Contacts of the helix formed by residues 1803 - 1821 (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 ASP1803 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1685A LYS* 2.8 37.8 + - - -
1689A GLN* 4.1 17.1 + - - +
1799A LEU 4.5 0.7 - - - +
1800A TYR* 3.2 18.5 + - + +
1802A LYS* 1.3 88.5 - - - +
1804A ILE* 1.3 66.5 + - - +
1805A PRO* 3.3 2.5 - - - -
1806A ASN* 3.1 19.8 + - - +
1807A TYR* 3.1 38.4 + - + -
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Residues in contact with ILE1804 (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 THR* 3.4 38.1 - - + +
1780A ASP* 4.0 24.5 - - + +
1781A SER* 3.5 9.9 - - - +
1796A ASN* 5.9 0.9 - - - +
1797A LYS* 5.8 3.4 - - - +
1800A TYR* 2.9 24.1 + - + +
1801A ALA* 4.6 3.8 - - - +
1803A ASP* 1.3 77.2 - - - +
1805A PRO* 1.3 68.8 - - + +
1807A TYR* 3.5 4.3 + - - +
1808A LYS* 3.1 47.0 + - + +
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Residues in contact with PRO1805 (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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1801A ALA 3.4 18.8 - - - +
1802A LYS* 4.0 4.5 - - - -
1803A ASP 3.3 7.0 - - - +
1804A ILE* 1.3 96.5 - - + +
1806A ASN* 1.3 66.4 + - - +
1808A LYS* 3.3 12.4 - - + +
1809A SER* 3.3 19.2 + - - -
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Residues in contact with ASN1806 (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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1802A LYS 4.0 15.2 - - - +
1803A ASP* 3.1 10.5 + - - +
1805A PRO* 1.3 82.3 - - - +
1807A TYR* 1.3 66.1 + - + +
1808A LYS 2.9 4.7 - - - -
1809A SER* 2.6 30.4 + - - +
1810A TRP* 3.2 23.2 + - + +
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Residues in contact with TYR1807 (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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1689A GLN* 3.9 13.6 + - - -
1692A VAL* 4.3 9.9 - - + +
1693A ASP* 2.8 28.0 + - - -
1696A PHE* 3.8 24.7 - + + -
1700A PHE* 4.1 6.9 - - + -
1777A THR* 4.2 18.2 - - + -
1781A SER* 3.1 32.7 - - - +
1800A TYR* 4.5 6.6 - + - -
1803A ASP* 3.1 41.3 + - + +
1804A ILE 4.0 2.2 - - - +
1806A ASN* 1.3 76.2 - - + +
1808A LYS* 1.3 61.0 + - - +
1810A TRP* 3.5 43.0 - + + +
1811A VAL* 3.4 18.5 + - - +
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Residues in contact with LYS1808 (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 ASP 3.5 13.5 - - - -
1781A SER* 3.2 22.7 - - - +
1783A SER 3.3 20.3 + - - +
1784A THR* 4.2 5.5 + - - +
1785A SER 3.0 27.5 + - - -
1786A GLU* 4.0 8.9 - - - +
1804A ILE* 3.1 35.1 + - + +
1805A PRO* 3.3 13.0 - - + +
1806A ASN 2.9 0.2 - - - -
1807A TYR* 1.3 73.3 - - - +
1809A SER* 1.3 66.8 + - - +
1810A TRP 3.0 1.3 - - - -
1811A VAL* 2.8 24.8 + - + +
1812A GLU* 3.0 16.8 + - + +
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Residues in contact with SER1809 (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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1805A PRO 3.3 7.8 + - - -
1806A ASN* 2.6 25.9 + - - +
1808A LYS* 1.3 78.4 - - - +
1810A TRP* 1.3 70.8 + - - +
1812A GLU* 3.5 18.2 + - - +
1813A ARG* 3.1 24.6 + - - +
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Residues in contact with TRP1810 (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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1693A ASP* 4.0 23.1 - - + -
1696A PHE* 3.7 36.8 - - + -
1697A GLU* 3.9 12.8 - - + -
1700A PHE* 3.9 11.0 - + + -
1806A ASN* 3.2 27.2 + - + +
1807A TYR* 3.5 40.6 - + - +
1808A LYS 3.0 0.6 - - - -
1809A SER* 1.3 87.2 + - - +
1811A VAL* 1.3 53.5 + - - +
1813A ARG* 3.4 26.2 + - - +
1814A TYR* 2.7 38.4 + - - +
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Residues in contact with VAL1811 (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* 3.8 30.9 - - + -
1736A HIS* 3.7 20.9 - - + +
1740A SER* 4.7 0.2 - - - +
1781A SER 3.6 20.4 - - - +
1782A CYS* 4.5 11.4 - - - -
1807A TYR 3.4 6.8 + - - +
1808A LYS* 2.8 20.2 + - + +
1810A TRP* 1.3 79.0 - - - +
1812A GLU* 1.3 58.8 + - + +
1814A TYR* 4.0 5.8 - - - -
1815A TYR* 3.0 62.0 + - + +
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Residues in contact with GLU1812 (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* 4.0 24.0 + - + +
1808A LYS* 3.0 23.4 + - - +
1809A SER* 3.6 15.6 - - - +
1811A VAL* 1.3 75.2 - - + +
1813A ARG* 1.3 66.4 + - - +
1814A TYR 3.0 0.9 - - - -
1815A TYR* 2.9 7.9 + - - +
1816A ALA* 2.8 24.4 + - - +
