Contacts of the helix formed by residues 1813 - 1830 (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 TYR1813 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A NDP 2.6 52.0 + + - -
1754A ALA* 5.1 0.2 - - + -
1755A THR 3.4 26.2 - - - -
1756A LEU* 3.7 30.5 - - + -
1757A ASP* 4.0 9.0 + - - +
1776A LYS* 4.1 11.6 + - - -
1800A SER* 3.6 15.7 - - - -
1801A PHE* 6.2 0.7 - + - -
1802A ALA* 3.6 15.9 - - + -
1810A LEU* 2.8 21.3 + - + +
1812A GLY* 1.3 76.8 - - - +
1814A ALA* 1.3 63.6 + - - +
1815A PRO* 3.3 3.6 - - - -
1816A GLY* 3.6 8.0 + - - -
1817A ASN* 3.0 42.7 + - - -
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Residues in contact with ALA1814 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1594A GLY* 3.6 26.7 - - - +
1598A VAL* 4.4 5.2 - - + -
1802A ALA* 3.3 33.3 - - - +
1803A SER* 3.8 2.3 - - - -
1810A LEU 2.9 13.4 + - - +
1811A GLY 4.3 2.5 - - - +
1813A TYR* 1.3 78.4 - - - +
1815A PRO* 1.3 67.7 - - + +
1817A ASN* 3.2 5.4 + - - +
1818A ALA* 3.0 23.1 + - - +
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Residues in contact with PRO1815 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1544A LEU* 4.3 5.6 - - + +
1549A LEU* 5.0 2.5 - - + -
1591A ALA* 4.0 30.7 - - + +
1595A VAL* 4.2 14.1 - - + -
1769A ILE* 3.6 37.2 - - + -
1811A GLY 3.0 23.3 - - - +
1812A GLY 3.5 5.6 - - - +
1813A TYR 3.3 4.7 - - - -
1814A ALA* 1.3 90.5 - - + +
1816A GLY* 1.3 62.5 + - - +
1818A ALA* 3.2 4.0 + - + +
1819A TYR* 3.2 21.3 + - - +
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Residues in contact with GLY1816 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1544A LEU* 4.1 4.7 - - - +
1773A SER* 4.4 8.9 - - - -
1776A LYS* 3.5 14.6 - - - +
1777A VAL* 3.7 24.4 - - - +
1812A GLY 5.1 0.8 + - - -
1813A TYR 3.6 6.2 + - - -
1814A ALA 3.4 0.6 - - - -
1815A PRO* 1.3 79.7 - - - +
1817A ASN* 1.3 62.2 + - - +
1819A TYR* 3.4 5.0 + - - +
1820A LEU* 3.3 24.1 + - - +
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Residues in contact with ASN1817 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A NDP 4.2 0.2 + - - -
1776A LYS* 3.0 27.3 + - - +
1799A SER* 3.2 34.9 + - - +
1800A SER* 3.6 12.2 - - - +
1802A ALA* 4.4 1.0 - - - +
1803A SER* 3.2 20.6 - - - +
1813A TYR* 3.0 54.4 + - - -
1814A ALA 3.2 6.5 + - - +
1816A GLY* 1.3 77.3 - - - +
1818A ALA* 1.3 61.3 + - - +
1820A LEU* 3.2 12.5 + - - +
1821A ASP* 3.2 7.6 + - - -
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Residues in contact with ALA1818 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1587A ALA 4.3 3.3 - - - +
1590A GLY* 3.3 34.5 - - - +
1591A ALA* 3.9 2.7 - - - +
1594A GLY* 4.4 6.5 - - - +
1597A ARG* 5.2 3.4 - - - +
1803A SER* 3.7 7.8 - - - -
1814A ALA 3.0 12.7 + - - +
1815A PRO 3.2 6.7 + - - +
1817A ASN* 1.3 73.0 - - - +
1819A TYR* 1.3 67.7 + - - +
1821A ASP* 3.1 23.7 + - - +
1822A GLY* 3.1 10.4 + - - -
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Residues in contact with TYR1819 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1543A PRO* 3.9 27.8 - - + +
