Contacts of the strand formed by residues 1777 - 1784 (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 ILE1777 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1771B LEU* 3.5 32.3 - - + +
1772B PHE* 4.0 21.1 - - + -
1775B GLN* 3.5 20.1 + - - +
1776B ILE* 1.3 74.8 - - - +
1778B TRP* 1.3 74.6 + - - +
1779B PHE* 4.3 8.7 - - + -
1811B ASN* 3.4 8.3 + - - +
1812B PRO* 3.2 24.3 - - + +
1860B GLN* 3.5 25.4 - - + +
1862B ILE* 3.4 34.8 - - + -
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Residues in contact with TRP1778 (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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1776B ILE* 3.8 17.5 - - + +
1777B ILE* 1.3 85.6 - - - +
1779B PHE* 1.3 59.0 + - - +
1780B VAL* 4.6 2.7 - - + -
1809B ILE* 3.3 30.3 - - + -
1810B PHE 3.3 5.8 - - - +
1811B ASN* 4.3 13.5 - - + +
1816B GLN* 5.6 0.4 + - - -
1818B PHE* 3.8 21.7 - + - -
1845B VAL* 4.5 7.9 - - + -
1848B LEU* 3.7 15.7 - - + -
1849B ILE* 3.6 25.8 - - + -
1852B LEU* 3.7 32.5 - - + -
1856B GLU 4.1 5.5 + - - -
1858B PRO* 3.6 29.2 - - + -
1860B GLN 3.0 11.3 + - - +
1861B ILE* 3.2 16.1 - - + +
1862B ILE* 2.7 32.2 + - - +
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Residues in contact with PHE1779 (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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1772B PHE* 5.5 2.5 - + - -
1777B ILE* 4.3 0.7 - - + -
1778B TRP* 1.3 73.9 - - - +
1780B VAL* 1.3 60.4 + - - +
1808B PHE 3.6 1.4 - - - +
1809B ILE* 3.4 3.8 - - - -
1810B PHE* 2.8 40.2 + + + +
1812B PRO* 3.9 27.1 - - + -
1862B ILE* 3.4 52.3 - - + -
1864B THR* 4.8 9.2 - - + -
1887B SER* 4.9 6.5 - - - -
1889B LEU* 3.9 20.9 - - + -
1891B LEU* 4.3 13.0 - - + -
1893B PHE* 4.4 18.0 - - + -
1933B PHE* 3.9 27.4 - + - -
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Residues in contact with VAL1780 (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* 4.6 3.6 - - + -
1779B PHE* 1.3 79.0 - - - +
1781B ASP* 1.3 67.0 + - - +
1807B ILE* 4.7 1.8 - - + -
1808B PHE 3.3 5.8 - - - +
1809B ILE* 4.2 22.2 - - + -
1841B THR* 3.9 28.3 - - + -
1845B VAL* 4.0 18.6 - - + -
1861B ILE* 3.7 21.5 - - + -
1862B ILE 2.9 12.7 + - - +
1863B VAL* 4.0 29.7 - - + +
1864B THR* 4.3 6.2 + - - +
1865B ARG* 5.4 1.6 + - - +
1868B MET* 5.6 0.9 - - + -
1872B LEU* 5.1 2.7 - - + -
1893B PHE* 5.5 0.4 - - - -
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Residues in contact with ASP1781 (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 4.3 0.2 - - - -
1780B VAL* 1.3 77.6 - - - +
1782B ASP* 1.3 82.3 + - - +
1807B ILE* 3.5 6.4 - - - +
1808B PHE* 2.9 31.8 + - + +
1864B THR* 4.4 8.1 + - - +
1865B ARG* 5.3 5.2 - - - +
1891B LEU 3.4 20.6 - - - +
1893B PHE* 3.4 37.8 + - + +
1894B GLN* 3.7 5.5 - - - +
2001B MG 2.2 31.5 - - - -
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Residues in contact with ASP1782 (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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1781B ASP* 1.3 92.1 + - - +
1783B THR* 1.3 65.9 + - - +
1806B ALA 3.2 13.0 - - - +
1807B ILE* 4.3 2.7 - - + -
1808B PHE* 4.3 4.2 - - - -
1834B GLY 5.0 0.5 - - - +
1835B GLN* 4.5 6.6 - - - +
1836B LEU* 3.9 12.8 + - + -
1841B THR* 2.5 36.7 + - + +
1865B ARG* 2.8 42.0 + - - +
1868B MET* 4.6 1.9 - - - +
1894B GLN* 5.2 2.4 - - - +
2001B MG 4.2 3.6 - - - -
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Residues in contact with THR1783 (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* 1.3 78.3 - - - +
1784B ASN* 1.3 78.4 + - - +
1785B VAL* 4.3 0.2 - - + -
1805B GLY* 3.4 2.4 - - - -
1806B ALA* 2.9 41.1 + - + +
1808B PHE* 3.9 21.1 - - + -
1834B GLY 3.7 10.8 + - - -
1836B LEU* 3.7 9.5 - - - +
1894B GLN* 4.0 21.6 - - + +
1897B LEU* 4.0 19.7 - - + +
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Residues in contact with ASN1784 (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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1783B THR* 1.3 91.6 + - - +
1785B VAL* 1.3 61.6 + - - +
1786B TYR* 3.5 50.3 + - + +
1804B ASN* 3.3 13.8 - - - +
1824B THR* 4.2 2.8 - - - +
1827B TRP* 3.1 40.9 - - - +
1834B GLY* 2.9 33.6 + - - +
1835B GLN 5.1 0.9 - - - -
1836B LEU* 4.2 7.0 - - + +
1897B LEU* 4.3 4.0 - - - +
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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