Contacts of the helix formed by residues 1782 - 1793 (chain A) in PDB entry 2H04
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 THR1782 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1729A GLY 4.5 1.8 - - - +
1730A LYS* 4.0 35.9 - - + +
1758A ILE* 5.1 5.6 - - - +
1776A GLN* 4.4 5.5 + - - +
1778A PRO* 3.9 5.8 - - - +
1779A LEU* 2.9 38.0 + - + +
1781A GLY* 1.3 83.0 - - - +
1783A LYS* 1.3 63.3 + - - +
1784A ASP 3.3 3.1 - - - +
1785A ASP* 3.2 24.8 + - - +
1786A PHE* 3.0 20.8 + - - +
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Residues in contact with LYS1783 (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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1778A PRO* 4.2 4.0 - - + -
1779A LEU 3.1 9.7 + - - +
1780A PRO* 3.9 18.8 + - - +
1781A GLY 3.8 1.2 - - - -
1782A THR* 1.3 77.2 - - - +
1784A ASP* 1.3 72.2 + - - +
1786A PHE* 3.1 15.6 + - + +
1787A TRP* 3.1 21.7 + - + -
1813A ASP* 3.3 24.3 + - - +
1814A HIS 4.6 7.3 + - - -
1815A TYR* 3.8 29.2 - - + +
1823A LEU* 6.2 1.4 - - - +
1825A TYR* 4.2 21.6 + - + -
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Residues in contact with ASP1784 (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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1781A GLY 5.5 0.4 - - - -
1782A THR 3.3 0.8 - - - -
1783A LYS* 1.3 82.5 - - - +
1785A ASP* 1.3 60.2 + - - +
1787A TRP* 3.5 2.1 + - - +
1788A LYS* 2.8 29.3 + - - +
1824A TYR 4.7 0.7 - - - +
1825A TYR* 3.4 32.8 - - - +
1826A GLY* 3.3 29.7 + - - +
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Residues in contact with ASP1785 (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 LYS* 5.0 8.7 - - - +
1746A LEU* 3.7 29.6 - - + +
1757A TYR 4.5 7.0 - - - +
1758A ILE* 3.8 14.0 - - + +
1781A GLY 4.5 3.2 - - - +
1782A THR* 3.2 31.9 + - - +
1784A ASP* 1.3 79.5 - - - +
1786A PHE* 1.3 57.9 + - - +
1788A LYS* 3.2 11.4 + - - +
1789A MET* 3.0 28.9 + - - +
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Residues in contact with PHE1786 (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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1758A ILE* 3.9 11.4 - - + -
1775A THR* 3.9 25.1 - - + -
1778A PRO* 3.6 26.5 - - + -
1782A THR* 3.0 13.1 + - - +
1783A LYS* 3.1 7.4 + - - +
1785A ASP* 1.3 77.4 - - - +
1787A TRP* 1.3 77.0 + + - +
1789A MET* 3.2 18.1 + - + +
1790A VAL* 3.1 49.4 + - + +
1798A ILE* 4.0 18.2 - - + -
1815A TYR* 3.4 38.6 - + - -
1901A VAL* 4.0 10.5 - - + -
1903A HIS* 4.5 4.0 - + - -
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Residues in contact with TRP1787 (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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1783A LYS* 3.1 23.1 + - + +
1784A ASP 4.0 3.1 - - - +
1786A PHE* 1.3 81.2 - + - +
1788A LYS* 1.3 64.7 + - - +
1790A VAL* 3.6 20.2 - - + +
1791A TRP 3.0 17.8 + - - -
1798A ILE* 3.6 31.2 - - + -
1815A TYR* 2.9 48.3 + + - +
1816A TRP* 4.0 6.3 - - + -
1825A TYR* 3.4 35.0 - + + -
1828A LEU* 3.2 22.3 - - + +
1830A LEU* 3.5 32.8 - - + -
1846A PHE* 4.2 15.3 - + - -
1848A ILE* 4.1 13.6 - - + +
1860A ILE* 4.3 7.6 - - + -
