Contacts of the helix formed by residues 1764 - 1783 (chain A) in PDB entry 3RYT
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 ASN1764 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1463A TYR* 5.7 0.2 - - - -
1467A LYS* 4.3 18.2 - - - +
1471A GLU* 5.0 4.2 - - - +
1475A ILE* 6.2 0.9 - - - -
1762A HIS* 3.2 12.5 + - - +
1763A LYS* 1.3 88.1 - - - +
1765A SER* 1.3 67.5 + - - +
1766A ILE* 3.3 14.2 - - - +
1767A THR* 2.8 47.6 + - - +
1768A ASP* 3.6 5.2 + - - +
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Residues in contact with SER1765 (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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1475A ILE* 6.2 1.8 - - - -
1480A GLY* 3.5 27.5 + - - -
1490A LYS* 4.2 15.2 + - - -
1764A ASN* 1.3 82.4 - - - +
1766A ILE* 1.3 64.9 + - - +
1768A ASP* 3.2 15.0 + - - +
1769A ALA* 3.6 6.1 + - - +
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Residues in contact with ILE1766 (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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1470A MET* 3.4 31.9 - - + -
1475A ILE* 3.7 30.7 - - + -
1480A GLY 3.6 14.8 - - - +
1482A ALA* 3.5 18.4 - - + -
1485A SER* 3.4 27.6 - - - +
1490A LYS* 4.0 16.6 - - + +
1764A ASN* 3.3 12.3 - - - +
1765A SER* 1.3 79.4 + - - +
1767A THR* 1.3 65.6 + - - +
1769A ALA* 2.9 15.9 + - + -
1770A CYS* 3.2 13.5 - - - -
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Residues in contact with THR1767 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1463A TYR* 4.2 28.0 - - + -
1466A ILE* 4.0 25.3 - - + +
1467A LYS* 4.0 17.8 + - - +
1470A MET* 4.9 0.5 - - - +
1763A LYS* 4.3 10.3 - - + -
1764A ASN* 2.8 35.7 + - - +
1766A ILE* 1.3 78.9 - - - +
1768A ASP* 1.3 61.3 + - - +
1770A CYS* 3.2 12.1 + - - +
1771A LEU* 3.3 21.2 + - + +
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Residues in contact with ASP1768 (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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1753A LYS* 2.8 34.1 + - - +
1763A LYS* 3.1 42.7 + - + +
1764A ASN 3.6 6.5 + - - +
1765A SER* 3.2 12.2 + - - +
1766A ILE 3.1 0.6 - - - -
1767A THR* 1.3 78.2 - - - +
1769A ALA* 1.3 58.8 + - - +
1770A CYS 3.1 2.2 + - - -
1771A LEU* 3.8 2.7 + - - +
1772A SER* 2.9 27.5 + - - -
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Residues in contact with ALA1769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1487A SER* 3.1 26.9 + - - -
1490A LYS* 3.4 46.4 - - + -
1765A SER 3.6 1.0 + - - -
1766A ILE* 2.9 13.6 + - + +
1768A ASP* 1.3 77.2 - - - +
1770A CYS* 1.3 60.1 + - - +
1772A SER* 4.4 7.5 - - - -
1773A VAL* 3.6 7.1 - - - +
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Residues in contact with CYS1770 (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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1466A ILE* 3.8 30.5 - - + -
1470A MET* 3.9 19.7 - - - -
1486A LEU* 3.6 36.6 - - + +
1487A SER 5.1 0.2 - - - -
1766A ILE* 3.2 22.0 - - - -
1767A THR 3.2 5.4 + - - +
1768A ASP 3.1 0.4 - - - -
1769A ALA* 1.3 81.5 - - - +
1771A LEU* 1.3 64.9 + - - +
1772A SER 3.1 1.6 - - - -
1773A VAL* 3.2 13.6 + - - +
1774A VAL* 3.2 18.9 + - - +
