Contacts of the helix formed by residues 1773 - 1788 (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 SER1773 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1544A LEU* 2.9 33.5 - - - +
1755A THR* 4.8 0.2 - - - -
1769A ILE* 3.0 15.8 + - - -
1770A GLU 3.6 3.7 + - - -
1771A ARG 3.4 0.6 - - - -
1772A ALA* 1.3 77.3 - - - +
1774A ARG* 1.3 58.6 + - - +
1775A ALA 3.4 2.5 - - - -
1776A LYS* 3.4 8.8 + - - +
1777A VAL* 2.9 33.1 + - - +
1816A GLY* 4.4 10.8 - - - -
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Residues in contact with ARG1774 (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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1728A THR* 3.3 12.0 - - + +
1770A GLU* 3.7 21.8 + - - +
1771A ARG* 3.0 65.7 + - - +
1772A ALA 3.4 2.6 - - - -
1773A SER* 1.3 78.6 - - - +
1775A ALA* 1.3 59.2 + - - +
1777A VAL* 4.9 0.9 - - - -
1778A LEU* 2.8 63.0 + - + +
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Residues in contact with ALA1775 (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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301A NDP 3.4 41.5 - - + +
1727A VAL* 3.7 1.9 - - + +
1728A THR* 3.7 10.4 - - - +
1751A HIS* 3.3 9.7 - - - -
1753A ALA 3.9 3.4 - - - +
1754A ALA* 4.2 17.3 - - - +
1755A THR* 5.0 6.0 - - + +
1772A ALA 5.1 1.0 + - - -
1773A SER 3.4 0.8 - - - -
1774A ARG* 1.3 77.9 - - - +
1776A LYS* 1.3 61.3 + - - +
1779A GLY* 3.2 21.3 + - - -
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Residues in contact with LYS1776 (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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301A NDP 3.5 19.2 + - - -
1751A HIS* 3.0 20.5 + - + +
1752A ALA 6.1 0.8 - - - -
1753A ALA 3.6 14.2 + - - +
1754A ALA* 3.9 16.8 - - + +
1755A THR 5.6 0.4 - - - +
1773A SER* 3.4 10.3 + - - +
1774A ARG 3.3 0.2 - - - -
1775A ALA* 1.3 79.6 - - - +
1777A VAL* 1.3 59.1 + - + +
1780A ALA* 3.3 15.2 + - - +
1798A PHE* 2.9 27.3 + - - +
1813A TYR* 4.1 10.3 - - - -
1816A GLY* 3.5 32.3 - - - +
1817A ASN* 3.0 24.9 + - - +
1820A LEU* 3.5 17.7 - - + +
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Residues in contact with VAL1777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1543A PRO* 3.4 35.9 - - + -
1544A LEU* 3.7 31.6 - - + -
1770A GLU* 6.1 0.9 - - - +
1773A SER* 2.9 21.2 + - - +
1774A ARG* 4.9 0.9 - - - -
1776A LYS* 1.3 74.6 - - - +
1778A LEU* 1.3 62.4 + - + +
1779A GLY 3.2 0.2 - - - -
1780A ALA* 3.3 3.6 + - - +
1781A ARG* 3.0 25.6 + - - +
1816A GLY* 3.7 20.9 - - - +
1819A TYR* 3.7 25.1 - - + -
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Residues in contact with LEU1778 (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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1541A GLU 3.3 26.7 - - - +
1542A ALA* 4.5 4.5 - - + -
1543A PRO* 4.1 16.4 - - + -
1728A THR* 4.1 25.8 - - + +
1770A GLU* 5.0 4.0 - - - +
1774A ARG* 2.8 52.4 + - + +
1777A VAL* 1.3 72.1 - - + +
1779A GLY* 1.3 66.2 + - - +
1781A ARG* 3.8 13.4 - - - +
1782A ASN* 2.9 34.9 + - - +
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Residues in contact with GLY1779 (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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1727A VAL* 3.5 28.8 + - - -
1751A HIS* 3.9 6.7 - - - -
1774A ARG 3.4 1.0 + - - -
1775A ALA 3.2 21.8 + - - -
1778A LEU* 1.3 80.6 - - - +
1780A ALA* 1.3 62.0 + - - +
1782A ASN* 3.8 1.0 - - - +
1783A LEU* 3.0 29.4 + - - +
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Residues in contact with ALA1780 (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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1751A HIS* 3.4 8.3 + - + -
1776A LYS 3.3 21.1 + - - +
1777A VAL 3.6 3.4 - - - +
1778A LEU 3.2 0.2 - - - -
1779A GLY* 1.3 77.3 - - - +
1781A ARG* 1.3 63.0 + - - +
1783A LEU* 3.3 3.9 + - - +
1784A HIS* 2.9 25.1 + - - +
1795A PHE* 4.1 1.9 - - - -
1797A LEU* 3.7 19.3 - - + -
1819A TYR* 4.5 0.4 - - + -
1820A LEU* 3.7 21.1 - - + -
1823A LEU* 3.8 12.8 - - + +
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Residues in contact with ARG1781 (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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1541A GLU* 2.8 44.7 + - - +
