Contacts of the helix formed by residues 1795 - 1812 (chain A) in PDB entry 2D4Q
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 GLU1795 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1719A PHE* 3.6 27.8 - - + -
1793A HIS* 3.1 19.2 + - + +
1794A GLN* 1.3 84.1 - - + +
1796A CYS* 1.3 64.6 + - - +
1797A GLU* 3.3 4.3 - - - -
1798A ALA* 3.1 12.0 + - + +
1799A ILE* 3.0 22.8 + - - +
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Residues in contact with CYS1796 (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 LEU* 3.9 17.5 - - + -
1775A GLU 3.4 13.6 + - - +
1776A ASN 3.5 18.2 - - - -
1777A GLN* 3.5 6.3 - - - +
1778A PHE* 3.6 25.4 - - + -
1791A PHE 4.4 0.9 - - - -
1793A HIS* 3.1 33.2 - - - -
1794A GLN 3.4 3.8 + - - -
1795A GLU* 1.3 73.0 - - - +
1797A GLU* 1.3 66.9 + - - +
1799A ILE* 2.9 6.8 + - - +
1800A VAL* 2.9 27.5 + - - +
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Residues in contact with GLU1797 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1772A LEU* 3.9 27.6 - - + +
1775A GLU* 3.0 53.4 - - - +
1794A GLN 4.1 5.9 - - - +
1795A GLU* 4.2 1.2 - - - -
1796A CYS* 1.3 75.2 + - - +
1798A ALA* 1.3 57.7 + - - +
1800A VAL* 3.5 2.4 + - - +
1801A GLN* 2.9 29.6 + - - +
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Residues in contact with ALA1798 (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 LYS* 5.6 0.2 - - - +
1719A PHE* 4.3 16.5 - - + -
1795A GLU* 3.1 15.9 + - + +
1797A GLU* 1.3 78.6 - - - +
1799A ILE* 1.3 64.4 + - - +
1801A GLN* 3.8 8.8 + - - +
1802A SER* 3.0 25.5 + - - -
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Residues in contact with ILE1799 (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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1719A PHE* 3.6 44.9 - - + -
1734A ILE* 4.2 17.7 - - + -
1736A VAL* 4.8 1.1 - - + -
1778A PHE* 3.5 40.8 - - + -
1793A HIS* 4.0 26.0 - - + -
1795A GLU 3.0 13.0 + - - +
1796A CYS* 2.9 9.0 + - - +
1798A ALA* 1.3 75.9 - - - +
1800A VAL* 1.3 62.5 + - - +
1802A SER* 3.4 2.6 + - - -
1803A ILE* 3.1 40.6 + - + +
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Residues in contact with VAL1800 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1770A ILE* 3.8 22.2 - - + +
1772A LEU* 3.8 27.6 - - + +
1778A PHE* 3.5 36.6 - - + -
1796A CYS 2.9 18.9 + - - +
1797A GLU* 3.8 4.7 - - - +
1799A ILE* 1.3 73.5 - - - +
1801A GLN* 1.3 67.3 + - - +
1803A ILE* 3.1 3.6 + - - +
1804A ILE* 2.8 48.7 + - + +
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Residues in contact with GLN1801 (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 LYS* 5.2 6.3 - - - +
1797A GLU 2.9 18.7 + - - +
1798A ALA* 3.8 9.3 + - - +
1799A ILE 3.4 0.2 - - - -
1800A VAL* 1.3 76.4 - - - +
1802A SER* 1.3 71.8 + - - +
1804A ILE* 3.4 9.3 + - - +
1805A HIS* 3.1 27.3 + - - +
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Residues in contact with SER1802 (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 LYS* 4.1 27.6 + - - +
1719A PHE* 4.9 0.7 - - - -
1736A VAL* 3.2 25.2 - - - +
1798A ALA 3.0 17.7 + - - -
1799A ILE* 3.7 5.8 - - - -
1801A GLN* 1.3 88.5 - - - +
1803A ILE* 1.3 59.3 + - - +
1805A HIS* 3.6 4.9 + - - +
1806A ILE* 3.1 30.3 + - - +
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Residues in contact with ILE1803 (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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1734A ILE* 5.0 0.7 - - + -
1736A VAL* 4.0 11.9 - - + -
1741A VAL* 3.7 33.9 - - + -
1767A ILE* 3.8 37.2 - - + -
1770A ILE* 4.3 11.7 - - + -
1778A PHE* 4.3 16.8 - - + -
1780A LEU* 4.4 8.5 - - + -
1799A ILE* 3.1 34.7 + - + +
1800A VAL* 3.9 4.7 - - - +
1802A SER* 1.3 73.4 - - - +
1804A ILE* 1.3 67.3 + - - +
1806A ILE* 3.3 6.8 + - + +
1807A ARG* 3.0 21.8 + - - +
