Contacts of the helix formed by residues 1935 - 1949 (chain J) in PDB entry 2BT4
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 VAL1935 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544C ARG* 5.7 0.2 - - - +
1820J LEU* 4.4 5.4 - - + -
1828J TYR 4.5 10.3 + - - +
1829J GLY* 6.1 0.2 - - - -
1831J ASP* 3.9 23.6 - - + +
1836J VAL* 3.6 30.2 - - + +
1839J LEU* 3.7 27.9 - - + +
1907J ILE* 4.1 19.7 - - + +
1934J GLY* 1.3 68.9 - - - -
1936J GLN* 1.3 63.9 + - + +
1937J GLY 2.9 7.4 + - - -
1938J TYR* 3.0 27.0 + - + +
1939J VAL 3.9 1.4 + - - -
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Residues in contact with GLN1936 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543C GLU* 3.4 22.2 + - - +
544C ARG* 2.7 40.1 + - - +
547C ALA* 3.2 15.1 - - - +
1839J LEU* 5.4 2.0 - - - -
1933J CYS 3.3 10.1 - - - +
1934J GLY* 3.1 1.0 - - - -
1935J VAL* 1.3 81.4 - - + +
1937J GLY* 1.3 57.4 + - - +
1938J TYR 3.1 0.2 - - - -
1939J VAL* 2.9 30.5 + - + +
1940J PHE* 3.0 40.5 + - + -
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Residues in contact with GLY1937 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1905J VAL* 3.6 17.7 - - - +
1930J VAL* 4.0 23.6 - - - +
1933J CYS* 3.4 6.4 + - - -
1934J GLY 3.1 11.5 + - - -
1935J VAL 2.9 2.4 - - - -
1936J GLN* 1.3 79.6 - - - +
1938J TYR* 1.3 56.5 + - - +
1940J PHE* 3.2 9.1 + - - +
1941J GLY 2.9 22.3 + - - -
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Residues in contact with TYR1938 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1811J ILE* 4.1 23.6 - - + -
1813J ASN* 2.7 31.0 + - - -
1817J LEU* 4.1 3.6 - - - +
1833J LEU* 4.6 3.9 - - + +
1836J VAL* 3.8 27.8 - - + -
1839J LEU* 6.2 0.7 - - + -
1840J CYS* 3.7 16.6 - - - -
1877J VAL* 4.6 8.3 - - + +
1879J ASN* 3.0 33.6 + - + +
1905J VAL* 4.0 17.3 - - + -
1907J ILE* 4.0 28.0 - - + +
1935J VAL* 3.0 22.2 + - + +
1937J GLY* 1.3 78.3 - - - +
1939J VAL* 1.3 58.4 + - + +
1941J GLY* 3.2 2.4 + - - +
1942J VAL* 3.0 31.8 + - - +
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Residues in contact with VAL1939 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1839J LEU* 4.3 32.3 - - + +
1840J CYS* 5.2 1.1 - - - +
1843J ALA* 4.0 24.7 - - + -
1935J VAL 4.6 5.4 - - - +
1936J GLN* 2.9 20.7 + - + +
1938J TYR* 1.3 78.3 - - + +
1940J PHE* 1.3 60.7 + - + +
1942J VAL* 3.1 7.2 + - - +
1943J GLU* 2.8 54.2 + - - +
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Residues in contact with PHE1940 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530C VAL* 5.1 0.9 - - + -
540C PHE* 3.3 64.6 - + + -
543C GLU* 3.3 34.3 - - + -
544C ARG* 3.8 8.1 - - + -
1903J VAL* 5.3 0.2 - - - -
1930J VAL* 4.4 12.1 - - + -
1933J CYS* 3.9 31.6 - - + -
1936J GLN* 3.0 42.4 + - + -
1937J GLY* 3.2 13.0 + - - +
1939J VAL* 1.3 76.4 - - + +
1941J GLY* 1.3 66.4 + - - +
1943J GLU* 3.1 3.8 + - - -
1944J ARG* 2.8 22.0 + - - +
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Residues in contact with GLY1941 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1877J VAL* 3.8 15.9 - - - +
1903J VAL* 3.8 27.6 - - - +
1930J VAL* 5.1 0.2 - - - +
1937J GLY 2.9 14.1 + - - -
1938J TYR 3.2 4.2 + - - -
1940J PHE* 1.3 79.1 - - - +
1942J VAL* 1.3 61.6 + - - +
1944J ARG* 3.2 1.9 + - - +
1945J ILE* 3.0 27.4 + - - +
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Residues in contact with VAL1942 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1804J LEU* 6.0 0.2 - - + -
1809J ILE* 4.1 18.0 - - + +
