Contacts of the helix formed by residues 1804 - 1826 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1691F GLN* 4.3 14.8 - - - +
1695F LEU* 6.3 1.1 - - + -
1803F ILE* 1.3 93.8 - - + +
1805F LEU* 1.3 63.1 + - - +
1806F GLU* 3.4 1.6 - - + +
1807F ALA* 4.4 18.8 - - + +
1808F LEU* 3.4 27.2 + - + +
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Residues in contact with LEU1805 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1720F LEU* 6.3 4.0 - - + -
1776F HIS* 5.0 1.8 - - + -
1778F PHE* 4.4 27.6 - - + -
1803F ILE* 3.1 27.8 + - + +
1804F PRO* 1.3 71.6 - - - +
1806F GLU* 1.3 61.0 + - - +
1808F LEU* 3.4 6.3 + - + +
1809F ARG* 2.9 30.3 + - - +
1849F LEU* 5.4 6.9 - - + +
1854F ILE* 3.7 50.2 - - + +
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Residues in contact with GLU1806 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1804F PRO* 3.4 1.0 - - + +
1805F LEU* 1.3 79.3 - - - +
1807F ALA* 1.3 57.1 + - - +
1809F ARG* 3.3 31.1 + - - +
1810F ASP* 2.9 29.3 + - - +
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Residues in contact with ALA1807 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1695F LEU* 4.9 13.3 - - + +
1804F PRO* 3.8 23.0 + - + +
1805F LEU 3.4 0.4 - - - -
1806F GLU* 1.3 79.3 - - - +
1808F LEU* 1.3 61.3 + - + +
1810F ASP* 3.3 6.5 + - - +
1811F LYS* 2.9 30.2 + - - +
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Residues in contact with LEU1808 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1695F LEU* 3.8 33.7 - - + -
1698F LEU* 4.9 7.9 - - + -
1715F LEU* 4.2 28.5 - - + -
1719F HIS* 5.8 0.7 - - + -
1803F ILE* 3.7 27.8 - - + -
1804F PRO* 3.4 20.9 + - + +
1805F LEU* 3.8 8.5 - - + +
1806F GLU 3.3 0.6 - - - -
1807F ALA* 1.3 80.5 - - + +
1809F ARG* 1.3 58.4 + - - +
1811F LYS* 3.7 6.3 - - + +
1812F ALA* 2.9 30.8 + - - +
1849F LEU* 4.1 18.1 - - + +
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Residues in contact with ARG1809 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1805F LEU 2.9 17.1 + - - +
1806F GLU* 3.5 33.2 + - - +
1807F ALA 3.3 0.2 - - - -
1808F LEU* 1.3 76.6 - - - +
1810F ASP* 1.3 59.4 + - - +
1812F ALA* 3.3 2.3 + - - +
1813F LEU* 2.9 44.3 + - + +
1849F LEU* 4.3 4.6 - - + +
1854F ILE* 4.6 12.1 + - + +
1855F PHE* 3.5 46.1 - - + +
1856F GLY* 4.6 3.1 - - - +
1859F ASP* 4.1 14.6 - - - +
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Residues in contact with ASP1810 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1806F GLU 2.9 16.9 + - - +
1807F ALA* 3.7 6.7 - - - +
1808F LEU 3.3 0.2 - - - -
1809F ARG* 1.3 80.6 - - - +
1811F LYS* 1.3 58.3 + - - +
1813F LEU* 3.3 8.6 + - - +
1814F ARG* 2.9 30.8 + - - +
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Residues in contact with LYS1811 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1695F LEU* 5.2 14.1 - - + -
1698F LEU* 5.5 11.7 - - + -
1807F ALA 2.9 17.9 + - - +
1808F LEU* 3.7 10.1 - - + +
1810F ASP* 1.3 76.0 - - - +
1812F ALA* 1.3 58.3 + - - +
1814F ARG* 3.4 21.2 + - - +
1815F MET* 2.9 30.4 + - - +
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Residues in contact with ALA1812 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1698F LEU* 6.5 0.7 - - - -
1808F LEU 2.9 17.2 + - - +
