3.0 20.1 + - - +
1939B ALA 4.1 1.3 - - - +
1941B ALA* 1.3 74.5 - - + +
1943B TYR* 1.3 57.2 + - - +
1945B ALA* 3.7 6.2 - - - +
1946B LEU* 2.7 36.6 + - - +
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Residues in contact with TYR1943 (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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1808B PHE* 3.2 38.4 - + + -
1811B ALA* 4.2 2.2 - - + -
1812B HIS* 2.9 55.9 + - + -
1815B VAL* 3.5 14.1 - - + +
1830B LEU* 3.3 47.2 - - + +
1833B LEU* 3.5 17.9 - - + +
1834B ARG* 4.4 5.6 - - + -
1939B ALA 3.0 17.7 + - - +
1940B MET 3.5 2.0 - - - +
1942B LYS* 1.3 77.9 - - - +
1944B MET* 1.3 61.5 + - - +
1946B LEU* 3.2 3.3 + - - +
1947B ILE* 2.8 48.2 + - + +
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Residues in contact with MET1944 (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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1799B LYS* 5.5 1.3 - - - +
1804B PHE* 3.3 41.7 - - + -
1807B MET* 4.0 19.5 - - + +
1808B PHE* 3.8 28.9 - - + +
1811B ALA* 4.1 12.6 - - + -
1940B MET 3.1 8.6 + - - +
1941B ALA 3.9 1.8 - - - +
1943B TYR* 1.3 84.3 - - - +
1945B ALA* 1.3 59.7 + - - +
1947B ILE* 3.1 6.5 + - + +
1948B LYS* 2.8 44.4 + - - +
1953B TYR* 3.2 40.6 - - + +
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Residues in contact with ALA1945 (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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1799B LYS* 5.6 3.8 - - - +
1941B ALA 2.9 19.1 + - - +
1942B LYS* 3.7 7.9 - - - +
1944B MET* 1.3 77.6 - - - +
1946B LEU* 1.3 65.6 + - - +
1948B LYS* 3.3 14.7 + - - +
1949B GLU* 3.3 15.4 + - - +
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Residues in contact with LEU1946 (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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1820B HIS* 4.9 1.8 + - - -
1826B ASN* 3.1 40.8 + - - +
1829B VAL* 3.6 33.4 - - + -
1830B LEU* 3.4 31.9 - - + -
1833B LEU* 4.5 4.7 - - + -
1942B LYS 2.7 22.3 + - - +
1943B TYR 3.4 4.3 - - - +
1945B ALA* 1.3 73.2 - - - +
1947B ILE* 1.3 63.8 + - - +
1949B GLU* 3.0 39.3 + - - +
1950B TRP 4.4 0.2 + - - -
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Residues in contact with ILE1947 (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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1811B ALA* 4.3 10.3 - - + -
1815B VAL* 3.6 26.5 - - + -
1820B HIS* 3.4 41.6 - - + +
1830B LEU* 3.8 9.9 - - + -
1943B TYR* 2.8 40.2 + - + +
1944B MET* 3.1 11.6 + - + +
1946B LEU* 1.3 72.7 - - - +
1948B LYS* 1.3 60.0 + - - +
1949B GLU 2.7 6.8 + - - -
1950B TRP* 2.9 14.9 + - - +
1953B TYR* 3.4 38.7 - - + +
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Residues in contact with LYS1948 (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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1794B THR* 2.5 33.6 + - - +
1795B ASP* 4.2 17.4 + - - +
1797B VAL* 5.7 2.8 + - - +
1799B LYS* 6.0 1.6 - - - +
1804B PHE* 5.0 10.3 - - - -
1807B MET* 4.8 2.2 - - - +
1944B MET* 2.8 37.5 + - + +
1945B ALA* 3.3 9.1 + - - +
1947B ILE* 1.3 70.2 - - + +
1949B GLU* 1.3 58.8 + - - +
1950B TRP 2.9 18.2 + - - +
1951B PRO* 5.2 0.7 - - - +
1953B TYR* 3.8 33.7 - - + -
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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
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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