Contacts of the helix formed by residues 1865 - 1879 (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 PRO1865 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1449A GLU* 4.3 13.2 - - - +
1843A ALA* 4.1 6.3 - - + -
1863A GLU 4.2 4.0 - - - +
1864A MET* 1.3 87.8 - - + +
1866A PRO* 1.3 74.8 - - + +
1867A GLU* 4.2 8.7 - - + +
1868A THR* 3.0 26.9 + - + +
1869A ALA* 3.0 19.5 + - - +
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Residues in contact with PRO1866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1680A GLN* 3.4 45.5 - - + +
1687A ARG* 5.4 0.9 - - - -
1842A TRP* 4.0 17.0 - - + -
1843A ALA* 3.7 23.8 - - + +
1864A MET 3.5 4.0 - - - +
1865A PRO* 1.3 81.5 - - + +
1867A GLU* 1.3 75.8 + - - +
1869A ALA* 3.3 2.6 + - + +
1870A CYS* 3.1 30.6 + - - -
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Residues in contact with GLU1867 (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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1680A GLN* 4.1 7.6 + - - -
1684A TRP* 5.7 0.2 - - - -
1687A ARG* 4.1 29.6 + - - +
1865A PRO* 4.2 7.7 - - + +
1866A PRO* 1.3 99.1 - - - +
1868A THR* 1.3 64.6 + - - +
1870A CYS* 3.6 3.2 + - - +
1871A ARG* 3.3 53.5 + - - +
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Residues in contact with THR1868 (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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1449A GLU* 4.1 23.2 + - + +
1450A VAL* 3.7 21.7 - - + +
1453A LEU* 3.8 23.1 - - + -
1864A MET* 5.2 0.2 - - - -
1865A PRO* 3.0 31.8 + - + +
1867A GLU* 1.3 75.6 - - - +
1869A ALA* 1.3 66.8 + - - +
1871A ARG* 3.1 12.2 + - - +
1872A ALA* 3.1 20.8 + - - +
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Residues in contact with ALA1869 (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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1839A TRP* 3.4 30.8 - - + -
1842A TRP* 3.9 16.2 - - + -
1864A MET* 4.0 22.2 - - + +
1865A PRO 3.0 11.7 + - - +
1866A PRO 3.6 8.3 - - - +
1868A THR* 1.3 77.5 - - - +
1870A CYS* 1.3 61.1 + - - +
1872A ALA* 3.2 8.8 + - - +
1873A LEU 3.1 16.5 + - - -
1886A VAL* 4.6 4.3 - - - -
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Residues in contact with CYS1870 (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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1680A GLN* 4.2 7.6 - - - -
1681A ILE* 3.8 25.8 - - - -
1684A TRP* 3.4 49.8 - - + -
1687A ARG* 5.3 0.7 - - - -
1839A TRP* 4.7 1.1 - - - -
1842A TRP* 4.0 10.5 - - - -
1866A PRO 3.1 22.7 + - - +
1867A GLU* 4.0 5.2 - - - +
1868A THR 3.3 0.2 - - - -
1869A ALA* 1.3 76.9 - - - +
1871A ARG* 1.3 58.5 + - - +
1873A LEU* 3.4 8.7 + - - +
1874A GLN* 3.0 25.8 + - - +
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Residues in contact with ARG1871 (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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1450A VAL* 4.0 16.8 - - + -
1684A TRP* 5.2 7.9 - - + +
1687A ARG* 4.6 13.9 - - - +
1867A GLU* 3.3 41.9 + - - +
1868A THR* 3.1 12.4 + - - +
1870A CYS* 1.3 77.3 - - + +
1872A ALA* 1.3 65.4 + - - +
1874A GLN* 3.4 8.6 + - + +
1875A ASN* 3.1 29.4 + - - +
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Residues in contact with ALA1872 (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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1450A VAL* 3.3 30.2 - - + +
1453A LEU* 5.1 2.2 - - + -
1454A ARG* 3.9 11.5 + - + +
1868A THR 3.1 9.8 + - - +
1869A ALA 3.2 3.8 + - - +
1871A ARG* 1.3 77.6 - - - +
1873A LEU* 1.3 64.1 + - - +
1875A ASN* 3.2 5.7 + - - +
1876A ALA* 3.0 19.9 + - - +
1886A VAL* 3.4 36.4 - - + +
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Residues in contact with LEU1873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1681A ILE* 4.4 9.9 - - + -
