Contacts of the helix formed by residues 1899 - 1909 (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 VAL1899 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1895B ALA 4.0 4.0 - - - +
1896B CYS* 2.9 16.5 + - - +
1897B LEU 4.8 0.2 - - - -
1898B LYS* 1.3 82.2 - - - +
1900B GLU* 1.3 67.4 + - - +
1901B LYS* 4.3 7.2 - - + +
1902B PHE* 3.0 16.1 + - + +
1903B GLY* 3.0 18.6 + - - -
1943B LEU* 3.9 16.6 - - + -
1951B LYS* 4.5 3.4 - - - +
1967B ILE* 3.9 33.7 - - + +
1968B TRP* 3.9 28.0 - - + -
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Residues in contact with GLU1900 (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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1898B LYS 3.8 3.4 + - - -
1899B VAL* 1.3 73.6 - - - +
1901B LYS* 1.3 54.6 + - - +
1903B GLY* 3.1 2.2 + - - +
1904B ASP* 2.7 62.4 + - - +
1951B LYS* 5.5 2.0 - - - +
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Residues in contact with LYS1901 (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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1899B VAL* 3.2 7.0 + - + +
1900B GLU* 1.3 78.5 - - - +
1902B PHE* 1.3 67.5 + - + +
1904B ASP* 3.8 8.6 + - - +
1905B LEU* 3.3 21.0 + - - +
1917B PHE* 4.0 23.4 - - + -
1964B PRO 2.6 29.9 + - - -
1965B HIS* 3.3 14.6 + - - +
1966B HIS 2.9 23.8 + - - +
1967B ILE* 3.8 24.0 - - + -
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Residues in contact with PHE1902 (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* 5.4 0.4 - + - -
1817B LEU* 3.9 13.9 - - + -
1819B LEU* 3.6 22.9 - - + -
1896B CYS* 3.2 49.4 - - + +
1897B LEU* 4.5 7.9 - - + -
1899B VAL* 3.0 14.1 + - + -
1901B LYS* 1.3 76.5 - - + +
1903B GLY* 1.3 68.6 + - - +
1905B LEU* 3.2 8.0 + - - +
1906B ILE* 3.1 26.7 + - + +
1917B PHE* 3.7 36.3 - + - -
1919B LEU* 3.8 24.0 - - + -
1967B ILE* 3.9 28.0 - - + -
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Residues in contact with GLY1903 (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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1897B LEU* 4.3 14.5 + - - -
1899B VAL 3.0 12.5 + - - -
1900B GLU* 3.6 3.4 - - - -
1902B PHE* 1.3 75.1 - - - +
1904B ASP* 1.3 57.9 + - - +
1906B ILE* 3.3 8.9 + - - +
1907B LEU* 2.9 39.2 + - - +
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Residues in contact with ASP1904 (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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1900B GLU* 2.7 48.1 + - - +
1901B LYS* 3.9 8.6 + - - +
1903B GLY* 1.3 72.6 - - - +
1905B LEU* 1.3 57.3 + - - +
1907B LEU* 3.3 11.8 + - - +
1908B LYS* 2.9 35.8 + - + +
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Residues in contact with LEU1905 (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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1819B LEU* 3.9 28.0 - - + -
1821B ILE* 4.2 16.2 - - + -
1901B LYS 3.3 11.9 + - - +
1902B PHE* 3.2 10.4 + - - +
1904B ASP* 1.3 79.3 - - - +
1906B ILE* 1.3 59.0 + - + +
1908B LYS* 3.1 4.5 + - + -
1909B ALA* 2.9 44.9 + - + +
1913B GLN* 4.9 4.0 - - - +
1915B VAL* 3.9 30.1 - - + -
1917B PHE* 4.2 13.0 - - + -
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Residues in contact with ILE1906 (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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1785B VAL* 4.1 26.0 - - + -
1787B ARG* 3.5 34.7 + - - +
1803B ILE* 4.0 17.4 - - + +
1805B GLY 5.2 0.7 - - - +
1806B ALA* 5.3 1.3 - - + -
1819B LEU* 5.7 2.0 - - + -
1821B ILE* 3.5 32.3 - - + -
1897B LEU* 4.5 22.2 - - + -
1902B PHE* 3.1 15.3 + - + +
1903B GLY* 3.6 9.6 - - - +
1905B LEU* 1.3 79.9 - - + +
1907B LEU* 1.3 66.5 + - + +
1908B LYS 3.4 0.2 + - - -
1909B ALA* 3.6 12.2 - - - +
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Residues in contact with LEU1907 (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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1787B ARG* 3.8 28.8 + - - +
1903B GLY* 2.9 25.5 + - - +
1904B ASP* 3.8 11.0 - - - +
1905B LEU 3.2 0.2 - - - -
1906B ILE* 1.3 79.5 - - + +
1908B LYS* 1.3 60.1 + - - +
1909B ALA 4.7 1.1 - - - +
1910B THR* 5.9 0.5 - - - +
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Residues in contact with LYS1908 (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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1911A GLU* 4.1 3.1 - - - +
1904B ASP* 2.9 19.3 + - + +
1905B LEU* 3.9 4.5 - - + +
1907B LEU* 1.3 79.7 - - - +
1909B ALA* 1.3 63.5 + - - +
1910B THR* 3.7 11.3 + - - +
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Residues in contact with ALA1909 (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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1911A GLU* 3.7 6.7 - - - -
1787B ARG* 5.1 1.7 + - - -
1803B ILE* 3.7 9.6 - - + +
1821B ILE* 3.6 27.1 - - + -
1905B LEU* 2.9 23.6 + - + +
1906B ILE 3.6 12.7 - - - +
1907B LEU 4.7 0.9 - - - +
1908B LYS* 1.3 79.0 - - - +
1910B THR* 1.3 63.7 + - - +
1911B GLU 4.6 1.1 - - - +
1913B GLN* 3.7 17.5 - - - +
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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