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Residues in contact with LYS1788 (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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1746A LEU* 3.9 25.6 - - + +
1747A SER* 3.1 22.5 + - - -
1748A ASN* 4.6 6.7 + - - -
1755A SER 5.2 1.4 + - - -
1784A ASP 2.8 22.4 + - - +
1785A ASP* 3.2 10.5 + - - +
1787A TRP* 1.3 72.9 - - - +
1789A MET* 1.3 58.4 + - - +
1791A TRP* 3.4 2.6 + - + +
1792A GLU* 3.0 63.5 + - + +
1827A ASP* 5.9 4.0 - - - +
1828A LEU* 4.0 10.7 - - + +
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Residues in contact with MET1789 (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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1744A VAL* 3.8 17.5 - - + -
1745A LYS 6.0 0.2 - - - +
1746A LEU* 4.2 12.8 - - + +
1758A ILE* 4.0 21.5 - - + -
1760A ALA* 3.7 26.0 - - + -
1773A ILE* 3.9 23.6 - - + -
1775A THR* 4.4 7.2 - - + -
1785A ASP 3.0 12.2 + - - +
1786A PHE* 3.4 28.7 - - + +
1788A LYS* 1.3 76.6 - - - +
1790A VAL* 1.3 57.6 + - + +
1792A GLU* 4.6 5.4 - - - -
1793A GLN* 2.9 52.8 + - + +
1795A VAL* 5.2 0.2 - - - -
1901A VAL* 4.7 6.5 - - + -
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Residues in contact with VAL1790 (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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1786A PHE* 3.1 46.1 + - + +
1787A TRP* 3.6 19.5 - - + +
1788A LYS 3.2 0.2 - - - -
1789A MET* 1.3 78.0 - - + +
1791A TRP* 1.3 60.1 + - - +
1794A ASN 3.4 1.7 + - - -
1795A VAL* 3.0 44.8 + - + +
1798A ILE* 4.2 8.7 - - + -
1848A ILE* 5.0 1.1 - - + -
1858A ARG* 2.9 15.7 + - - +
1860A ILE* 3.8 29.6 - - + -
1901A VAL* 4.4 7.4 - - + -
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Residues in contact with TRP1791 (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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1787A TRP 3.0 16.7 + - - +
1788A LYS* 3.6 4.7 - - + +
1790A VAL* 1.3 77.8 - - - +
1792A GLU* 1.3 72.2 + - + +
1794A ASN* 3.2 4.0 + - - +
1828A LEU* 3.6 26.7 - - + +
1848A ILE* 3.6 49.1 - - + +
1849A CYS* 4.3 0.9 - - - -
1850A GLY* 3.8 24.0 - - - -
1857A HIS 5.0 7.0 - - - -
1858A ARG* 2.8 59.3 + - + +
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Residues in contact with GLU1792 (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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1745A LYS 4.3 3.1 - - - +
1746A LEU* 3.8 7.3 - - - -
1747A SER* 2.9 49.5 + - - -
1788A LYS* 3.0 48.6 + - + +
1789A MET* 4.0 5.2 - - - +
1791A TRP* 1.3 85.0 - - + +
1793A GLN* 1.3 70.1 + - - +
1794A ASN* 3.2 2.4 + - - +
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Residues in contact with GLN1793 (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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1744A VAL* 4.1 10.3 - - + +
1745A LYS 4.2 11.9 + - - -
1762A TYR* 3.0 35.7 + - - -
1770A ARG* 4.9 2.1 + - - -
1773A ILE* 3.6 27.1 - - + +
1789A MET* 2.9 30.2 + - + +
1792A GLU* 1.3 86.3 + - - +
1794A ASN* 1.3 70.1 + - - +
1795A VAL* 3.3 5.2 - - + -
1898A GLY* 3.6 0.7 - - - -
1899A PRO* 3.4 23.0 - - + +
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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
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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