Contacts of the helix formed by residues 1804 - 1826 (chain D) in PDB entry 6X34
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 PRO1804 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1691D GLN* 4.3 15.0 - - - +
1695D LEU* 6.3 1.1 - - + -
1803D ILE* 1.3 93.4 - - + +
1805D LEU* 1.3 65.6 + - - +
1806D GLU 3.4 1.6 - - - +
1807D ALA* 4.4 19.1 - - + +
1808D LEU* 3.4 26.3 + - + +
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Residues in contact with LEU1805 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1720D LEU* 6.3 4.0 - - + -
1776D HIS* 5.0 1.6 - - + -
1778D PHE* 4.4 27.8 - - + -
1803D ILE* 3.7 27.4 - - + +
1804D PRO* 1.3 71.2 - - - +
1806D GLU* 1.3 61.2 + - - +
1808D LEU* 3.4 6.3 + - + +
1809D ARG* 2.9 29.7 + - - +
1849D LEU* 5.4 7.9 - - + +
1854D ILE* 3.7 49.7 - - + +
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Residues in contact with GLU1806 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1804D PRO* 3.4 1.2 - - + +
1805D LEU* 1.3 79.9 - - - +
1807D ALA* 1.3 57.7 + - - +
1809D ARG* 3.3 32.0 + - - +
1810D ASP* 2.9 30.4 + - - +
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Residues in contact with ALA1807 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1695D LEU* 4.9 13.3 - - + +
1804D PRO* 3.8 22.8 + - + +
1805D LEU 3.4 0.6 - - - -
1806D GLU* 1.3 78.3 - - - +
1808D LEU* 1.3 62.5 + - + +
1810D ASP* 3.3 5.9 + - - +
1811D LYS* 2.9 30.2 + - - +
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Residues in contact with LEU1808 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1695D LEU* 3.8 33.2 - - + -
1698D LEU* 4.9 8.1 - - + -
1715D LEU* 4.2 28.5 - - + -
1719D HIS* 5.8 0.4 - - + -
1803D ILE* 3.7 27.4 - - + -
1804D PRO* 3.4 21.8 + - + +
1805D LEU* 3.8 7.9 - - + +
1806D GLU 3.3 0.4 - - - -
1807D ALA* 1.3 81.2 - - + +
1809D ARG* 1.3 58.7 + - - +
1811D LYS* 3.3 6.4 + - + +
1812D ALA* 2.9 30.1 + - - +
1849D LEU* 4.1 18.4 - - + +
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Residues in contact with ARG1809 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1805D LEU 2.9 17.0 + - - +
1806D GLU* 3.5 31.7 + - - +
1808D LEU* 1.3 76.0 - - - +
1810D ASP* 1.3 60.2 + - - +
1812D ALA* 3.3 2.3 + - - +
1813D LEU* 2.9 44.1 + - + +
1849D LEU* 4.3 5.3 - - + +
1854D ILE* 4.6 11.0 + - + +
1855D PHE* 3.5 46.2 - - + +
1856D GLY 4.6 3.1 - - - +
1859D ASP* 4.1 15.1 - - - +
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Residues in contact with ASP1810 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1806D GLU 2.9 17.4 + - - +
1807D ALA* 3.7 6.7 - - - +
1809D ARG* 1.3 80.7 - - - +
1811D LYS* 1.3 57.7 + - - +
1813D LEU* 3.3 9.7 + - - +
1814D ARG* 2.9 30.4 + - - +
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Residues in contact with LYS1811 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1695D LEU* 5.2 14.4 - - + -
1698D LEU* 5.6 11.4 - - + -
1807D ALA 2.9 17.4 + - - +
1808D LEU* 3.7 10.3 - - + +
1810D ASP* 1.3 76.9 - - - +
1812D ALA* 1.3 58.6 + - - +
1814D ARG* 3.4 20.9 + - - +
1815D MET* 2.9 30.1 + - - +
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Residues in contact with ALA1812 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1698D LEU* 6.3 0.6 - - - +
1808D LEU 2.9 18.0 + - - +
1809D ARG* 3.7 3.8 - - - +
1810D ASP 3.3 0.2 - - - -
1811D LYS* 1.3 75.5 - - - +
1813D LEU* 1.3 59.5 + - - +
1815D MET* 3.3 6.1 + - - +
1816D LEU* 2.9 29.6 + - - +
1842D VAL* 4.5 2.0 - - + +
1845D LEU* 5.4 6.5 - - + -
1846D VAL* 4.4 24.4 - - + +
1849D LEU* 4.4 15.5 - - + -
1855D PHE* 4.8 5.8 - - + -
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Residues in contact with LEU1813 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1809D ARG* 2.9 40.7 + - + +
1810D ASP* 3.7 8.1 - - - +
1812D ALA* 1.3 76.9 - - - +
1814D ARG* 1.3 57.4 + - - +
1816D LEU* 3.3 7.6 + - + +
1817D GLY* 2.9 25.8 + - - -
1846D VAL* 6.1 2.7 - - + -
1855D PHE* 5.1 8.5 - - + -
1859D ASP* 4.7 20.6 - - + +
1862D GLN* 5.1 11.4 - - + -
1863D ILE* 4.6 23.1 - - + -
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Residues in contact with ARG1814 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1699D GLU* 3.9 32.5 + - - +
1810D ASP 2.9 16.7 + - - +
1811D LYS* 3.8 19.8 + - - +
1813D LEU* 1.3 75.4 - - - +
1815D MET* 1.3 58.3 + - - +
1817D GLY* 3.3 2.1 + - - -
1818D GLU* 2.9 29.7 + - + +
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Residues in contact with MET1815 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1698D LEU* 5.5 4.3 - - + +
1708D ARG* 4.6 9.0 - - - +
1712D TYR* 4.5 12.1 - - - +
