Contacts of the helix formed by residues 1892 - 1898 (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 PRO1892 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1781B ASP* 4.5 0.4 - - - +
1890B GLN* 3.8 8.5 - - + +
1891B LEU* 1.3 86.3 - - + +
1893B PHE* 1.3 64.3 + - - +
1894B GLN* 3.1 21.5 - - - +
1895B ALA* 2.9 16.8 + - - +
1940B LEU* 3.6 32.8 - - + +
1941B ARG* 3.8 18.4 - - + +
1944B HIS* 3.7 32.1 - - + +
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Residues in contact with PHE1893 (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* 4.4 13.7 - - + -
1780B VAL 5.6 0.2 - - - -
1781B ASP* 3.4 26.8 + - + +
1808B PHE* 3.3 45.0 - + + -
1810B PHE* 3.6 39.7 - + + -
1817B LEU* 4.9 1.1 - - + -
1891B LEU* 3.0 47.1 + - + -
1892B PRO* 1.3 70.5 - - - +
1894B GLN* 1.3 58.5 + - - +
1895B ALA 3.0 0.2 - - - -
1896B CYS* 2.9 36.5 + - - +
1919B LEU* 4.2 12.3 - - + -
1936B LEU* 4.9 1.1 - - + -
1940B LEU* 4.1 20.9 - - + -
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Residues in contact with GLN1894 (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* 3.7 10.1 + - - +
1782B ASP 5.2 1.9 - - - +
1783B THR* 4.0 30.5 - - + +
1808B PHE* 4.2 10.1 - - - -
1892B PRO* 3.3 22.2 - - - +
1893B PHE* 1.3 73.4 + - - +
1895B ALA* 1.3 62.5 + - - +
1897B LEU* 3.1 26.8 + - + +
1898B LYS* 4.5 1.4 + - - +
1944B HIS* 3.4 34.8 + - + +
2001B MG 4.1 4.2 - - - -
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Residues in contact with ALA1895 (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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1892B PRO 2.9 12.9 + - - +
1894B GLN* 1.3 79.2 - - - +
1896B CYS* 1.3 62.0 + - - +
1897B LEU 3.1 0.4 - - - -
1898B LYS* 3.0 28.1 + - - +
1899B VAL* 4.0 6.2 - - - +
1940B LEU* 3.4 33.0 - - + +
1943B LEU* 3.8 10.6 - - + +
1944B HIS* 3.8 21.8 - - + +
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Residues in contact with CYS1896 (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* 3.9 20.4 - - + -
1817B LEU* 5.1 0.2 - - - -
1893B PHE* 2.9 29.0 + - - +
1895B ALA* 1.3 78.0 - - - +
1897B LEU* 1.3 56.4 + - + +
1899B VAL* 2.9 28.8 + - - +
1902B PHE* 3.2 44.0 - - + +
1919B LEU* 4.8 10.8 - - - -
1940B LEU* 3.9 21.0 - - - +
1968B TRP* 5.5 3.6 - - - -
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Residues in contact with LEU1897 (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* 4.0 15.3 - - + +
1784B ASN 4.3 4.9 - - - +
1785B VAL* 3.9 40.2 - - + -
1806B ALA* 4.9 8.5 - - + -
1808B PHE* 4.9 7.0 - - + -
1819B LEU* 6.4 0.4 - - + -
1894B GLN* 3.1 23.9 + - + +
1896B CYS* 1.3 76.4 - - + +
1898B LYS* 1.3 59.8 + - + +
1899B VAL 3.3 5.9 + - - +
1902B PHE* 4.5 8.3 - - + -
1903B GLY* 4.3 11.8 - - - +
1906B ILE* 4.5 20.0 - - + -
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Residues in contact with LYS1898 (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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1894B GLN 5.2 0.7 - - - +
1895B ALA* 3.0 20.6 + - - +
1897B LEU* 1.3 78.8 - - + +
1899B VAL* 1.3 60.6 + - - +
1900B GLU* 3.8 1.2 + - - -
1943B LEU* 3.0 35.5 + - + +
1944B HIS* 3.2 24.0 + - - +
1947B ASN* 3.6 36.3 + - - +
1951B LYS* 2.7 27.8 + - - +
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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