Contacts of the helix formed by residues 1765 - 1785 (chain A) in PDB entry 5XJY
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 THR1765 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742A ARG* 4.2 12.8 - - - +
744A ASN* 4.3 23.8 - - + +
745A LEU* 5.2 0.9 - - - -
748A ALA* 6.1 2.2 - - + -
1760A PHE* 3.1 22.3 - - - -
1762A ILE* 3.4 19.8 - - + +
1763A PRO 3.2 7.5 - - - +
1764A SER* 1.3 83.0 - - - +
1766A ALA* 1.3 59.7 + - - +
1767A TYR 3.1 2.5 - - - +
1768A VAL* 2.9 29.0 + - + +
1769A VAL* 3.0 15.3 + - - +
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Residues in contact with ALA1766 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1670A ALA* 4.3 2.4 - - - +
1673A VAL* 3.9 18.4 - - + -
1674A VAL* 4.8 1.5 - - + +
1677A ILE* 4.1 8.3 - - + -
1756A ALA 5.5 0.2 - - - +
1760A PHE* 3.3 34.6 - - + -
1764A SER* 4.7 0.6 - - - +
1765A THR* 1.3 73.0 - - - +
1767A TYR* 1.3 59.0 + - - +
1769A VAL* 3.8 3.8 - - - -
1770A LEU* 2.8 57.1 + - + +
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Residues in contact with TYR1767 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745A LEU* 5.9 7.2 - - + -
1347A PHE* 6.3 3.4 - + - -
1349A ALA* 5.7 1.9 - - - +
1350A GLN* 3.3 39.3 + - - -
1353A LEU* 5.7 1.0 - - - +
1667A PHE* 3.3 27.5 - + - -
1670A ALA* 3.7 19.5 - - + +
1674A VAL* 3.8 25.5 - - + +
1764A SER* 4.6 11.2 - - - +
1765A THR 4.3 4.3 - - - -
1766A ALA* 1.3 73.3 - - - +
1768A VAL* 1.3 74.4 + - + +
1771A THR* 2.4 35.2 + - - -
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Residues in contact with VAL1768 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745A LEU* 6.1 4.7 - - + -
748A ALA* 4.3 30.1 - - + -
749A CYS* 5.9 1.1 - - + +
752A ILE* 5.4 13.7 - - + -
1764A SER 5.2 1.6 - - - +
1765A THR* 2.9 21.3 + - + +
1767A TYR* 1.3 92.6 - - + +
1769A VAL* 1.3 61.5 + - + +
1771A THR* 3.2 7.2 + - - -
1772A SER* 2.9 26.6 + - - -
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Residues in contact with VAL1769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1760A PHE* 3.5 37.9 - - + -
1765A THR 3.0 11.6 + - - +
1766A ALA* 3.8 4.0 - - - -
1768A VAL* 1.3 81.1 - - + +
1770A LEU* 1.3 66.8 + - + +
1772A SER* 2.3 31.4 + - - +
1773A VAL* 2.9 15.6 + - + +
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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
----------------------------------------------------------
1666A SER 5.5 1.1 - - - -
1670A ALA* 5.0 5.4 - - + -
1673A VAL* 4.1 15.5 - - + -
1753A MET* 3.7 35.6 - - + +
1756A ALA* 4.5 27.8 - - + +
1760A PHE* 6.1 0.9 - - + -
1766A ALA* 2.8 39.4 + - + +
1769A VAL* 1.3 80.1 - - + +
1771A THR* 1.3 60.2 + - - +
1773A VAL* 3.7 19.3 - - + +
1774A ASN* 3.0 33.6 + - - +
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Residues in contact with THR1771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1663A PHE* 3.6 31.2 - - + -
1666A SER* 4.2 12.5 + - - +
1667A PHE* 3.4 33.3 - - + -
1670A ALA* 4.5 5.3 - - - +
1767A TYR* 2.4 28.0 + - - -
1768A VAL* 3.4 6.3 - - - -
1770A LEU* 1.3 76.8 - - - +
1772A SER* 1.3 56.2 + - - +
1774A ASN* 3.9 0.9 - - - +
1775A LEU* 3.0 31.0 + - + +
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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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1768A VAL* 2.9 14.1 + - - -
1769A VAL* 2.3 36.6 + - - +
1771A THR* 1.3 74.3 - - - +
1773A VAL* 1.3 64.3 + - - +
1775A LEU* 3.0 25.1 + - - +
1776A PHE* 3.0 28.1 + - - -
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Residues in contact with VAL1773 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1769A VAL* 2.9 18.0 + - + +
1770A LEU* 3.7 27.4 - - + +
1772A SER* 1.3 82.4 + - - +
1774A ASN* 1.3 60.4 + - + +
1776A PHE* 3.3 13.9 + - + +
1777A ILE* 3.0 33.9 + - + +
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Residues in contact with ASN1774 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1662A ILE* 5.6 3.1 - - - +
1666A SER* 2.9 48.0 + - - +
1669A PRO* 4.9 4.6 - - - +
1749A ILE* 4.5 10.7 - - - +
1753A MET* 5.3 6.6 - - + +
1770A LEU 3.0 22.2 + - - +
1771A THR 4.0 0.2 - - - +
1773A VAL* 1.3 78.0 - - + +
1775A LEU* 1.3 63.4 + - - +
1777A ILE* 3.2 8.6 + - - +
1778A GLY* 3.0 17.8 + - - -
1814A CYS* 3.2 32.6 - - - +
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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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1659A ILE* 4.9 13.5 - - + +