1544A LEU* 4.6 8.1 - - + -
1586A ASN* 5.6 1.1 - - - -
1587A ALA* 3.6 41.8 + - + +
1588A ALA* 3.9 8.3 - - - -
1591A ALA* 4.9 1.0 - - + +
1777A VAL* 3.7 37.0 - - + -
1780A ALA* 4.5 1.8 - - + -
1781A ARG* 3.2 30.1 - - - +
1815A PRO 3.2 9.7 + - - +
1816A GLY 3.5 8.5 - - - +
1817A ASN 3.3 0.2 - - - -
1818A ALA* 1.3 78.7 - - - +
1820A LEU* 1.3 74.6 + - + +
1822A GLY* 3.1 2.9 + - - -
1823A LEU* 2.9 49.7 + - + +
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Residues in contact with LEU1820 (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* 4.8 3.6 - - + +
1776A LYS* 3.5 31.9 - - + +
1780A ALA* 3.7 29.6 - - + -
1797A LEU* 3.6 30.2 - - + +
1798A PHE 3.2 35.2 - - - +
1799A SER* 4.1 9.0 - - - +
1816A GLY 3.3 13.5 - - - +
1817A ASN* 3.4 6.3 - - - +
1818A ALA 3.2 0.4 - - - -
1819A TYR* 1.3 86.0 - - + +
1821A ASP* 1.3 63.5 + - - +
1823A LEU* 3.2 1.2 + - - -
1824A ALA* 3.0 22.9 + - - +
1836A ALA* 4.0 2.5 - - + -
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Residues in contact with ASP1821 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1597A ARG* 5.8 0.9 + - - -
1799A SER* 3.0 24.4 + - - -
1803A SER* 3.5 18.4 + - - +
1804A ALA* 5.8 0.2 - - - -
1817A ASN 3.3 11.4 - - - +
1818A ALA* 3.1 14.2 + - - +
1820A LEU* 1.3 76.8 - - - +
1822A GLY* 1.3 62.9 + - - +
1824A ALA* 3.4 3.8 + - - +
1825A GLN* 3.0 32.0 + - - +
1836A ALA* 3.5 16.2 - - - +
1838A ALA* 5.4 3.1 - - - +
1883A CYS* 3.7 13.8 - - - +
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Residues in contact with GLY1822 (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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1584A VAL* 4.4 10.3 - - - +
1587A ALA* 3.8 18.6 - - - -
1590A GLY* 6.5 0.2 - - - -
1818A ALA 3.1 8.9 + - - -
1819A TYR 3.1 3.3 + - - -
1821A ASP* 1.3 76.4 - - - +
1823A LEU* 1.3 65.1 + - - +
1825A GLN* 3.1 14.7 + - - +
1826A GLN* 2.9 25.5 + - - +
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Residues in contact with LEU1823 (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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1587A ALA* 3.6 2.9 - - - +
1780A ALA* 3.8 39.5 - - + +
1781A ARG* 4.2 1.3 - - + +
1784A HIS* 3.8 37.5 - - + +
1795A PHE* 4.9 1.3 - - + -
1797A LEU* 4.0 11.7 - - + -
1819A TYR* 2.9 46.3 + - + +
1820A LEU 3.7 4.0 - - - +
1822A GLY* 1.3 69.6 - - - +
1824A ALA* 1.3 65.0 + - - +
1826A GLN* 3.1 20.6 + - + +
1827A ARG* 2.9 27.0 + - + +
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Residues in contact with ALA1824 (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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1797A LEU* 4.4 6.9 - - + +
1820A LEU 3.0 12.4 + - - +
1821A ASP 3.6 8.7 - - - +
1823A LEU* 1.3 78.8 - - - +
1825A GLN* 1.3 62.2 + - - +
1827A ARG* 3.2 2.2 + - - +
1828A ARG* 3.0 26.2 + - - +
1834A ALA* 3.5 22.6 - - + +
1835A THR 4.2 1.3 - - - +
1836A ALA* 3.8 27.6 - - + +
1882A VAL* 3.9 11.0 - - + -
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Residues in contact with GLN1825 (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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1576A VAL* 6.1 0.8 - - - +