1811J ILE* 3.8 28.3 - - + -
1840J CYS* 4.5 11.2 - - - +
1843J ALA* 3.8 12.8 - - + +
1844J ALA* 3.6 33.4 - - - +
1847J HIS* 5.0 3.8 - - + -
1851J VAL* 4.9 0.7 - - + -
1877J VAL* 4.4 7.6 - - + -
1938J TYR 3.0 16.6 + - - +
1939J VAL 3.6 6.5 - - - +
1941J GLY* 1.3 75.8 - - - +
1943J GLU* 1.3 65.3 + - - +
1945J ILE* 3.3 2.9 + - - +
1946J ALA* 2.9 23.5 + - + +
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Residues in contact with GLU1943 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536C GLN* 3.4 14.6 + - - +
540C PHE* 3.1 20.6 - - + -
543C GLU* 2.7 36.2 - - - +
1843J ALA* 5.7 0.9 - - + -
1847J HIS* 3.8 26.4 + - + +
1939J VAL* 2.8 42.5 + - + +
1940J PHE* 3.1 4.4 + - - +
1942J VAL* 1.3 73.9 - - + +
1944J ARG* 1.3 57.8 + - - +
1946J ALA* 3.5 7.8 + - - +
1947J ALA* 3.0 21.1 + - - +
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Residues in contact with ARG1944 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532C GLY 4.5 5.4 + - - +
533C CYS* 3.1 49.9 + - - +
534C GLY* 3.7 9.3 - - - +
536C GLN* 2.8 30.5 + - - +
540C PHE* 3.8 9.1 - - + -
1903J VAL* 3.9 20.6 - - + -
1927J ASP* 6.3 0.6 - - - +
1928J GLY* 5.9 1.1 - - - +
1940J PHE 2.8 20.2 + - - +
1941J GLY* 3.7 4.0 - - - +
1943J GLU* 1.3 72.3 - - - +
1945J ILE* 1.3 66.8 + - - +
1947J ALA* 3.2 5.9 + - - +
1948J LEU* 2.8 62.9 + - + +
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Residues in contact with ILE1945 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1804J LEU* 4.2 8.3 - - + -
1809J ILE* 4.2 20.4 - - + -
1874J CYS* 4.1 19.3 - - - +
1875J GLY* 4.1 4.5 - - - -
1876J ILE 3.9 15.9 - - - +
1877J VAL* 4.0 13.7 - - + -
1901J PRO* 3.7 35.4 - - + +
1903J VAL* 4.1 11.7 - - + -
1941J GLY 3.0 17.9 + - - +
1942J VAL* 3.8 5.6 - - - +
1944J ARG* 1.3 77.5 - - - +
1946J ALA* 1.3 55.3 + - - +
1948J LEU* 4.4 4.5 - - - +
1949J ALA* 2.6 40.4 + - + +
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Residues in contact with ALA1946 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1804J LEU* 3.6 32.6 - - + +
1847J HIS* 3.9 25.1 - - + +
1942J VAL* 2.9 17.9 + - + +
1943J GLU 3.6 6.3 - - - +
1945J ILE* 1.3 78.2 - - - +
1947J ALA* 1.3 61.4 + - - +
1949J ALA 3.7 5.4 + - - -
1950J GLY* 3.8 9.5 + - - -
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Residues in contact with ALA1947 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536C GLN* 3.2 31.9 - - - +
1943J GLU 3.0 12.5 + - - +
1944J ARG* 3.2 8.9 + - - +
1946J ALA* 1.3 78.7 - - - +
1948J LEU* 1.3 60.9 + - - +
1950J GLY 3.8 14.0 + - - +
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Residues in contact with LEU1948 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1901J PRO* 3.7 32.3 - - + +
1902J VAL 5.5 0.2 - - - +
1903J VAL* 5.6 1.1 - - + -
1927J ASP* 4.9 15.3 - - + -
1944J ARG* 2.8 64.6 + - + +
1945J ILE* 3.9 2.7 - - + +
1947J ALA* 1.3 75.1 - - - +
1949J ALA* 1.3 58.1 + - - +
1950J GLY 3.0 15.9 + - - +
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Residues in contact with ALA1949 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1802J ARG 4.0 16.9 - - - +
1803J SER* 3.7 22.0 - - - -
1804J LEU* 3.4 22.3 + - + +
1874J CYS* 4.1 10.1 - - - +
1901J PRO* 4.7 4.3 - - + -
1945J ILE* 2.6 30.6 + - + +
1946J ALA 4.1 4.3 - - - -
1947J ALA 3.4 0.4 - - - -
1948J LEU* 1.3 70.4 - - - +
1950J GLY* 1.3 54.7 + - - +
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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