Contacts of the strand formed by residues 1816 - 1822 (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 GLN1816 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1851A SER 5.5 0.6 + - - -
1852A LEU* 3.7 28.3 - - - +
1853A PRO* 3.8 18.5 - - + +
1856A GLU* 4.8 13.0 - - - +
1778B TRP* 5.6 0.3 + - - -
1809B ILE 3.7 1.0 - - - +
1810B PHE* 3.4 4.8 - - - -
1811B ASN* 2.9 38.6 + - + +
1814B THR* 3.2 17.6 + - - +
1815B GLY* 1.3 75.8 - - - +
1817B LEU* 1.3 65.8 + - - +
1818B PHE* 3.3 42.1 - - + -
1856B GLU* 5.1 4.9 - - - +
1916B LEU* 4.4 9.0 - - + +
1917B PHE 3.5 9.0 - - - +
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Residues in contact with LEU1817 (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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1808B PHE* 4.0 25.6 - - + -
1809B ILE 3.4 25.4 - - - +
1810B PHE* 4.2 9.0 - - + -
1815B GLY 3.3 0.6 + - - -
1816B GLN* 1.3 75.7 - - - +
1818B PHE* 1.3 74.0 + - - +
1819B LEU* 4.1 6.3 - - + +
1893B PHE* 4.9 1.3 - - + -
1896B CYS* 5.1 0.9 - - - -
1902B PHE* 3.9 29.6 - - + -
1915B VAL 3.7 0.7 - - - +
1916B LEU* 3.5 6.4 - - - +
1917B PHE* 2.9 44.3 + - + +
1919B LEU* 3.9 35.2 - - + -
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Residues in contact with PHE1818 (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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1916A LEU* 4.4 9.6 - - + -
1778B TRP* 3.8 32.3 - + - -
1807B ILE 3.6 3.6 - - - +
1809B ILE* 2.8 56.6 + - + +
1811B ASN* 5.8 1.3 - - + -
1816B GLN* 3.3 33.4 - - + -
1817B LEU* 1.3 75.0 - - - +
1819B LEU* 1.3 59.9 + - - +
1820B LYS 3.9 0.8 + - - -
1848B LEU* 3.8 21.8 - - + -
1852B LEU* 4.5 11.4 - - + -
1856B GLU* 5.9 0.4 - - - -
1914B MET* 3.8 25.1 - - + -
1915B VAL 3.9 2.9 - - - -
1916B LEU* 3.4 29.4 - - + -
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Residues in contact with LEU1819 (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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1806B ALA* 4.1 16.8 - - + -
1807B ILE 3.5 12.3 - - - +
1808B PHE* 3.6 32.5 - - + -
1817B LEU* 3.8 6.4 - - + -
1818B PHE* 1.3 71.0 - - - +
1820B LYS* 1.3 62.3 + - - +
1821B ILE* 3.9 13.0 + - + +
1897B LEU* 6.4 0.2 - - + -
1902B PHE* 3.6 28.7 - - + +
1905B LEU* 3.9 18.6 - - + -
1906B ILE* 5.7 2.5 - - + -
1913B GLN 3.8 1.0 - - - +
1914B MET* 3.3 2.6 - - - +
1915B VAL* 2.8 45.6 + - - +
1917B PHE* 3.8 19.1 - - + -
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Residues in contact with LYS1820 (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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1806B ALA* 3.3 5.9 - - - +
1807B ILE* 2.8 44.3 + - + +
1809B ILE* 4.5 13.2 - - + -
1818B PHE 3.9 0.2 + - - -
1819B LEU* 1.3 71.4 - - - +
1821B ILE* 1.3 62.5 + - - +
1822B ILE* 4.0 11.4 + - + +
1844B GLU* 2.8 61.4 + - + +
1847B ALA* 4.2 5.5 - - - +
1848B LEU* 3.9 23.6 - - - +
1913B GLN 3.5 5.8 - - - +
1914B MET* 3.9 31.1 - - + +
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Residues in contact with ILE1821 (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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1803B ILE* 3.8 21.3 - - + -
1805B GLY 3.6 4.9 - - - +
1806B ALA* 4.7 2.7 - - + -
1819B LEU* 3.9 24.9 + - + +
1820B LYS* 1.3 75.3 - - - +
1822B ILE* 1.3 62.6 + - - +
1905B LEU* 4.2 19.1 - - + +
1906B ILE* 3.5 23.6 - - + -
1909B ALA* 3.6 31.0 - - + -
1911B GLU 4.4 4.0 - - - +
1912B PRO* 3.2 7.2 - - - +
1913B GLN* 3.0 56.6 + - + +
1915B VAL* 5.5 0.9 - - + -
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Residues in contact with ILE1822 (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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1803B ILE* 3.5 9.2 - - - -
1804B ASN 3.0 23.6 + - - -
1805B GLY* 3.0 39.6 + - - +
1806B ALA* 4.1 1.8 - - - +
1807B ILE* 4.2 11.7 - - + -
1820B LYS* 4.2 13.5 - - + +
1821B ILE* 1.3 81.6 - - - +
1823B HIS* 1.3 75.9 + - - +
1824B THR* 3.8 12.3 - - + +
1836B LEU* 4.1 17.5 - - + -
1840B LYS* 3.8 20.4 - - + +
1844B GLU* 4.0 23.1 - - - +
1912B PRO* 4.2 7.6 - - + -
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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