1662A ILE* 5.3 4.3 - - + +
1663A PHE* 3.5 53.2 - - + +
1666A SER* 4.3 2.8 + - - +
1771A THR* 3.0 19.9 + - + +
1772A SER* 3.0 12.6 + - - +
1774A ASN* 1.3 76.3 - - - +
1776A PHE* 1.3 63.1 + - + +
1778A GLY* 3.0 3.3 + - - +
1779A ILE* 2.9 40.2 + - + +
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Residues in contact with PHE1776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1772A SER* 3.0 25.2 + - - -
1773A VAL* 3.7 16.4 - - + +
1774A ASN 3.3 0.2 - - - -
1775A LEU* 1.3 77.4 - - + +
1777A ILE* 1.3 61.8 + - - +
1779A ILE* 4.4 18.1 - - + +
1780A ASN* 3.0 30.0 + - - +
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Residues in contact with ILE1777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1773A VAL* 3.0 20.6 + - + +
1774A ASN* 3.3 13.2 - - - +
1775A LEU 3.2 0.2 - - - -
1776A PHE* 1.3 77.9 - - - +
1778A GLY* 1.3 55.7 + - - +
1780A ASN* 3.3 13.1 - - - +
1781A GLY* 3.0 21.8 + - - -
1812A HIS* 3.4 40.8 - - + +
1814A CYS* 3.8 25.6 - - + +
1815A LEU* 4.0 11.2 - - - +
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Residues in contact with GLY1778 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1659A ILE* 3.5 20.0 - - - +
1662A ILE* 4.3 18.6 - - - -
1774A ASN 3.0 9.8 + - - -
1775A LEU 3.0 8.6 + - - -
1777A ILE* 1.3 77.9 - - - +
1779A ILE* 1.3 53.8 + - - +
1781A GLY* 2.7 22.6 + - - -
1782A SER 3.0 9.0 + - - -
1814A CYS 5.8 0.9 - - - -
1815A LEU* 5.9 1.6 - - - -
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Residues in contact with ILE1779 (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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1659A ILE* 3.9 20.6 - - + -
1775A LEU* 2.9 23.7 + - + +
1776A PHE* 4.4 20.0 - - + +
1778A GLY* 1.3 71.4 - - - +
1780A ASN* 1.3 59.5 + - - +
1782A SER* 2.4 40.5 + - - +
1783A VAL* 3.0 16.3 + - + +
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Residues in contact with ASN1780 (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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1776A PHE 3.0 21.2 + - - +
1777A ILE* 3.3 19.1 - - - +
1779A ILE* 1.3 76.1 - - - +
1781A GLY* 1.3 55.5 + - - +
1783A VAL* 3.8 5.6 + - - +
1784A ALA* 2.9 29.3 + - - +
1812A HIS* 5.0 3.6 + - - -
1815A LEU* 4.1 9.9 - - + +
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Residues in contact with GLY1781 (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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1777A ILE 3.0 8.2 + - - -
1778A GLY* 2.7 17.5 + - - -
1780A ASN* 1.3 71.0 - - - +
1782A SER* 1.3 54.1 + - - -
1784A ALA* 2.7 19.6 + - - -
1785A THR 3.0 10.7 + - - -
1815A LEU* 3.7 25.7 - - - +
1819A LEU* 3.2 21.1 - - - +
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Residues in contact with SER1782 (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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1655A VAL* 4.8 13.0 - - - +
1659A ILE* 4.9 9.0 - - - -
1778A GLY 3.0 5.5 + - - -
1779A ILE* 2.4 43.7 + - - +
1781A GLY* 1.3 75.3 - - - +
1783A VAL* 1.3 64.5 + - - +
1785A THR* 3.5 1.6 + - - -
1786A PHE* 3.0 53.1 + - - -
1819A LEU* 4.3 4.7 - - - +
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Residues in contact with VAL1783 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1779A ILE* 3.0 18.4 + - + +
1780A ASN* 4.4 5.8 - - - +
1782A SER* 1.3 87.0 + - - +
1784A ALA* 1.3 61.3 + - - +
1786A PHE* 3.2 27.7 + - + +
1787A VAL* 5.5 0.5 - - - +
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Residues in contact with ALA1784 (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 ASN* 2.9 23.7 + - - +
1781A GLY* 2.7 15.7 + - - +
1783A VAL* 1.3 72.2 - - - +
1785A THR* 1.3 65.5 + - - +
1787A VAL* 5.5 1.1 - - - +
1802A ILE* 5.3 6.4 - - - +
1805A SER* 4.3 18.2 - - - -
1815A LEU* 4.2 10.3 - - + -
1819A LEU* 3.8 11.6 - - + +
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Residues in contact with THR1785 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1655A VAL* 5.8 4.2 - - - +
1781A GLY 3.0 5.3 + - - -
1782A SER 3.6 3.4 + - - -
1784A ALA* 1.3 82.0 - - - +
1786A PHE* 1.3 62.4 + - - +
1787A VAL* 3.2 14.0 + - - +
1788A LEU* 6.0 0.3 - - - +
1802A ILE* 5.6 7.2 - - + +
1805A SER* 5.5 5.8 - - - -
1819A LEU* 3.2 40.9 + - + +
1822A MET* 5.5 4.2 - - - +
1823A VAL* 6.2 2.9 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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