Contacts of the helix formed by residues 1782 - 1793 (chain B) in PDB entry 2H02
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1729B GLY 4.4 1.8 - - - +
1730B LYS* 3.6 44.9 - - + +
1758B ILE* 5.2 6.2 - - - +
1776B GLN* 4.1 7.0 + - - -
1778B PRO* 3.8 6.3 - - - +
1779B LEU* 2.9 34.6 + - + +
1781B GLY* 1.3 82.0 - - - +
1783B LYS* 1.3 66.4 + - - +
1784B ASP 3.2 2.9 - - - -
1785B ASP* 3.1 18.7 - - - +
1786B PHE* 3.0 21.1 + - - +
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Residues in contact with LYS1783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1778B PRO* 4.2 7.9 - - + -
1779B LEU 3.1 8.4 + - - +
1780B PRO* 3.5 21.3 - - - +
1781B GLY 3.7 0.2 - - - -
1782B THR* 1.3 78.5 - - - +
1784B ASP* 1.3 70.5 + - - +
1786B PHE* 3.3 3.2 + - - +
1787B TRP* 3.0 35.7 + - - -
1813B ASP* 3.4 24.2 + - - +
1814B HIS 4.0 11.5 + - - -
1815B TYR* 3.9 22.4 - - + +
1823B LEU* 6.3 0.6 - - - +
1825B TYR* 3.9 27.0 + - + -
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Residues in contact with ASP1784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1781B GLY 5.4 1.3 + - - +
1782B THR 3.2 0.6 - - - -
1783B LYS* 1.3 83.2 - - - +
1785B ASP* 1.3 60.9 + - - +
1787B TRP* 3.3 2.1 + - - +
1788B LYS* 2.9 31.3 + - - +
1824B TYR 4.8 0.3 - - - +
1825B TYR* 3.3 35.5 - - - +
1826B GLY* 3.5 27.8 + - - +
1828B LEU* 5.5 0.2 - - - +
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Residues in contact with ASP1785 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1730B LYS* 4.7 11.6 + - - +
1746B LEU* 3.5 34.6 - - + +
1757B TYR 4.3 8.4 - - - +
1758B ILE* 4.0 11.0 - - + -
1781B GLY 4.6 3.4 - - - +
1782B THR* 3.1 28.5 - - - +
1784B ASP* 1.3 77.3 - - - +
1786B PHE* 1.3 59.6 + - - +
1788B LYS* 3.4 11.4 - - - +
1789B MET* 2.9 25.6 + - - +
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Residues in contact with PHE1786 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1758B ILE* 3.8 14.1 - - + +
1775B THR* 4.0 28.0 - - + -
1778B PRO* 3.5 26.2 - - + -
1782B THR* 3.0 13.1 + - - +
1783B LYS 3.5 7.4 - - - +
1784B ASP 3.3 0.2 - - - -
1785B ASP* 1.3 77.8 - - - +
1787B TRP* 1.3 81.1 + + - +
1789B MET* 3.3 10.4 + - + +
1790B VAL* 3.0 46.7 + - + +
1798B ILE* 3.9 14.6 - - + -
1815B TYR* 3.4 40.4 - + - -
1901B VAL* 4.1 11.4 - - + -
1903B HIS* 4.3 4.5 - + - -
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Residues in contact with TRP1787 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1783B LYS* 3.0 27.0 + - + +
1784B ASP 4.0 3.1 - - - +
1786B PHE* 1.3 85.7 - + - +
1788B LYS* 1.3 52.6 + - - +
1790B VAL* 3.1 19.9 + - + +
1791B TRP* 2.8 30.0 + - - +
1798B ILE* 3.7 30.3 - - + -
1815B TYR* 2.9 47.5 + + - -
1816B TRP* 4.2 9.4 - - + -
1825B TYR* 3.4 34.4 - + + -
1828B LEU* 3.5 21.6 - - + +
1830B LEU* 3.5 39.5 - - + -
1846B PHE* 4.2 14.1 - + - -
1848B ILE* 4.6 3.4 - - + +
1860B ILE* 4.9 7.9 - - + -
