Contacts of the helix formed by residues 1837 - 1852 (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 ALA1837 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1824B THR* 5.7 2.6 + - - +
1826B VAL* 4.7 4.0 - - + +
1830B GLN* 3.4 34.0 + - - +
1835B GLN 3.8 0.6 + - - -
1836B LEU* 1.3 77.0 - - - +
1838B LYS* 1.3 64.7 + - - +
1839B TRP* 3.2 39.9 - - + +
1840B LYS* 3.0 23.1 + - + +
1841B THR* 3.3 5.7 + - - -
1865B ARG* 4.9 0.2 - - - +
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Residues in contact with LYS1838 (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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1832B ARG* 5.2 9.9 - - - +
1836B LEU 3.3 2.6 + - - -
1837B ALA* 1.3 71.1 - - - +
1839B TRP* 1.3 58.3 + - - +
1841B THR 3.4 1.1 + - - +
1842B ALA* 3.0 30.4 + - - +
1865B ARG* 3.6 27.7 - - - +
1867B GLY* 3.3 36.5 - - - +
1868B MET* 3.8 24.8 - - - +
1871B PRO* 3.8 16.3 - - + +
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Residues in contact with TRP1839 (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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1824B THR* 5.9 2.0 - - - -
1826B VAL* 4.2 24.9 - - + +
1830B GLN* 5.4 0.8 - - - +
1837B ALA* 3.2 27.7 - - + +
1838B LYS* 1.3 78.4 - - - +
1840B LYS* 1.3 88.2 + - + +
1843B GLU* 2.9 63.8 + - - +
1871B PRO* 5.2 1.1 - - - +
1875B HIS* 4.0 21.9 + - + +
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Residues in contact with LYS1840 (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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1807B ILE* 4.4 1.8 - - + -
1822B ILE* 3.8 28.8 - - + +
1823B HIS 3.8 18.3 + - - +
1824B THR* 5.3 6.1 - - - -
1836B LEU* 4.4 18.4 - - + -
1837B ALA* 3.0 22.0 + - + +
1839B TRP* 1.3 99.7 - - + +
1841B THR* 1.3 65.6 + - - +
1843B GLU* 3.3 19.0 + - - +
1844B GLU* 3.1 55.0 + - - +
1912B PRO* 6.4 0.2 - - - +
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Residues in contact with THR1841 (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* 3.9 25.8 - - + -
1782B ASP* 2.5 38.3 + - - +
1807B ILE* 3.9 19.2 - - + +
1836B LEU* 3.9 11.8 - - - +
1837B ALA 3.3 3.5 + - - -
1838B LYS 3.4 2.7 + - - -
1840B LYS* 1.3 77.2 - - - +
1842B ALA* 1.3 63.2 + - - +
1844B GLU* 3.2 3.1 + - - +
1845B VAL* 3.0 28.0 + - + +
1868B MET* 3.8 22.4 - - + -
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Residues in contact with ALA1842 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1838B LYS 3.0 19.3 + - - +
1839B TRP 4.1 0.2 - - - +
1841B THR* 1.3 77.9 - - - +
1843B GLU* 1.3 56.4 + - - +
1845B VAL* 3.3 2.6 + - - +
1846B ALA* 3.0 28.1 + - - +
1868B MET* 4.0 6.9 - - + +
1871B PRO* 3.8 16.4 - - + +
1872B LEU* 4.0 13.8 - - + +
1875B HIS* 3.4 36.5 - - + +
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Residues in contact with GLU1843 (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* 2.9 46.1 + - - +
1840B LYS* 3.3 29.9 + - - +
1842B ALA* 1.3 75.7 - - - +
1844B GLU* 1.3 68.6 + - + +
1846B ALA* 3.4 4.4 + - - +
1847B ALA* 2.9 28.9 + - - +
1875B HIS* 3.9 15.7 + - + -
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Residues in contact with GLU1844 (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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1807B ILE* 3.5 28.3 - - + -
1820B LYS* 2.8 53.4 + - + +
1822B ILE* 4.0 11.7 - - - +
1840B LYS* 3.1 51.7 + - - +
1841B THR 3.7 1.3 - - - +
1843B GLU* 1.3 80.9 - - + +
1845B VAL* 1.3 65.4 + - - +
1847B ALA* 3.4 5.4 + - - +
1848B LEU* 3.1 10.6 + - - +
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Residues in contact with VAL1845 (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* 4.5 10.5 - - + -
1780B VAL* 4.0 31.9 - - + -
1807B ILE* 4.6 2.5 - - + -
1809B ILE* 4.3 14.6 - - + -
