Contacts of the helix formed by residues 1764 - 1781 (chain A) in PDB entry 5A31
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 LYS1764 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1761A MET* 4.2 14.7 - - + +
1762A GLY 2.7 11.9 + - - +
1763A GLN* 1.3 71.4 - - - +
1765A GLN* 1.3 61.6 + - - +
1766A GLU 3.3 1.7 + - - -
1767A ILE* 3.7 15.0 + - + +
1768A LEU* 3.7 16.1 + - - +
635O GLY 4.8 13.7 - - - +
636O ILE* 5.3 2.7 - - - +
637O PRO* 5.2 2.7 - - + -
638O GLU* 3.9 22.4 - - - +
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Residues in contact with GLN1765 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1757A PRO* 4.5 13.5 - - - +
1760A ASN 5.2 1.3 - - - +
1761A MET* 4.0 10.1 - - + +
1762A GLY* 3.7 28.3 - - - +
1763A GLN 3.1 2.3 - - - +
1764A LYS* 1.3 75.4 - - - +
1766A GLU* 1.3 71.2 + - - +
1768A LEU* 3.1 23.8 + - - +
1769A ASP* 3.0 46.4 + - - +
167N ARG* 3.9 24.2 - - - +
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Residues in contact with GLU1766 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1763A GLN* 3.7 22.4 + - - +
1764A LYS 3.3 0.8 - - - -
1765A GLN* 1.3 82.1 - - - +
1767A ILE* 1.3 63.7 + - + +
1769A ASP* 3.4 16.0 + - - +
1770A LEU* 3.3 18.0 + - - +
1798A ARG* 4.0 11.6 + - - +
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Residues in contact with ILE1767 (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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1763A GLN 4.8 2.0 + - - +
1764A LYS* 3.7 16.0 + - - +
1765A GLN 3.2 0.2 - - - -
1766A GLU* 1.3 81.1 - - + +
1768A LEU* 1.3 63.1 + - + +
1770A LEU* 3.3 15.0 + - + +
1771A PHE* 3.2 37.1 + - + -
1798A ARG* 3.2 45.8 - - + +
634O LEU 4.2 14.6 - - - +
635O GLY* 4.4 19.3 - - - +
636O ILE* 4.5 6.7 - - + -
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Residues in contact with LEU1768 (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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1754A PHE 3.4 18.4 - - - +
1755A CYS* 3.0 31.4 - - - +
1756A LYS 4.1 3.8 - - - +
1757A PRO* 3.9 24.7 - - + -
1761A MET* 4.1 16.6 - - + -
1764A LYS 3.7 6.6 + - - +
1765A GLN* 3.1 25.4 + - - +
1767A ILE* 1.3 77.0 - - - +
1769A ASP* 1.3 66.5 + - - +
1771A PHE* 3.5 12.7 - - - +
1772A SER* 3.3 18.7 + - - +
636O ILE* 4.1 21.5 - - + -
639O GLN* 4.7 1.3 - - - +
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Residues in contact with ASP1769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1731A ARG* 5.6 11.9 - - - +
1765A GLN* 3.0 51.1 + - - +
1766A GLU* 3.4 20.7 - - - +
1768A LEU* 1.3 76.6 - - - +
1770A LEU* 1.3 62.6 + - - +
1772A SER* 2.5 25.5 + - - -
1773A SER* 3.2 13.2 + - - +
167N ARG* 5.4 1.6 + - - -
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Residues in contact with LEU1770 (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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1766A GLU 3.3 8.8 + - - +
1767A ILE* 3.3 14.1 + - + +
1769A ASP* 1.3 79.6 - - - +
1771A PHE* 1.3 83.7 + - + +
1773A SER* 3.4 8.0 + - - -
1774A VAL* 2.9 35.0 + - + +
1791A ILE* 5.0 1.6 - - + -
1794A ASP* 3.0 42.6 - - + +
1797A ILE* 5.1 7.2 - - + -
1798A ARG* 3.6 27.8 - - - +
1844A PHE* 5.4 5.2 - - + -
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Residues in contact with PHE1771 (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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1750A PHE* 3.6 25.1 - + - -
1754A PHE* 4.5 11.7 - + + +
1755A CYS* 4.1 12.3 - - - -
1767A ILE* 3.2 40.5 + - + -
1768A LEU* 3.5 13.5 - - - +
1770A LEU* 1.3 88.8 - - + +
1772A SER* 1.3 59.9 + - - +
1774A VAL* 3.4 5.9 + - - +
1775A LEU* 2.9 30.0 + - - +
1791A ILE* 3.4 37.7 - - + -
1794A ASP* 6.4 0.2 - - + -
1795A GLN* 4.4 4.3 - - - -
634O LEU* 3.9 37.2 - - + -
636O ILE* 4.2 14.1 - - + -
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Residues in contact with SER1772 (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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1733A PHE* 4.6 11.8 - - - -
1734A LYS 3.7 24.7 - - - -
1755A CYS* 3.9 20.2 - - - -
1768A LEU* 3.3 7.8 + - - +
1769A ASP* 2.5 28.5 + - - -
1771A PHE* 1.3 77.5 - - - +
1773A SER* 1.3 56.7 + - - +
1775A LEU* 3.3 8.9 + - - +
1776A TYR* 3.1 26.3 + - - +
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Residues in contact with SER1773 (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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1731A ARG* 3.0 56.6 + - - +
1733A PHE* 5.6 0.2 - - - +
1769A ASP 3.2 12.4 + - - -
1770A LEU* 3.5 11.8 - - - -