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Residues in contact with LEU1771 (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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1459A LEU* 6.0 3.1 - - + -
1462A LEU* 4.6 25.1 - - + -
1463A TYR* 5.1 7.6 - - + +
1466A ILE* 4.7 12.6 - - + -
1752A ILE* 3.4 21.6 - - + +
1753A LYS* 4.2 8.5 - - - +
1755A PRO* 3.5 39.5 - - + -
1763A LYS* 4.1 14.4 - - + -
1767A THR* 3.3 24.8 + - + +
1768A ASP* 3.8 4.5 + - - +
1770A CYS* 1.3 74.0 - - - +
1772A SER* 1.3 59.8 + - - +
1773A VAL 3.3 0.2 - - - -
1774A VAL* 3.5 6.8 + - + +
1775A ALA* 2.8 31.1 + - - +
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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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1753A LYS* 2.7 37.5 + - - +
1768A ASP 2.9 9.4 + - - -
1769A ALA* 4.6 7.7 - - - -
1770A CYS 3.1 0.2 - - - -
1771A LEU* 1.3 79.0 - - - +
1773A VAL* 1.3 54.0 + - - +
1775A ALA* 3.2 6.8 + - - +
1776A GLN* 2.8 42.6 + - - +
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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
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1486A LEU* 4.3 18.8 - - + +
1487A SER* 3.6 27.4 - - - +
1769A ALA 3.6 20.2 - - - +
1770A CYS* 3.2 7.9 + - - +
1772A SER* 1.3 78.3 - - - +
1774A VAL* 1.3 60.4 + - - +
1776A GLN* 4.4 0.2 - - - -
1777A THR* 3.1 23.4 + - - -
1796A ASN* 3.3 27.2 + - + +
1799A LEU* 5.1 5.2 - - + -
1800A TYR* 4.3 19.9 - - + -
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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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1462A LEU* 4.6 16.4 - - + -
1466A ILE* 5.8 3.4 - - + -
1486A LEU* 4.2 13.9 - - + -
1692A VAL* 4.3 24.7 - - + -
1696A PHE* 3.9 26.8 - - + -
1752A ILE* 4.5 11.4 - - + -
1770A CYS 3.2 15.8 + - - +
1771A LEU* 3.8 9.6 - - + +
1772A SER 3.2 0.2 - - - -
1773A VAL* 1.3 74.8 - - - +
1775A ALA* 1.3 61.5 + - - +
1776A GLN 3.1 0.2 - - - -
1777A THR* 3.2 7.2 + - - +
1778A PHE* 2.8 27.9 + - - +
1800A TYR* 4.9 8.5 - - + +
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Residues in contact with ALA1775 (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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1749A VAL* 3.9 16.9 - - + +
1752A ILE* 4.1 15.0 - - + +
1753A LYS* 4.2 14.4 - - + +
1771A LEU 2.8 20.2 + - - +
1772A SER* 3.5 8.7 - - - +
1774A VAL* 1.3 77.3 - - - +
1776A GLN* 1.3 62.6 + - - +
1778A PHE* 3.4 8.9 + - - +
1779A MET* 3.2 29.6 + - - +
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Residues in contact with GLN1776 (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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1772A SER* 2.8 20.8 + - - +
1773A VAL* 3.7 0.6 - - - +
1774A VAL 3.1 0.2 - - - -
1775A ALA* 1.3 76.0 - - - +
1777A THR* 1.3 63.4 + - - +
1779A MET* 3.3 17.1 + - - +
1780A ASP* 3.1 37.2 + - - +
1796A ASN* 3.1 32.2 - - + +
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Residues in contact with THR1777 (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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1696A PHE* 4.8 4.7 - - + -
1773A VAL 3.1 13.0 + - - -
1774A VAL* 3.2 11.1 + - - -
1776A GLN* 1.3 77.8 - - - +
1778A PHE* 1.3 58.3 + - - +
1780A ASP* 3.5 7.7 + - - -
1781A SER* 2.7 37.5 + - - +
1796A ASN* 3.5 13.6 + - - -
1800A TYR* 3.5 32.1 - - + -
