Contacts of the helix formed by residues 1868 - 1876 (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 MET1868 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1780B VAL* 6.1 0.7 - - + -
1782B ASP* 4.7 2.7 - - - +
1838B LYS* 3.8 42.0 - - - +
1841B THR* 3.8 29.4 - - + -
1842B ALA* 4.0 8.7 - - + +
1863B VAL* 4.1 19.7 - - + -
1865B ARG* 3.3 41.8 + - + +
1866B LYS 3.0 1.6 - - - -
1867B GLY* 1.3 77.5 - - - +
1869B LEU* 1.3 65.5 + - - +
1870B ASP 3.5 0.4 - - - -
1871B PRO* 3.5 3.3 - - + +
1872B LEU* 3.0 54.6 + - + +
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Residues in contact with LEU1869 (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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1863B VAL* 3.4 27.6 - - + -
1866B LYS* 3.3 22.3 + - + +
1867B GLY 3.3 1.0 - - - -
1868B MET* 1.3 78.0 - - - +
1870B ASP* 1.3 63.9 + - - +
1872B LEU* 3.4 2.3 + - - +
1873B GLU* 3.1 34.6 + - - +
1884B ILE* 3.7 19.3 - - + +
1885B LYS* 3.7 21.3 - - - -
1886B GLY* 3.7 9.9 - - - +
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Residues in contact with ASP1870 (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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1867B GLY 4.4 1.0 + - - +
1869B LEU* 1.3 77.7 - - - +
1871B PRO* 1.4 77.5 - - + +
1873B GLU* 3.1 15.9 + - - +
1874B VAL* 3.0 37.4 + - - +
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Residues in contact with PRO1871 (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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1838B LYS* 3.8 30.7 - - + +
1839B TRP* 5.2 0.7 - - - +
1842B ALA* 4.1 13.5 - - + -
1867B GLY 3.2 23.3 - - - +
1868B MET* 3.5 10.1 - - + +
1870B ASP* 1.4 96.3 - - + +
1872B LEU* 1.3 55.2 + - - +
1874B VAL* 3.4 4.8 + - + +
1875B HIS* 2.8 45.5 + - + +
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Residues in contact with LEU1872 (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* 5.1 3.8 - - + -
1842B ALA* 4.0 24.9 - - + +
1845B VAL* 4.1 26.7 - - + -
1861B ILE* 4.0 12.8 - - + -
1863B VAL* 3.5 31.4 - - + -
1868B MET* 3.0 30.8 + - + +
1869B LEU 3.8 3.1 - - - +
1871B PRO* 1.3 73.6 - - - +
1873B GLU* 1.3 67.4 + - - +
1875B HIS* 3.8 0.6 - - + -
1876B LEU* 2.9 41.2 + - + +
1884B ILE* 4.0 22.7 - - + -
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Residues in contact with GLU1873 (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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1869B LEU* 3.1 23.5 + - - +
1870B ASP* 3.1 17.3 + - - +
1872B LEU* 1.3 74.4 - - - +
1874B VAL* 1.3 62.7 + - + +
1876B LEU* 3.5 2.7 + - - +
1877B LEU* 3.3 21.0 + - - +
1884B ILE* 3.6 38.4 + - + +
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Residues in contact with VAL1874 (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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1870B ASP* 3.0 38.1 + - - +
1871B PRO* 3.7 6.5 - - + +
1873B GLU* 1.3 78.4 - - + +
1875B HIS* 1.3 70.7 + - + +
1877B LEU* 3.2 21.4 + - - +
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Residues in contact with HIS1875 (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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1839B TRP* 4.0 26.5 + - + +
1842B ALA* 3.4 29.7 - - + +
1843B GLU* 3.9 24.4 + - + +
1846B ALA* 4.1 11.8 - - + +
1850B ARG* 4.3 14.0 + - - -
1871B PRO* 2.8 34.8 + - + +
1872B LEU* 4.1 2.5 - - - +
1874B VAL* 1.3 84.5 - - + +
1876B LEU* 1.3 63.3 + - + +
1877B LEU* 3.3 2.4 + - - +
1878B ASP 5.0 0.2 + - - -
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Residues in contact with LEU1876 (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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1845B VAL* 4.7 0.7 - - + -
1846B ALA* 3.8 35.9 - - + +
1849B ILE* 3.9 16.4 - - + -
1861B ILE* 3.7 30.3 - - + -
1872B LEU* 2.9 32.3 + - + +
1873B GLU* 3.6 6.7 - - - +
1875B HIS* 1.3 77.5 - - + +
1877B LEU* 1.3 65.3 + - - +
1878B ASP 3.2 2.7 - - - -
1879B PHE* 2.9 42.3 + - + +
1880B PRO* 5.0 0.5 - - - +
1882B ILE* 4.4 11.7 - - + -
1884B ILE* 4.6 10.5 - - + -
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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