1772A SER* 1.3 77.0 + - - +
1774A VAL* 1.3 66.0 + - - +
1776A TYR* 3.3 8.9 + - - +
1777A GLU* 3.2 27.7 + - - +
163N PHE* 5.7 3.1 - - - -
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Residues in contact with VAL1774 (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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1770A LEU* 2.9 24.5 + - + +
1771A PHE* 3.5 6.1 - - - +
1773A SER* 1.3 70.8 - - - +
1775A LEU* 1.3 68.8 + - - +
1777A GLU* 3.1 20.6 + - + +
1778A CYS* 3.3 11.4 + - - -
1787A LEU* 4.7 9.9 - - + -
1790A TYR* 3.8 23.0 - - + -
1791A ILE* 3.7 24.2 - - + -
1794A ASP* 3.5 22.4 - - - +
1844A PHE* 4.3 23.8 - - + -
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Residues in contact with LEU1775 (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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1733A PHE* 3.7 29.4 - - + -
1739A SER* 4.9 3.4 - - - +
1747A LEU* 3.8 21.9 - - + +
1750A PHE* 3.5 33.7 - - + -
1751A ALA* 4.2 15.5 - - + +
1755A CYS* 4.6 2.5 - - + -
1771A PHE 2.9 15.0 + - - +
1772A SER* 3.4 13.0 - - - +
1774A VAL* 1.3 76.6 - - - +
1776A TYR* 1.3 62.5 + - - +
1778A CYS* 3.1 5.6 + - - +
1779A VAL* 2.8 42.0 + - + +
1787A LEU* 4.1 16.6 - - + -
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Residues in contact with TYR1776 (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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1729A GLU* 4.5 12.2 + - + -
1730A ALA 3.5 26.0 + - - -
1731A ARG* 5.2 6.3 - - - +
1732A ALA 5.4 2.0 - - - -
1733A PHE* 3.2 50.5 - + + -
1741A PHE* 4.0 21.7 - + - -
1772A SER 3.1 9.8 + - - +
1773A SER* 3.4 12.6 - - - +
1774A VAL 3.1 0.4 - - - -
1775A LEU* 1.3 86.2 - - - +
1777A GLU* 1.3 62.7 + - + +
1779A VAL* 3.7 4.5 - - + +
1780A THR* 2.8 46.2 + - + +
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Residues in contact with GLU1777 (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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1731A ARG* 5.7 4.3 - - + +
1773A SER* 3.2 16.8 + - - +
1774A VAL* 3.1 10.8 + - - +
1776A TYR* 1.3 81.6 - - + +
1778A CYS* 1.3 57.3 + - - +
1780A THR* 3.2 11.4 - - - +
1781A GLN* 3.2 32.8 + - + +
1783A THR* 4.6 1.2 - - - +
1790A TYR* 4.1 18.5 + - + +
1842A SER* 3.0 33.6 + - - -
1843A GLU 5.0 0.5 - - - -
1844A PHE* 3.4 32.4 + - - +
163N PHE* 5.5 5.9 - - - -
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Residues in contact with CYS1778 (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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1703A ALA* 5.7 0.3 - - - +
1747A LEU* 4.8 4.7 - - + -
1774A VAL* 3.3 6.6 + - - +
1775A LEU 3.1 9.3 + - - +
1777A GLU* 1.3 77.0 - - - +
1779A VAL* 1.3 57.6 + - - +
1781A GLN 2.6 24.7 - - - +
1783A THR* 3.4 26.9 + - - +
1784A PRO* 4.1 8.9 - - + +
1786A MET* 3.8 0.7 - - - -
1787A LEU* 3.4 49.1 - - + -
1790A TYR* 3.7 24.9 - - - -
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Residues in contact with VAL1779 (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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1703A ALA* 4.1 0.6 - - - -
1704A GLY* 3.0 29.3 + - - +
1733A PHE* 5.5 3.8 - - + -
1739A SER* 5.5 3.8 - - - +
1741A PHE* 4.0 26.9 - - + -
1742A THR* 3.5 25.8 - - - +
1747A LEU* 3.5 30.3 - - + -
1775A LEU* 2.8 41.5 + - + +
1776A TYR* 3.2 7.2 + - + +
1778A CYS* 1.3 73.1 - - - +
1780A THR* 1.3 62.9 + - - +
1781A GLN 3.4 4.5 - - - +
1784A PRO* 6.0 0.2 - - - -
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Residues in contact with THR1780 (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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1703A ALA 4.6 1.7 - - - +
1704A GLY* 4.8 6.6 - - - +
1729A GLU* 4.1 17.2 + - - +
1741A PHE* 6.2 3.8 - - - -
1776A TYR* 2.8 34.5 + - + +
1777A GLU* 3.2 19.5 - - - +
1779A VAL* 1.3 79.6 - - - +
1781A GLN* 1.3 86.8 + - - +
1782A GLU* 4.5 8.3 - - - +
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Residues in contact with GLN1781 (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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960A TYR* 4.7 13.2 + - + +
1703A ALA 4.4 1.6 - - - +
1729A GLU* 3.9 20.8 + - - +
1777A GLU* 3.2 14.9 + - + +
1778A CYS 2.6 24.6 - - - +
1779A VAL 3.4 4.2 - - - +
1780A THR* 1.3 102.2 + - - +
1782A GLU* 1.3 62.5 + - - +
1783A THR* 2.8 24.8 + - + -
1784A PRO* 4.4 0.7 - - - +
1790A TYR* 5.9 2.0 - - - +
1839A PHE 5.3 9.4 - - - +
1840A MET* 6.4 1.1 - - - -
1842A SER* 5.1 10.6 - - - +
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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