1577A ALA* 3.9 27.8 + - + +
1582A GLU 6.2 0.4 - - - +
1584A VAL* 4.2 18.6 - - + +
1821A ASP* 3.0 29.8 + - - +
1822A GLY* 3.1 12.4 + - - +
1824A ALA* 1.3 75.9 - - - +
1826A GLN* 1.3 63.3 + - - +
1828A ARG* 3.3 5.1 + - - +
1829A SER* 3.0 26.3 + - - -
1882A VAL* 4.0 18.4 - - + +
1883A CYS* 4.0 19.5 - - - -
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Residues in contact with GLN1826 (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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1583A ARG* 3.6 22.6 + - - +
1584A VAL* 2.9 33.6 + - + +
1585A ARG 3.1 20.6 + - - -
1586A ASN* 4.3 0.2 - - - +
1587A ALA* 3.9 23.0 + - - +
1784A HIS* 6.0 2.5 - - + -
1822A GLY 2.9 16.5 + - - +
1823A LEU* 3.1 20.2 + - + +
1825A GLN* 1.3 72.8 - - - +
1827A ARG* 1.3 67.2 + - - +
1829A SER* 3.3 9.4 + - - -
1830A ASP* 3.2 26.9 + - - +
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Residues in contact with ARG1827 (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* 3.1 61.9 + - + +
1787A THR* 4.2 7.1 + - - -
1788A ARG* 4.5 3.4 - - - +
1792A LEU* 4.6 7.7 - - - +
1795A PHE* 3.3 42.7 - - - +
1823A LEU* 2.9 18.8 + - + +
1824A ALA* 3.2 8.0 + - - +
1826A GLN* 1.3 77.3 - - - +
1828A ARG* 1.3 64.2 + - - +
1830A ASP* 2.9 16.0 + - - -
1832A LEU* 2.9 46.8 + - + +
1833A PRO* 2.8 41.4 + - - +
1834A ALA* 3.7 8.7 - - + -
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Residues in contact with ARG1828 (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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1824A ALA 3.0 14.0 + - - +
1825A GLN* 3.7 9.0 - - - +
1826A GLN 3.3 0.2 - - - -
1827A ARG* 1.3 76.6 - - - +
1829A SER* 1.3 56.8 + - - +
1831A GLY* 2.9 20.1 + - - -
1832A LEU 3.2 19.5 - - - -
1833A PRO* 4.3 2.2 - - - -
1834A ALA* 3.1 29.6 + - + +
1835A THR* 5.3 0.2 + - - -
1880A ALA* 2.9 42.2 + - - +
1881A GLU 4.0 1.6 + - - -
1882A VAL* 3.6 28.8 - - + +
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Residues in contact with SER1829 (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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1580A PRO 4.5 9.8 + - - -
1582A GLU 4.2 9.4 + - - -
1583A ARG* 3.7 34.5 - - - +
1825A GLN* 3.0 14.8 + - - +
1826A GLN 3.5 9.0 - - - -
1827A ARG 3.2 0.2 - - - -
1828A ARG* 1.3 75.4 - - - +
1830A ASP* 1.3 64.5 + - - +
1831A GLY 3.3 1.4 + - - -
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Residues in contact with ASP1830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1583A ARG* 3.8 25.5 + - - -
1784A HIS* 5.6 1.4 + - - -
1788A ARG* 4.7 12.3 + - - -
1826A GLN 3.2 13.8 + - - +
1827A ARG* 2.9 11.2 + - - +
1829A SER* 1.3 83.0 - - - +
1831A GLY* 1.3 61.2 + - - +
1832A LEU* 3.3 17.7 + - + +
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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
------------------------------------------------------------
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