Contacts of the strand formed by residues 1809 - 1813 (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 ILE1809 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1804J LEU* 4.5 16.4 - - + -
1807J ALA 5.2 0.2 - - - +
1808J PRO* 1.3 72.9 - - - +
1810J MET* 1.3 70.5 + - - +
1811J ILE* 3.5 11.4 + - + -
1844J ALA* 4.4 9.4 - - + -
1850J THR 2.9 15.0 + - - +
1851J VAL* 3.2 7.4 - - + +
1852J ASP 2.8 24.0 + - - -
1873J HIS* 4.2 0.4 - - - -
1874J CYS* 3.8 18.8 - - - -
1875J GLY 3.8 15.0 - - - +
1877J VAL* 4.2 15.7 - - + -
1942J VAL* 4.1 29.2 - - + +
1945J ILE* 4.2 20.2 - - + -
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Residues in contact with MET1810 (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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1808J PRO 3.7 2.4 + - - -
1809J ILE* 1.3 72.6 - - - +
1811J ILE* 1.3 61.6 + - - +
1812J LEU* 3.6 28.0 + - + -
1852J ASP* 3.5 20.6 - - - +
1854J ARG* 3.6 33.9 - - - +
1865J TRP* 3.7 22.4 - - + +
1868J GLU* 4.5 2.0 - - + -
1869J ALA* 3.8 19.7 - - + +
1873J HIS* 3.4 36.6 - - + +
1875J GLY 3.0 14.1 + - - +
1876J ILE* 3.3 5.1 - - + +
1877J VAL 2.8 26.3 + - - +
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Residues in contact with ILE1811 (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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1809J ILE* 4.0 14.8 - - + +
1810J MET* 1.3 77.5 - - - +
1812J LEU* 1.3 62.2 + - - +
1813J ASN* 3.9 1.6 + - - +
1840J CYS* 3.7 33.2 - - + -
1851J VAL* 3.7 20.6 - - + -
1852J ASP 2.8 11.3 + - - +
1853J PHE* 3.5 26.0 - - + -
1854J ARG 3.0 28.6 + - - +
1877J VAL* 3.2 16.4 - - + +
1938J TYR* 4.1 22.4 - - + -
1942J VAL* 3.8 15.7 - - + -
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Residues in contact with LEU1812 (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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1810J MET* 3.6 35.7 - - + -
1811J ILE* 1.3 78.5 - - - +
1813J ASN* 1.3 64.0 + - - +
1814J GLY 4.3 0.2 - - - -
1854J ARG* 3.6 5.2 - - + -
1862J LEU* 4.5 11.0 - - + +
1865J TRP* 4.0 36.1 - - + -
1866J ILE* 3.7 34.5 - - + +
1876J ILE* 4.4 12.6 - - + -
1877J VAL 2.8 10.5 + - - +
1878J ILE* 3.4 19.2 - - + +
1879J ASN 2.9 26.2 + - - +
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Residues in contact with ASN1813 (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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1811J ILE* 3.9 4.4 + - - +
1812J LEU* 1.3 79.0 - - - +
1814J GLY* 1.3 60.1 + - - +
1817J LEU* 3.8 10.2 - - + +
1833J LEU* 4.0 8.7 - - + +
1853J PHE* 3.2 34.6 - - - -
1854J ARG 2.9 24.9 + - - +
1855J GLN* 3.2 16.0 - - + -
1856J SER 3.0 25.3 + - - +
1862J LEU* 3.8 7.9 - - - +
1879J ASN* 3.4 3.9 - - - +
1938J TYR* 2.7 37.5 + - - -
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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