1804A ILE* 3.4 23.4 - - + +
1807A TYR* 4.2 14.8 - - + -
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Residues in contact with PHE1778 (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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1696A PHE* 3.6 32.7 - + + -
1699A ILE* 4.1 19.3 - - + -
1700A PHE* 3.9 22.0 - + - -
1744A PRO* 3.4 39.5 - - + -
1745A LEU* 5.1 0.7 - - + -
1748A TRP* 3.6 20.9 - + + -
1749A VAL* 3.6 27.6 - - + -
1752A ILE* 4.0 11.9 - - + -
1774A VAL 2.8 17.2 + - - +
1775A ALA* 3.4 8.5 - - - +
1777A THR* 1.3 73.6 - - - +
1779A MET* 1.3 68.8 + - + +
1781A SER* 3.4 5.1 + - - -
1782A CYS* 3.4 22.2 + - - -
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Residues in contact with MET1779 (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 LEU* 3.4 32.9 - - + +
1749A VAL* 3.8 20.6 - - + -
1775A ALA 3.2 15.8 + - - +
1776A GLN* 3.3 19.9 + - - +
1778A PHE* 1.3 77.6 - - - +
1780A ASP* 1.3 59.5 + - - +
1782A CYS* 2.8 25.6 + - - +
1783A SER* 3.0 12.1 + - - -
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Residues in contact with ASP1780 (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 GLN* 3.1 30.1 + - - +
1777A THR* 3.8 7.3 - - - +
1778A PHE 3.4 0.4 - - - -
1779A MET* 1.3 77.8 - - - +
1781A SER* 1.3 60.0 + - - +
1782A CYS 3.4 0.3 + - - -
1783A SER* 3.5 15.9 + - - +
1785A SER 4.9 0.7 - - - +
1796A ASN* 4.2 10.6 - - - +
1797A LYS* 5.7 4.7 - - - +
1804A ILE* 4.0 19.9 - - + +
1808A LYS* 3.5 19.1 + - - -
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Residues in contact with SER1781 (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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1696A PHE* 4.6 3.5 - - - -
1700A PHE* 5.5 3.8 - - - -
1777A THR 2.7 21.9 + - - -
1778A PHE* 3.7 8.2 - - - -
1779A MET 3.1 0.8 - - - -
1780A ASP* 1.3 76.2 - - - +
1782A CYS* 1.3 62.0 + - - +
1783A SER 4.1 0.2 - - - +
1804A ILE* 3.5 14.1 - - - +
1807A TYR* 3.1 39.4 - - - +
1808A LYS* 3.2 32.8 - - - +
1811A VAL* 3.6 8.2 - - - +
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Residues in contact with CYS1782 (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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1700A PHE* 4.2 18.6 - - - -
1736A HIS* 3.5 15.1 + - - -
1737A THR* 5.7 0.3 + - - -
1740A SER* 3.3 25.4 + - - +
1744A PRO* 3.4 32.5 - - - -
1745A LEU* 4.1 19.1 - - + -
1778A PHE* 3.4 18.1 + - - -
1779A MET 2.8 9.3 + - - +
1781A SER* 1.3 78.0 - - - +
1783A SER* 1.3 64.7 + - - +
1784A THR* 3.5 0.9 + - - +
1811A VAL* 4.5 7.6 - - - -
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Residues in contact with SER1783 (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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1736A HIS* 5.3 0.2 - - - -
1737A THR* 5.9 0.4 - - - -
1740A SER* 5.8 0.4 - - - -
1745A LEU* 5.2 6.2 - - - +
1779A MET 3.0 10.1 + - - -
1780A ASP* 3.5 14.1 + - - -
1781A SER 4.1 0.2 - - - +
1782A CYS* 1.3 79.3 - - - +
1784A THR* 1.3 63.4 + - - +
1785A SER* 3.3 24.1 + - - -
1808A LYS* 3.3 24.3 - - - +
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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
------------------------------------------------------------
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