1841B THR* 3.0 24.5 + - + +
1842B ALA 3.8 3.6 - - - +
1843B GLU 3.3 0.2 - - - -
1844B GLU* 1.3 75.3 - - - +
1846B ALA* 1.3 62.3 + - - +
1848B LEU* 3.3 6.8 + - - +
1849B ILE* 3.0 40.5 + - + +
1861B ILE* 4.1 17.0 - - + -
1872B LEU* 4.1 15.7 - - + -
1876B LEU* 4.7 1.3 - - + -
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Residues in contact with ALA1846 (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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1842B ALA 3.0 17.2 + - - +
1843B GLU* 3.7 7.2 - - - +
1845B VAL* 1.3 77.6 - - - +
1847B ALA* 1.3 57.3 - - - +
1849B ILE* 3.3 2.5 + - - +
1850B ARG* 2.9 54.2 + - - +
1875B HIS* 4.1 11.4 - - + +
1876B LEU* 3.8 26.2 - - + +
1879B PHE* 4.9 0.4 - - - -
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Residues in contact with ALA1847 (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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1820B LYS* 4.2 8.3 - - - +
1843B GLU 2.9 17.5 + - - +
1844B GLU* 3.7 9.2 - - - +
1845B VAL 3.3 0.2 - - - -
1846B ALA* 1.3 74.8 - - - +
1848B LEU* 1.3 63.2 + - - +
1850B ARG* 3.3 10.2 + - - +
1851B SER* 3.1 23.0 + - - -
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Residues in contact with LEU1848 (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* 4.2 2.2 - - + -
1778B TRP* 3.7 26.2 - - + -
1809B ILE* 3.5 28.3 - - + -
1818B PHE* 3.8 26.0 - - + -
1820B LYS* 3.9 10.0 - - - +
1844B GLU 3.1 13.8 + - - +
1845B VAL* 3.6 7.6 - - - +
1847B ALA* 1.3 76.1 - - - +
1849B ILE* 1.3 63.2 + - - +
1851B SER* 2.7 31.2 + - - +
1852B LEU* 3.3 17.1 + - + +
1914B MET* 3.6 31.4 - - + -
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Residues in contact with ILE1849 (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* 3.6 23.6 - - + -
1845B VAL* 3.0 34.2 + - + +
1846B ALA* 3.7 4.9 - - - +
1848B LEU* 1.3 76.1 - - - +
1850B ARG* 1.3 63.2 + - - +
1852B LEU* 3.1 16.2 + - - +
1857B GLN* 3.1 35.7 + - + +
1858B PRO* 4.1 4.7 - - + -
1861B ILE* 4.0 4.9 - - + -
1876B LEU* 3.9 16.6 - - + -
1879B PHE* 3.7 33.2 - - + -
1882B ILE* 3.9 21.5 - - + -
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Residues in contact with ARG1850 (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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1918A ASN* 4.5 10.4 + - - +
1965A HIS* 3.8 55.4 + - + +
1846B ALA* 2.9 42.0 + - - +
1847B ALA* 3.7 8.7 - - - +
1848B LEU 3.2 0.2 - - - -
1849B ILE* 1.3 75.7 - - - +
1851B SER* 1.3 59.5 + - - +
1852B LEU 3.6 3.6 + - - +
1857B GLN* 4.9 1.5 + - - +
1875B HIS 4.3 10.9 + - - -
1878B ASP* 2.9 36.2 + - - +
1879B PHE* 3.7 26.4 - - + -
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Residues in contact with SER1851 (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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1816A GLN* 5.5 0.5 + - - -
1916A LEU* 3.6 31.6 - - - +
1917A PHE* 3.4 26.5 + - - +
1918A ASN* 3.5 7.3 + - - +
1847B ALA 3.1 10.5 + - - -
1848B LEU* 2.7 33.6 + - - +
1850B ARG* 1.3 77.7 - - - +
1852B LEU* 1.3 58.8 + - - +
1853B PRO* 4.2 1.2 - - - +
1914B MET* 5.6 0.2 - - - +
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Residues in contact with LEU1852 (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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1816A GLN* 3.8 23.3 - - - +
1916A LEU* 3.9 20.9 - - + -
1918A ASN* 4.4 7.6 + - - -
1778B TRP* 3.7 37.0 - - + -
1818B PHE* 4.5 11.4 - - + -
1848B LEU* 3.4 20.9 - - + +
1849B ILE* 3.1 9.1 + - - +
1850B ARG 4.2 3.5 - - - +
1851B SER* 1.3 81.3 - - - +
1853B PRO* 1.3 77.9 - - + +
1854B VAL 3.5 0.3 + - - -
1856B GLU* 3.9 20.2 - - + +
1857B GLN* 3.2 19.5 + - + -
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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