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Residues in contact with LYS1788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1746B LEU* 4.0 21.9 - - + +
1747B SER* 3.0 27.1 + - - +
1748B ASN 5.0 2.2 - - - -
1755B SER* 4.6 5.5 + - - -
1784B ASP 2.9 18.1 + - - +
1785B ASP* 3.4 11.4 - - - +
1787B TRP* 1.3 72.9 - - - +
1789B MET* 1.3 59.0 + - - +
1791B TRP* 3.1 4.0 + - + +
1792B GLU* 2.9 61.3 + - + +
1828B LEU* 3.9 12.2 - - + +
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Residues in contact with MET1789 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1744B VAL* 3.6 24.7 - - + -
1746B LEU* 3.6 15.3 - - + +
1758B ILE* 3.9 19.5 - - + -
1760B ALA* 3.7 19.7 - - + -
1773B ILE* 3.8 24.0 - - + -
1775B THR* 4.3 7.6 - - + -
1785B ASP 2.9 16.3 + - - +
1786B PHE* 3.5 25.8 - - + +
1788B LYS* 1.3 69.8 - - - +
1790B VAL* 1.3 67.2 + - + +
1792B GLU* 4.6 5.2 - - - -
1793B GLN* 3.0 44.6 + - + +
1795B VAL* 5.8 0.2 - - + -
1901B VAL* 4.5 11.2 - - + -
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Residues in contact with VAL1790 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1786B PHE* 3.0 46.3 + - + +
1787B TRP* 3.1 25.5 + - + +
1789B MET* 1.3 78.4 - - + +
1791B TRP* 1.3 61.8 + - - +
1794B ASN 3.3 1.0 + - - -
1795B VAL* 3.2 28.9 + - + -
1798B ILE* 4.2 9.0 - - + -
1848B ILE* 5.5 3.8 - - + -
1858B ARG* 3.0 18.1 + - - +
1860B ILE* 4.0 27.4 - - + -
1901B VAL* 4.4 16.4 - - + -
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Residues in contact with TRP1791 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1787B TRP 2.8 14.9 + - - +
1788B LYS* 3.5 5.6 - - + +
1789B MET 3.0 0.2 - - - -
1790B VAL* 1.3 75.9 - - - +
1792B GLU* 1.3 74.5 + - + +
1793B GLN 3.3 0.9 + - - -
1794B ASN* 3.3 5.0 + - - +
1828B LEU* 3.7 21.7 - - + +
1848B ILE* 3.5 46.2 - - + -
1850B GLY* 3.4 33.7 - - - -
1851B GLU* 4.2 15.4 - - - +
1852B GLU* 3.9 19.2 + - - +
1856B ALA 3.6 22.4 - - - -
1858B ARG* 2.8 56.8 + - + +
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Residues in contact with GLU1792 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1745B LYS 4.4 2.8 - - - +
1746B LEU* 3.6 12.3 - - - +
1747B SER* 2.9 48.8 + - - -
1788B LYS* 2.9 41.6 + - + +
1789B MET* 4.1 3.4 - - - +
1791B TRP* 1.3 80.8 - - + +
1793B GLN* 1.3 67.9 + - + +
1794B ASN* 3.3 15.3 + - - -
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Residues in contact with GLN1793 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1744B VAL* 4.2 2.8 - - - +
1745B LYS 4.2 14.8 + - - -
1762B TYR* 2.9 40.5 + - - -
1770B ARG* 4.6 3.0 + - - +
1773B ILE* 3.7 25.9 - - + +
1789B MET* 3.0 31.1 + - + +
1792B GLU* 1.3 85.5 + - + +
1794B ASN* 1.3 76.9 + - - +
1795B VAL* 3.3 7.1 + - + -
1898B GLY* 3.4 14.0 - - - -
1899B PRO* 3.5 8.3 - - + +
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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