1684A TRP* 4.1 23.6 - - + -
1750A PHE* 4.1 13.9 - - + -
1796A VAL* 4.2 11.0 - - + -
1798A PHE* 4.8 0.7 - - + -
1835A THR* 4.6 2.7 - - + -
1837A VAL* 3.3 32.5 - - + -
1839A TRP* 3.9 30.5 - - + -
1869A ALA 3.1 5.8 + - - +
1870A CYS* 3.6 7.9 - - - +
1872A ALA* 1.3 75.1 - - - +
1874A GLN* 1.3 66.0 + - - +
1876A ALA* 2.8 18.8 + - + +
1877A LEU* 2.9 31.9 + - + +
1886A VAL* 4.7 4.4 - - - +
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Residues in contact with GLN1874 (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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1661A GLU* 4.0 4.3 - - + +
1662A TRP* 3.2 28.1 + - - +
1684A TRP* 3.5 18.3 - - + +
1688A ARG* 3.1 38.2 + - - +
1870A CYS 3.0 14.9 + - - +
1871A ARG* 3.5 13.2 - - + +
1872A ALA 3.3 0.2 - - - -
1873A LEU* 1.3 76.9 - - - +
1875A ASN* 1.3 65.7 + - - +
1877A LEU* 3.1 7.1 + - - +
1878A ASP* 3.0 59.8 + - - +
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Residues in contact with ASN1875 (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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1450A VAL* 3.6 17.0 - - - +
1454A ARG* 4.0 20.8 + - - +
1656A PRO* 4.0 25.1 - - + +
1871A ARG* 3.1 18.5 + - - +
1872A ALA 3.5 9.2 - - - +
1873A LEU 3.1 0.2 - - - -
1874A GLN* 1.3 80.9 - - - +
1876A ALA* 1.3 59.7 + - - +
1878A ASP* 3.5 12.4 + - - +
1879A ARG* 3.2 22.5 + - - +
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Residues in contact with ALA1876 (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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1454A ARG* 3.6 10.3 - - - +
1835A THR* 5.0 1.1 - - + -
1872A ALA 3.0 11.6 + - - +
1873A LEU* 2.8 16.7 + - + +
1875A ASN* 1.3 75.3 - - - +
1877A LEU* 1.3 66.4 + - - +
1879A ARG 3.4 0.7 + - - -
1880A ALA 3.1 17.3 + - - -
1881A GLU* 3.1 33.6 + - - +
1884A PRO* 3.7 25.8 - - + -
1886A VAL* 5.7 0.9 - - + -
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Residues in contact with LEU1877 (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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1662A TRP* 3.8 46.3 - - + +
1684A TRP* 4.3 10.1 - - + -
1750A PHE* 4.6 7.9 - - + -
1794A ALA* 4.4 11.2 - - + -
1796A VAL* 4.0 15.5 - - + -
1835A THR* 3.4 29.4 - - + +
1873A LEU* 2.9 32.7 + - + +
1874A GLN* 3.6 7.6 - - - +
1876A ALA* 1.3 76.3 - - - +
1878A ASP* 1.3 63.7 + - - +
1880A ALA* 3.2 14.0 + - - +
1881A GLU 5.8 0.2 - - - -
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Residues in contact with ASP1878 (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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1656A PRO* 4.2 15.3 - - + +
1658A THR* 3.5 18.0 - - - +
1660A ASP* 3.5 31.7 - - - +
1661A GLU* 3.7 7.8 - - - +
1662A TRP 2.8 29.0 + - - +
1874A GLN* 3.0 39.0 + - - +
1875A ASN* 3.7 14.0 + - - +
1876A ALA 3.2 0.2 - - - -
1877A LEU* 1.3 78.5 - - - +
1879A ARG* 1.3 57.6 + - - +
1880A ALA* 3.3 1.8 + - - +
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Residues in contact with ARG1879 (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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1454A ARG* 3.8 2.5 - - - +
1456A ARG* 3.7 27.9 - - - +
1653A ALA* 3.7 2.4 - - - +
1654A ALA* 2.7 60.1 + - - +
1655A ALA 4.2 2.9 - - - -
1656A PRO* 3.5 23.1 - - + -
1658A THR* 5.0 3.6 - - + -
1875A ASN 3.2 16.3 + - - +
1876A ALA 3.4 0.2 + - - -
1877A LEU 3.3 0.2 - - - -
1878A ASP* 1.3 76.1 - - - +
1880A ALA* 1.3 71.5 + - - +
1881A GLU* 2.9 34.0 + - + +
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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
------------------------------------------------------------
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