1811D LYS 2.9 17.6 + - - +
1812D ALA* 3.7 6.7 - - - +
1813D LEU 3.3 0.2 - - - -
1814D ARG* 1.3 77.2 - - - +
1816D LEU* 1.3 57.1 + - - +
1818D GLU* 3.3 7.0 + - - +
1819D ALA* 2.9 29.3 + - - +
1842D VAL* 3.9 16.2 - - + +
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Residues in contact with LEU1816 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1812D ALA 2.9 17.3 + - - +
1813D LEU* 3.7 9.9 - - + +
1815D MET* 1.3 75.9 - - - +
1817D GLY* 1.3 57.8 + - - +
1819D ALA* 3.3 4.4 + - - +
1820D VAL* 2.9 32.6 + - - +
1842D VAL* 3.9 14.3 - - + +
1843D LEU* 6.3 2.0 - - + -
1846D VAL* 4.6 11.0 - - + -
1866D MET* 3.7 27.9 - - + +
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Residues in contact with GLY1817 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1813D LEU 2.9 15.1 + - - -
1814D ARG* 3.7 3.4 - - - -
1815D MET 3.3 0.2 - - - -
1816D LEU* 1.3 76.8 - - - +
1818D GLU* 1.3 55.9 + - - +
1820D VAL* 3.1 12.2 - - - +
1821D ARG* 2.9 30.4 + - - +
1866D MET* 4.8 2.2 - - - -
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Residues in contact with GLU1818 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1814D ARG* 2.9 19.6 + - + +
1815D MET* 3.7 6.7 - - - +
1817D GLY* 1.3 75.3 - - - +
1819D ALA* 1.3 57.8 + - - +
1821D ARG* 3.4 7.0 + - - +
1822D ASP* 2.9 30.0 + - - +
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Residues in contact with ALA1819 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1815D MET 2.9 18.1 + - - +
1816D LEU* 3.6 8.1 - - - +
1817D GLY 3.2 0.2 - - - -
1818D GLU* 1.3 77.9 - - - +
1820D VAL* 1.3 57.6 + - - +
1822D ASP* 3.3 5.7 + - - +
1823D GLY 2.9 23.6 + - - -
1838D GLN 4.8 2.9 - - - +
1839D PHE* 3.4 32.8 - - + -
1842D VAL* 4.6 17.0 - - + -
1866D MET* 5.9 1.3 - - + -
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Residues in contact with VAL1820 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1816D LEU 2.9 17.8 + - - +
1817D GLY* 3.1 22.7 - - - +
1819D ALA* 1.3 77.1 - - - +
1821D ARG* 1.3 57.0 + - + +
1823D GLY* 3.8 1.7 - - - +
1824D GLY* 2.9 25.6 + - - -
1839D PHE* 5.0 4.5 - - - -
1866D MET* 4.1 31.1 - - + +
1925D GLU* 4.0 28.3 - - + +
1926D GLY 5.8 0.2 - - - -
1927D LEU* 5.3 16.4 - - + +
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Residues in contact with ARG1821 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1817D GLY 2.9 19.6 + - - +
1818D GLU* 3.7 6.7 - - - +
1820D VAL* 1.3 78.9 - - + +
1822D ASP* 1.3 57.6 + - - +
1824D GLY* 3.3 1.7 + - - -
1825D GLN* 2.9 30.0 + - - +
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Residues in contact with ASP1822 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1232D ARG* 5.7 7.2 - - - +
1818D GLU 2.9 18.2 + - - +
1819D ALA* 3.3 6.7 + - - +
1821D ARG* 1.3 76.5 - - - +
1823D GLY* 1.3 61.8 + - - +
1825D GLN* 3.4 6.3 + - - +
1826D HIS* 3.2 17.3 + - - -
1827D ALA* 4.0 13.0 + - + +
1830D PRO* 6.5 0.9 - - + -
1831D VAL* 6.0 4.3 - - + -
1839D PHE* 5.7 2.9 - - + -
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Residues in contact with GLY1823 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1819D ALA 2.9 16.0 + - - -
1820D VAL* 3.3 2.2 + - - -
1822D ASP* 1.3 77.7 - - - +
1824D GLY* 1.3 60.7 + - - +
1826D HIS* 3.4 16.0 + - - +
1835D VAL* 6.5 0.4 - - - -
1839D PHE* 4.5 10.7 - - - -
1930D MET* 4.3 30.4 - - - +
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Residues in contact with GLY1824 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1820D VAL 2.9 16.2 + - - -
1821D ARG* 3.8 2.5 - - - -
1823D GLY* 1.3 75.6 - - - +
1825D GLN* 1.3 61.7 + - - +
1826D HIS* 3.4 3.6 + - - +
1925D GLU* 4.4 17.7 - - - +
1930D MET* 5.4 1.1 - - - -
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Residues in contact with GLN1825 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1231D GLN* 5.1 12.8 - - + +
1821D ARG 2.9 17.2 + - - +
1822D ASP* 3.8 7.6 - - - +
1824D GLY* 1.3 75.3 - - - +
1826D HIS* 1.3 71.3 + - - +
1827D ALA* 3.4 8.1 - - + +
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Residues in contact with HIS1826 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1229D ASN* 5.0 3.3 - - - +
1822D ASP 3.2 8.1 + - - -
1823D GLY 3.4 11.4 + - - +
1824D GLY 3.2 5.6 - - - +
1825D GLN* 1.3 80.4 - - - +
1827D ALA* 1.3 68.1 + - - +
1828D ARG 4.0 0.2 + - - -
1930D MET* 6.3 2.0 - - + -
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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
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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