Contacts of the strand formed by residues 1902 - 1906 (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 VAL1902 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1876J ILE* 3.3 18.6 - - + +
1878J ILE* 4.5 6.7 - - + -
1894J LEU* 4.1 38.4 - - + -
1897J CYS* 5.1 2.2 - - + -
1900J LEU* 3.7 12.1 - - + +
1901J PRO* 1.3 80.1 - - - +
1903J VAL* 1.3 69.2 + - - +
1925J ARG* 3.8 18.8 - - - +
1926J ALA* 3.6 19.0 - - + -
1927J ASP* 2.8 40.7 + - - +
1928J GLY 3.4 4.0 + - - -
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Residues in contact with VAL1903 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533C CYS* 5.1 2.5 - - - -
1876J ILE 2.9 9.3 + - - +
1877J VAL* 3.4 6.1 - - + +
1878J ILE* 3.0 24.8 + - - +
1902J VAL* 1.3 83.7 - - - +
1904J GLU* 1.3 71.8 + - - +
1905J VAL* 4.4 2.5 - - + -
1927J ASP* 5.6 0.4 - - + -
1928J GLY* 3.4 18.4 - - - +
1930J VAL* 4.4 13.0 - - + -
1941J GLY* 3.8 30.1 - - - +
1944J ARG* 3.9 31.6 - - + -
1945J ILE* 4.1 10.3 - - + -
1948J LEU* 5.6 2.7 - - + -
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Residues in contact with GLU1904 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1878J ILE* 3.2 12.1 - - + +
1880J PRO* 4.2 4.7 - - + -
1884J SER* 4.0 1.4 + - - -
1903J VAL* 1.3 74.6 - - - +
1905J VAL* 1.3 64.1 + - - +
1906J HIS* 2.5 34.9 + - + +
1920J SER* 2.5 23.0 + - - -
1922J VAL* 3.5 18.6 - - + +
1923J SER* 2.6 36.5 + - - -
1926J ALA* 3.8 13.8 - - + +
1928J GLY 3.0 8.6 + - - +
1929J VAL* 3.4 9.1 - - + +
1930J VAL 2.9 26.4 + - - -
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Residues in contact with VAL1905 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1877J VAL* 3.6 28.9 - - + -
1878J ILE 2.9 10.1 + - - +
1879J ASN* 3.1 31.4 - - + +
1880J PRO* 4.1 0.5 - - - +
1903J VAL* 4.3 8.3 - - + +
1904J GLU* 1.3 77.5 - - - +
1906J HIS* 1.3 77.4 + - - +
1907J ILE 4.5 0.4 - - - +
1930J VAL* 3.4 7.2 - - + +
1934J GLY 4.9 1.6 - - - +
1937J GLY* 3.6 23.8 - - - +
1938J TYR* 4.0 40.4 - - + +
1941J GLY* 4.7 0.2 - - - -
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Residues in contact with HIS1906 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1880J PRO* 3.8 9.9 - - + -
1881J ALA 4.7 0.2 - - - -
1884J SER* 2.9 34.2 - - - -
1885J HIS* 5.0 0.7 - + - -
1904J GLU* 2.5 30.9 + - + -
1905J VAL* 1.3 79.0 + - - +
1907J ILE* 1.3 66.2 + - - +
1908J SER 3.5 14.1 - - - +
1910J ILE* 4.0 31.0 - - + +
1920J SER* 4.4 0.4 + - - -
1929J VAL* 4.6 7.9 - - + -
1930J VAL* 2.9 14.7 + - - +
1931J ALA* 3.4 8.8 - - + -
1932J GLY 3.1 17.3 + - - -
1933J CYS 4.2 2.3 + - - -
1934J GLY 4.7 0.7 - - - +
1937J GLY* 5.8 0.3 - - - -
1960J CA2 3.1 32.3 + - + +
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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