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Residues in contact with ARG1813 (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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1697A GLU* 4.7 14.5 + - - +
1700A PHE* 2.9 27.5 + - - +
1701A SER* 4.1 12.7 - - - +
1702A THR* 5.0 3.6 + - - +
1809A SER 3.1 11.9 + - - +
1810A TRP* 3.4 35.7 - - - +
1812A GLU* 1.3 78.2 - - - +
1814A TYR* 1.3 66.4 + - - +
1816A ALA* 3.6 7.6 - - - +
1817A ASP* 2.9 55.5 + - - +
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Residues in contact with TYR1814 (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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1699A ILE 3.8 18.2 + - - -
1700A PHE* 3.4 46.9 - + + +
1701A SER 3.7 18.4 - - - -
1702A THR* 4.3 4.5 - - + -
1709A LEU* 3.6 6.8 - - + +
1713A ILE* 3.5 34.1 - - - +
1717A PHE* 4.8 0.7 - + - -
1743A LEU* 3.9 13.1 - - + +
1744A PRO* 5.9 0.7 - - + -
1748A TRP* 5.5 0.2 + - - -
1810A TRP 2.7 22.3 + - - +
1811A VAL 3.9 3.8 - - - +
1813A ARG* 1.3 80.5 - - - +
1815A TYR* 1.3 85.5 + + - +
1817A ASP* 3.7 5.2 + - - +
1818A ILE* 3.0 48.5 + - + +
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Residues in contact with TYR1815 (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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1717A PHE* 3.3 34.2 - + - -
1736A HIS* 3.6 48.7 - + + -
1739A LYS* 3.9 33.1 + - + +
1740A SER* 3.0 21.1 + - - -
1744A PRO* 3.3 22.8 - - + +
1811A VAL* 3.0 24.2 + - + +
1812A GLU* 2.9 6.3 + - - +
1814A TYR* 1.3 95.6 - + - +
1816A ALA* 1.3 66.8 + - - +
1818A ILE* 3.3 7.9 + - - +
1819A ALA* 3.2 20.1 + - - +
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Residues in contact with ALA1816 (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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1812A GLU 2.8 15.9 + - - +
1813A ARG* 3.6 9.2 - - - +
1815A TYR* 1.3 77.7 - - - +
1817A ASP* 1.3 59.7 + - - +
1819A ALA* 2.9 21.0 + - - +
1820A LYS* 2.9 32.4 + - + +
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Residues in contact with ASP1817 (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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1702A THR* 3.5 31.0 + - + +
1813A ARG* 2.9 49.6 + - - +
1814A TYR* 3.9 1.4 - - - +
1816A ALA* 1.3 77.9 - - - +
1818A ILE* 1.3 62.1 + - - +
1820A LYS* 3.3 11.7 + - - +
1821A MET* 3.1 29.8 + - + +
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Residues in contact with ILE1818 (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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1702A THR* 4.2 6.3 - - + -
1709A LEU* 3.6 25.8 - - + -
1713A ILE* 3.9 10.1 - - + -
1714A LYS* 2.7 66.8 + - + +
1717A PHE* 4.0 26.9 - - + -
1718A ASP* 4.3 1.1 - - - +
1814A TYR* 3.0 44.9 - - + +
1815A TYR* 3.3 6.0 + - - +
1816A ALA 3.3 0.6 - - - -
1817A ASP* 1.3 76.1 - - - +
1819A ALA* 1.3 53.9 + - - +
1821A MET* 3.7 9.5 - - - +
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Residues in contact with ALA1819 (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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1714A LYS* 4.4 2.9 + - - +
1718A ASP* 5.5 2.0 - - - -
1721A ASP* 4.4 17.3 - - - +
1739A LYS* 5.3 4.3 - - - +
1815A TYR 3.2 11.2 + - - +
1816A ALA* 2.9 13.1 + - - +
1818A ILE* 1.3 76.9 - - - +
1820A LYS* 1.3 67.4 + - + +
1821A MET 3.6 5.5 - - - +
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Residues in contact with LYS1820 (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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1816A ALA* 2.9 30.3 + - + +
1817A ASP* 3.3 12.2 + - - +
1819A ALA* 1.3 77.9 - - + +
1821A MET* 1.3 68.4 + - - +
1822A PRO* 3.7 1.6 - - - +
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Residues in contact with MET1821 (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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1702A THR* 3.5 40.6 - - + +
1703A ALA* 6.0 2.0 - - + -
1708A ALA* 6.4 0.9 - - + -
1709A LEU* 4.7 17.5 - - + +
1714A LYS* 3.2 26.9 + - - +
1817A ASP* 3.1 15.8 + - + +
1818A ILE* 3.7 18.4 - - - +
1819A ALA 3.3 4.8 - - - +
1820A LYS* 1.3 82.4 - - - +
1822A PRO* 1.3 72.6 - - + +
1823A ALA 3.7 0.9 + - - -
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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) + - + + + + + -
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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