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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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1770A ILE* 4.4 20.6 - - + +
1800A VAL* 2.8 41.5 + - + +
1801A GLN* 3.7 8.1 - - - +
1803A ILE* 1.3 77.8 - - - +
1805A HIS* 1.3 57.3 + - - +
1807A ARG* 3.2 6.9 + - - +
1808A THR* 2.9 43.6 + - - +
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Residues in contact with HIS1805 (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 GLN* 3.1 20.2 + - - +
1802A SER* 3.6 10.3 - - - +
1803A ILE 3.2 0.2 - - - -
1804A ILE* 1.3 77.2 - - - +
1806A ILE* 1.3 76.8 + - + +
1808A THR* 3.3 6.9 + - - -
1809A ARG* 3.0 57.0 + - + +
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Residues in contact with ILE1806 (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 VAL* 4.0 11.2 - - + -
1737A GLY 3.0 29.2 - - - +
1738A SER* 3.4 22.8 - - - +
1740A ALA 4.8 4.3 - - - +
1741A VAL* 5.1 2.9 - - + -
1764A ALA* 3.8 23.8 - - + +
1767A ILE* 5.1 3.8 - - + -
1802A SER* 3.1 26.4 + - - +
1803A ILE* 3.3 16.0 + - + +
1805A HIS* 1.3 95.5 - - + +
1807A ARG* 1.3 62.1 + - - +
1809A ARG* 3.8 9.2 + - - +
1810A TRP* 3.3 20.6 + - - +
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Residues in contact with ARG1807 (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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1764A ALA* 2.7 37.3 + - - +
1765A SER 3.3 19.6 + - - -
1767A ILE* 3.0 32.2 + - + +
1768A GLU* 4.5 13.1 + - - +
1770A ILE* 4.6 14.4 - - + -
1803A ILE* 3.0 17.7 + - + +
1804A ILE* 3.6 6.7 - - - +
1806A ILE* 1.3 79.3 - - + +
1808A THR* 1.3 65.9 + - - +
1810A TRP* 3.2 27.4 + - - +
1811A GLU* 2.9 57.7 + - - +
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Residues in contact with THR1808 (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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1804A ILE* 2.9 30.9 + - - +
1805A HIS* 3.7 7.2 - - - -
1807A ARG* 1.3 72.7 - - - +
1809A ARG* 1.3 68.4 + - + +
1811A GLU* 3.1 16.5 + - - +
1812A LEU* 3.0 44.8 + - + +
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Residues in contact with ARG1809 (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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1738A SER* 2.9 49.3 + - - +
1739A THR* 5.2 4.8 - - - +
1805A HIS* 3.0 46.1 + - + +
1806A ILE* 4.0 12.9 - - - +
1808A THR* 1.3 79.4 - - + +
1810A TRP* 1.3 64.2 + - - +
1812A LEU* 3.3 20.7 + - + +
1813A SER* 3.4 14.9 + - - -
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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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1764A ALA* 3.8 15.7 - - + -
1765A SER* 3.4 38.0 - - - -
1806A ILE 3.3 11.6 + - - +
1807A ARG* 3.2 41.2 + - - +
1808A THR 3.2 0.8 - - - -
1809A ARG* 1.3 80.0 - - - +
1811A GLU* 1.3 87.8 + - + +
1813A SER* 3.0 18.5 + - - -
1814A GLN* 3.5 34.7 + - + +
1813B SER 5.9 1.5 + - - -
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Residues in contact with GLU1811 (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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1807A ARG* 2.9 54.7 + - - +
1808A THR* 3.1 17.3 + - - +
1810A TRP* 1.3 86.0 - - + +
1812A LEU* 1.3 66.9 + - + +
1813A SER 3.1 1.6 + - - -
1814A GLN* 2.7 40.3 + - - +
1708B ALA* 5.4 1.2 - - - +
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Residues in contact with LEU1812 (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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1808A THR* 3.0 35.7 + - + +
1809A ARG* 3.5 17.9 - - + +
1810A TRP 3.2 0.4 - - - -
1811A GLU* 1.3 79.8 - - + +
1813A SER* 1.3 58.8 + - - +
1814A GLN 3.7 0.9 - - - +
1707B ALA* 3.9 26.0 - - + +
1708B ALA* 3.6 39.9 - - + +
1711B ALA* 4.2 21.3 - - + +
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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