1543A PRO* 4.5 9.7 - - + +
1730A ARG* 5.9 0.2 - - - +
1777A VAL 3.0 14.2 + - - +
1778A LEU* 3.3 14.5 + - + +
1780A ALA* 1.3 75.3 - - - +
1782A ASN* 1.3 90.3 + - - +
1784A HIS* 3.2 10.7 + - - +
1785A GLU* 2.9 65.6 + - - +
1819A TYR* 3.2 25.1 - - + +
1823A LEU* 4.2 2.4 - - + +
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Residues in contact with ASN1782 (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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1727A VAL 2.8 25.8 + - - +
1728A THR* 3.3 21.8 + - - +
1730A ARG* 3.6 30.0 - - - +
1733A VAL* 4.6 6.3 - - + -
1778A LEU* 2.9 22.1 + - - +
1779A GLY 3.8 2.9 - - - +
1781A ARG* 1.3 91.8 + - - +
1783A LEU* 1.3 57.8 + - - +
1785A GLU* 3.2 6.4 + - - +
1786A LEU* 2.8 47.7 + - + +
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Residues in contact with LEU1783 (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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1669A LEU* 3.9 26.5 - - + -
1671A THR* 3.9 15.7 - - + -
1727A VAL* 5.0 5.2 - - + -
1733A VAL* 4.0 21.3 - - + -
1736A LEU* 6.2 0.7 - - + -
1737A LEU* 5.4 0.9 - - + -
1749A VAL* 4.0 16.2 - - + -
1751A HIS* 3.7 31.9 - - + +
1779A GLY* 3.0 23.3 + - - +
1780A ALA* 3.7 4.7 - - - +
1782A ASN* 1.3 75.3 - - + +
1784A HIS* 1.3 56.9 + - - +
1786A LEU* 4.8 2.5 - - - -
1787A THR* 2.8 44.8 + - + +
1795A PHE* 3.9 14.4 - - + -
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Residues in contact with HIS1784 (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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1780A ALA 2.9 18.4 + - - +
1781A ARG* 3.3 9.7 + - - +
1783A LEU* 1.3 77.5 - - - +
1785A GLU* 1.3 69.5 + - + +
1787A THR* 3.7 0.9 + - - -
1788A ARG* 3.0 61.8 + - + +
1795A PHE* 3.6 14.7 - - + -
1823A LEU* 3.8 24.6 - - + +
1826A GLN* 6.0 2.0 - - + -
1827A ARG* 3.1 48.8 + - + +
1830A ASP* 5.6 2.3 + - - -
1832A LEU* 4.5 2.4 - - - +
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Residues in contact with GLU1785 (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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1730A ARG* 2.7 52.2 + - - +
1781A ARG* 2.9 53.2 + - - +
1782A ASN* 3.8 3.9 - - - +
1784A HIS* 1.3 81.8 - - - +
1786A LEU* 1.3 61.6 + - - +
1787A THR 3.5 0.9 + - - -
1788A ARG* 3.8 37.8 + - - +
1789A GLU* 5.2 3.3 + - - +
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Residues in contact with LEU1786 (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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1730A ARG* 3.6 52.5 - - + +
1733A VAL* 3.4 31.4 - - + -
1734A ARG* 3.7 32.5 - - + +
1737A LEU* 3.6 20.6 - - + +
1782A ASN 2.8 19.8 + - - +
1783A LEU 4.3 1.6 - - - +
1785A GLU* 1.3 77.5 - - - +
1787A THR* 1.3 61.7 + - - +
1788A ARG 3.6 0.2 - - - -
1789A GLU* 5.2 1.9 + - - +
1790A LEU* 4.1 7.6 - - - +
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Residues in contact with THR1787 (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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1737A LEU* 4.1 14.1 - - + -
1746A LEU* 4.2 11.9 - - + -
1749A VAL* 4.5 7.6 - - + -
1783A LEU* 2.8 27.1 + - + +
1784A HIS 3.7 2.1 + - - -
1786A LEU* 1.3 81.6 - - - +
1788A ARG* 1.3 65.0 + - - +
1789A GLU 3.0 6.1 - - - -
1790A LEU* 2.9 39.8 + - + +
1792A LEU* 3.5 27.2 - - + +
1795A PHE* 3.8 8.5 - - - -
1827A ARG* 4.2 5.6 + - - -
1832A LEU* 5.7 0.3 - - - +
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Residues in contact with ARG1788 (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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1784A HIS* 3.0 53.4 + - - +
1785A GLU* 3.8 31.4 + - - +
1786A LEU 3.6 0.8 - - - -
1787A THR* 1.3 77.7 - - - +
1789A GLU* 1.3 78.7 + - - +
1790A LEU 4.2 1.7 - - - +
1827A ARG* 4.5 6.7 - - - +
1830A ASP* 4.7 11.5 + - - -
1832A LEU* 3.6 39.2 - - + +
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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
------------------------------------------------------------
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