Contacts of the strand formed by residues 1805 - 1810 (chain B) in PDB entry 4JKE
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 GLY1805 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1783B THR 3.4 11.4 - - - -
1785B VAL* 3.8 9.3 - - - +
1803B ILE* 3.8 3.0 - - - +
1804B ASN* 1.3 80.0 - - - +
1806B ALA* 1.3 61.3 - - - +
1821B ILE* 3.6 5.5 - - - +
1822B ILE* 3.0 44.8 + - - +
1836B LEU* 4.2 3.1 - - - -
1906B ILE* 5.2 0.2 - - - +
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Residues in contact with ALA1806 (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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1782B ASP* 3.2 5.5 - - - +
1783B THR* 2.9 35.9 + - + +
1785B VAL* 4.2 12.6 - - + -
1805B GLY* 1.3 75.2 - - - +
1807B ILE* 1.3 63.4 + - - +
1808B PHE* 4.2 15.4 - - + -
1819B LEU* 4.1 17.0 - - + -
1820B LYS 3.3 9.9 - - - +
1821B ILE* 4.7 6.5 - - + -
1822B ILE* 4.1 1.4 - - - +
1836B LEU* 3.9 0.9 - - - +
1897B LEU* 4.9 5.4 - - + -
1906B ILE* 5.3 1.3 - - + -
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Residues in contact with ILE1807 (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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1780B VAL* 4.7 0.9 - - + -
1781B ASP 3.5 10.8 - - - +
1782B ASP* 4.3 0.9 - - + -
1806B ALA* 1.3 77.9 - - - +
1808B PHE* 1.3 63.1 - - - +
1809B ILE* 4.3 22.6 - - + +
1818B PHE 3.6 1.2 - - - +
1819B LEU* 3.5 6.1 - - - +
1820B LYS* 2.8 40.1 + - + +
1822B ILE* 4.2 14.1 - - + -
1836B LEU* 3.6 22.0 - - + -
1840B LYS* 4.1 2.2 - - + +
1841B THR* 3.9 33.0 - - + +
1844B GLU* 3.5 35.9 - - + -
1845B VAL* 4.6 5.8 - - + -
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Residues in contact with PHE1808 (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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1779B PHE 3.6 1.0 - - - +
1780B VAL* 3.3 6.2 - - - +
1781B ASP* 2.9 45.5 + - + +
1782B ASP* 4.3 2.5 - - - -
1783B THR* 3.9 23.8 - - + -
1806B ALA* 4.2 14.4 - - + -
1807B ILE* 1.3 72.5 - - - +
1809B ILE* 1.3 64.5 + - - +
1810B PHE 4.1 0.4 - - - -
1817B LEU* 4.0 17.5 - - + -
1818B PHE 3.8 3.4 - - - -
1819B LEU* 3.6 26.2 - - + -
1893B PHE* 3.3 63.5 - + + -
1894B GLN* 4.2 4.3 - - - -
1896B CYS* 3.9 17.0 - - + -
1897B LEU* 4.9 7.6 - - + -
1902B PHE* 5.3 0.9 - + - -
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Residues in contact with ILE1809 (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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1778B TRP* 3.3 50.3 - - + -
1779B PHE 3.4 2.7 - - - -
1780B VAL* 4.2 12.8 - - + -
1807B ILE* 4.3 18.6 - - + +
1808B PHE* 1.3 79.1 - - - +
1810B PHE* 1.3 59.5 + - - +
1817B LEU* 3.4 3.1 - - - +
1818B PHE* 2.8 56.0 + - + +
1820B LYS* 4.5 16.2 - - + -
1845B VAL* 4.3 13.9 - - + -
1848B LEU* 3.5 23.1 - - + -
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Residues in contact with PHE1810 (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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1778B TRP* 3.3 6.2 - - - -
1779B PHE* 2.8 44.4 + - + +
1809B ILE* 1.3 76.7 - - - +
1811B ASN* 1.3 63.3 + - - +
1812B PRO* 3.5 25.3 - - + +
1815B GLY* 3.5 25.8 - - - -
1816B GLN 3.4 13.5 - - - -
1817B LEU* 4.2 4.7 - - + -
1893B PHE* 3.6 32.3 - + + -
1919B LEU* 3.8 24.9 - - + -
1920B TYR* 3.5 17.9 - + - -
1933B PHE* 3.8 22.0 - + - -
1936B LEU* 3.4 20.4 - - + -
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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