Contacts of the helix formed by residues 1832 - 1846 (chain J) in PDB entry 2BT4
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 THR1832 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1820J LEU* 3.4 16.6 - - - +
1821J GLY* 5.0 2.9 - - - -
1822J GLN* 6.1 2.2 - - + -
1830J SER 4.6 4.7 - - - +
1831J ASP* 1.3 77.1 - - - +
1833J LEU* 1.3 66.2 + - - +
1834J ALA* 3.3 11.4 + - - +
1835J ASP* 2.8 36.4 + - - +
1836J VAL* 3.1 20.4 + - - +
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Residues in contact with LEU1833 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1813J ASN* 4.0 20.4 - - + +
1817J LEU* 3.6 31.0 - - + +
1818J ASN* 4.3 11.0 + - + +
1820J LEU* 4.0 21.6 + - + +
1832J THR* 1.3 75.6 - - - +
1834J ALA* 1.3 58.3 + - - +
1836J VAL* 3.2 9.9 + - + +
1837J GLU* 2.9 27.2 + - - +
1853J PHE* 3.8 20.5 - - + -
1855J GLN* 3.7 37.0 - - + -
1938J TYR* 4.6 3.1 - - - +
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Residues in contact with ALA1834 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1832J THR* 3.1 10.2 + - - +
1833J LEU* 1.3 76.0 - - - +
1835J ASP* 1.3 66.4 + - - +
1837J GLU* 3.2 13.8 + - - +
1838J ALA* 3.0 21.4 + - - +
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Residues in contact with ASP1835 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1830J SER 4.6 1.0 - - - +
1831J ASP* 3.5 28.5 - - + +
1832J THR* 2.8 39.0 + - - +
1834J ALA* 1.3 75.6 - - - +
1836J VAL* 1.3 58.3 + - - +
1838J ALA* 3.1 8.6 + - - +
1839J LEU* 2.9 31.1 + - + +
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Residues in contact with VAL1836 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1820J LEU* 3.9 12.8 - - + -
1831J ASP* 4.7 3.4 - - + -
1832J THR 3.1 13.4 + - - +
1833J LEU* 3.2 11.9 + - + +
1835J ASP* 1.3 73.6 - - - +
1837J GLU* 1.3 66.7 + - - +
1839J LEU* 3.0 10.2 + - + +
1840J CYS* 2.9 23.7 + - - -
1853J PHE* 4.0 15.0 - - + -
1935J VAL* 3.6 34.8 - - + -
1938J TYR* 3.8 36.6 - - + -
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Residues in contact with GLU1837 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1833J LEU 2.9 10.4 + - - +
1834J ALA* 3.2 14.3 + - - +
1836J VAL* 1.3 76.4 - - - +
1838J ALA* 1.3 57.3 + - - +
1840J CYS* 3.1 3.3 + - - +
1841J VAL* 2.9 39.5 + - + +
1851J VAL* 5.3 0.7 - - + +
1853J PHE* 3.5 57.4 + - + +
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Residues in contact with ALA1838 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1834J ALA 3.0 12.7 + - - +
1835J ASP* 3.1 11.9 + - - +
1837J GLU* 1.3 78.5 - - - +
1839J LEU* 1.3 61.7 + - - +
1841J VAL* 3.4 9.5 + - - +
1842J LYS* 3.2 22.9 + - - +
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Residues in contact with LEU1839 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1831J ASP* 5.1 5.8 - - - +
1835J ASP* 2.9 14.7 + - + +
1836J VAL* 3.4 12.3 - - + +
1838J ALA* 1.3 74.3 - - - +
1840J CYS* 1.3 60.8 + - - +
1842J LYS* 3.3 33.9 + - + +
1843J ALA* 2.9 29.0 + - - +
1935J VAL* 3.7 37.7 - - + +
1936J GLN* 5.2 1.8 - - - +
1938J TYR* 6.2 0.4 - - + -
1939J VAL* 4.3 17.9 - - + -
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Residues in contact with CYS1840 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1811J ILE* 3.7 32.3 - - + -
1836J VAL 2.9 14.9 + - - +
1837J GLU* 3.4 10.3 - - - +
1839J LEU* 1.3 78.6 - - - +
1841J VAL* 1.3 61.5 + - - +
1843J ALA* 3.7 6.1 - - - +
1844J ALA* 2.9 31.7 + - - +
1851J VAL* 3.6 5.3 - - + +
1853J PHE* 4.2 13.7 - - + -
1938J TYR* 3.7 35.2 - - - -
1939J VAL* 5.2 0.9 - - - -
1942J VAL* 4.5 3.2 - - - +
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Residues in contact with VAL1841 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1837J GLU* 2.9 25.9 + - + +
1838J ALA* 3.4 10.7 + - - +
1840J CYS* 1.3 78.0 - - - +
1842J LYS* 1.3 58.5 + - - +
1844J ALA* 3.9 2.5 - - - +
1845J ALA* 3.0 29.0 + - + +
1849J GLY 4.9 0.7 - - - +
1850J THR* 5.7 1.2 - - - +
1851J VAL* 3.7 25.1 - - + +
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Residues in contact with LYS1842 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1838J ALA 3.2 9.4 + - - +
1839J LEU* 3.5 34.3 - - + +
1840J CYS 3.2 0.2 - - - -
1841J VAL* 1.3 78.9 - - + +
1843J ALA* 1.3 69.3 + - + +
1845J ALA* 3.2 6.4 + - - +
1846J ALA* 2.9 24.7 + - + +
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Residues in contact with ALA1843 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1839J LEU 2.9 16.8 + - - +
1840J CYS* 3.3 6.3 + - - +
1842J LYS* 1.3 79.9 - - + +
1844J ALA* 1.3 64.2 + - - +
1846J ALA* 3.2 10.3 + - - +
1847J HIS* 3.2 26.6 - - + -
1939J VAL* 4.0 31.9 - - + -
1942J VAL* 3.8 15.3 - - + -
1943J GLU* 5.7 0.4 - - + -
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Residues in contact with ALA1844 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1804J LEU* 4.6 1.0 - - - +
1809J ILE* 4.4 5.2 - - + -
1840J CYS 2.9 18.8 + - - +
1841J VAL 3.9 2.7 - - - +
1843J ALA* 1.3 78.0 - - - +
1845J ALA* 1.3 52.0 + - - +
1847J HIS* 2.9 16.5 + - - +
1848J GLY 3.1 0.2 + - - -
1849J GLY* 2.7 44.4 + - - +
1850J THR* 3.9 2.7 - - - +
1851J VAL* 3.5 22.7 - - + -
1942J VAL* 3.6 14.3 - - + +
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Residues in contact with ALA1845 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1841J VAL* 3.0 20.8 + - + +
1842J LYS* 3.2 7.6 + - - +
1844J ALA* 1.3 70.6 - - - +
1846J ALA* 1.3 57.5 + - - +
1847J HIS 2.9 10.7 + - - -
1848J GLY* 3.0 12.7 + - - -
1849J GLY 3.4 12.9 + - - +
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Residues in contact with ALA1846 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1842J LYS* 2.9 13.8 + - + +
1843J ALA* 3.5 13.2 - - - +
1844J ALA 3.2 0.2 - - - -
1845J ALA* 1.3 74.5 - - - +
1847J HIS* 1.3 74.8 + - + +
1848J GLY 3.6 0.2 - - - -
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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