Contacts of the helix formed by residues 1890 - 1899 (chain A) in PDB entry 2FR1
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 ARG1890 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1860A GLY 2.8 12.0 + - - +
1862A ILE* 3.8 23.5 - - + +
1888A ASP* 3.2 37.6 + - - -
1889A VAL* 1.3 87.5 + - - +
1891A TRP* 1.3 60.0 + - - +
1892A ASP* 3.2 16.4 - - - +
1893A ARG* 3.0 36.1 + - + +
1894A PHE* 2.9 26.3 + - - +
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Residues in contact with TRP1891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1455A TYR* 3.2 42.7 + + - -
1650A TRP* 3.8 17.7 - + - -
1652A ARG* 3.6 9.2 - - - +
1889A VAL* 3.7 22.8 - - + +
1890A ARG* 1.3 69.4 - - - +
1892A ASP* 1.3 65.2 + - - +
1894A PHE* 3.6 23.8 - + - -
1895A LEU* 3.0 53.6 + - + +
1907A PHE* 3.3 40.4 - + + -
1910A ILE* 3.6 19.9 - - + +
1912A ASP* 3.5 44.2 - - + +
1913A ALA* 4.4 0.9 - - + -
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Residues in contact with ASP1892 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1890A ARG* 3.6 20.4 - - - +
1891A TRP* 1.3 75.2 + - - +
1893A ARG* 1.3 68.0 + - - +
1895A LEU* 5.3 2.0 - - - -
1896A LEU* 2.9 31.3 - - - +
1912A ASP 5.0 2.6 + - - +
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Residues in contact with ARG1893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1857A ARG 5.2 0.6 + - - -
1858A ARG* 3.5 41.7 - - - +
1859A HIS 4.1 3.0 - - - +
1860A GLY* 4.3 8.0 - - - -
1862A ILE* 4.8 10.7 - - - +
1890A ARG* 3.0 36.9 + - - +
1892A ASP* 1.3 90.4 + - - +
1894A PHE* 1.3 64.9 + - - +
1895A LEU 3.5 0.4 - - - -
1896A LEU* 3.9 4.4 + - - +
1897A ALA* 3.6 18.9 + - - +
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Residues in contact with PHE1894 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1805A PHE* 3.5 48.9 - + - -
1859A HIS* 3.7 33.3 + + - +
1860A GLY* 4.3 5.4 - - - -
1861A VAL* 4.8 8.5 - - + -
1889A VAL* 4.9 9.0 - - + -
1890A ARG 2.9 16.6 + - - +
1891A TRP* 3.4 31.2 + + + +
1893A ARG* 1.3 75.2 - - - +
1895A LEU* 1.3 63.5 + - + +
1897A ALA* 3.2 4.5 + - - +
1898A TYR* 2.9 51.2 + + + +
1907A PHE* 3.5 28.0 - + - -
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Residues in contact with LEU1895 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1891A TRP* 3.0 44.9 + - + +
1892A ASP* 5.3 1.3 - - - -
1894A PHE* 1.3 77.1 - - + +
1896A LEU* 1.3 62.1 + - + +
1898A TYR* 3.2 4.0 + - - -
1899A THR* 2.7 41.4 + - + +
1907A PHE* 3.9 30.5 - - + -
1912A ASP 4.6 0.7 - - - +
1913A ALA* 3.5 38.6 - - + +
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Residues in contact with LEU1896 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1892A ASP* 2.9 28.5 - - + +
1893A ARG* 3.9 6.2 + - - +
1894A PHE 3.4 0.6 - - - -
1895A LEU* 1.3 81.0 - - + +
1897A ALA* 1.3 57.5 + - - +
1899A THR* 3.6 4.4 + - - -
1900A ALA* 3.0 28.8 + - - +
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Residues in contact with ALA1897 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1601A LEU* 5.7 0.7 - - - +
1859A HIS* 3.8 34.5 - - + +
1893A ARG 3.6 10.4 + - - +
1894A PHE 3.2 8.1 + - - +
1896A LEU* 1.3 78.6 - - - +
1898A TYR* 1.3 63.1 + - - +
1900A ALA* 3.4 19.6 - - - +
1901A GLN* 5.0 3.6 - - - +
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Residues in contact with TYR1898 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1597A ARG* 4.7 7.1 + - - +
1601A LEU* 3.4 42.9 - - + +
1637A GLN* 4.8 3.6 + - - -
1805A PHE* 2.9 39.0 + + + -
1806A GLY 3.7 9.6 - - - -
1859A HIS* 5.3 5.1 + - - -
1894A PHE* 2.9 45.5 + + + +
1895A LEU* 3.8 5.6 - - - +
1897A ALA* 1.3 76.6 - - - +
1899A THR* 1.3 57.6 + - + +
1900A ALA 3.4 1.0 + - - -
1901A GLN* 5.4 1.4 - - - +
1902A ARG 3.6 6.4 + - - +
1904A THR* 3.6 36.8 - - + -
1906A LEU* 4.1 11.9 - - + +
1907A PHE* 3.7 16.2 - + + -
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Residues in contact with THR1899 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1895A LEU* 2.7 28.0 + - + +
1896A LEU* 3.6 4.9 + - - -
1898A TYR* 1.3 79.9 - - + +
1900A ALA* 1.3 64.4 + - - +
1901A GLN 3.2 3.0 + - - -
1902A ARG 3.0 20.9 + - - +
1903A PRO* 4.1 6.8 - - + +
1904A THR* 3.4 38.8 - - + +
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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