1809F ARG* 3.7 3.8 - - - +
1811F LYS* 1.3 76.7 - - - +
1813F LEU* 1.3 60.0 + - - +
1815F MET* 3.3 6.4 + - - +
1816F LEU* 2.9 30.4 + - - +
1842F VAL* 4.5 2.8 - - + +
1845F LEU* 5.4 6.7 - - + -
1846F VAL* 4.4 23.8 - - + +
1849F LEU* 4.4 16.2 - - + -
1855F PHE* 4.8 5.6 - - + -
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Residues in contact with LEU1813 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1809F ARG* 2.9 41.8 + - + +
1810F ASP* 3.7 7.4 - - - +
1812F ALA* 1.3 77.7 - - - +
1814F ARG* 1.3 56.8 + - - +
1816F LEU* 3.3 8.3 + - + +
1817F GLY* 2.9 25.6 + - - -
1846F VAL* 6.1 2.7 - - + -
1855F PHE* 5.1 9.0 - - + -
1859F ASP* 4.7 20.0 - - + +
1862F GLN* 5.1 12.1 - - + -
1863F ILE* 4.6 22.4 - - + -
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Residues in contact with ARG1814 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1699F GLU* 3.9 32.5 + - - +
1810F ASP 2.9 18.1 + - - +
1811F LYS* 3.8 20.0 + - - +
1813F LEU* 1.3 76.3 - - - +
1815F MET* 1.3 58.3 + - - +
1817F GLY* 3.3 1.7 + - - -
1818F GLU* 2.9 30.2 + - + +
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Residues in contact with MET1815 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1698F LEU* 5.5 3.6 - - + +
1708F ARG* 4.6 9.0 - - - +
1712F TYR* 4.5 12.3 - - - +
1811F LYS 2.9 18.3 + - - +
1812F ALA* 3.7 6.3 - - - +
1814F ARG* 1.3 78.5 - - - +
1816F LEU* 1.3 56.1 + - - +
1818F GLU* 3.3 6.3 + - - +
1819F ALA* 2.9 29.8 + - - +
1842F VAL* 3.9 15.8 - - + +
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Residues in contact with LEU1816 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1812F ALA 2.9 16.9 + - - +
1813F LEU* 3.3 9.6 + - + +
1815F MET* 1.3 75.2 - - - +
1817F GLY* 1.3 57.9 + - - +
1819F ALA* 3.3 5.1 + - - +
1820F VAL* 2.9 32.3 + - - +
1842F VAL* 3.9 14.5 - - + +
1843F LEU* 6.3 1.8 - - + -
1846F VAL* 4.6 10.5 - - + -
1866F MET* 3.7 28.1 - - + +
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Residues in contact with GLY1817 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1813F LEU 2.9 16.1 + - - -
1814F ARG* 3.7 2.9 - - - -
1816F LEU* 1.3 76.2 - - - +
1818F GLU* 1.3 56.2 + - - +
1820F VAL* 3.1 11.8 - - - +
1821F ARG* 2.9 30.4 + - - +
1866F MET* 4.8 2.8 - - - -
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Residues in contact with GLU1818 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1814F ARG* 2.9 18.9 + - + +
1815F MET* 3.3 7.6 + - - +
1817F GLY* 1.3 75.4 - - - +
1819F ALA* 1.3 58.2 + - - +
1821F ARG* 3.4 6.3 + - - +
1822F ASP* 2.9 30.0 + - - +
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Residues in contact with ALA1819 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1815F MET 2.9 17.4 + - - +
1816F LEU* 3.6 7.9 - - - +
1818F GLU* 1.3 77.3 - - - +
1820F VAL* 1.3 58.1 + - - +
1822F ASP* 3.3 5.7 + - - +
1823F GLY 2.9 23.7 + - - -
1838F GLN 4.8 3.6 - - - +
1839F PHE* 3.4 33.4 - - + -
1842F VAL* 4.6 16.4 - - + -
1866F MET* 5.9 1.6 - - + -
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Residues in contact with VAL1820 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1816F LEU 2.9 16.9 + - - +
1817F GLY* 3.1 22.4 - - - +
1819F ALA* 1.3 76.3 - - - +
1821F ARG* 1.3 58.6 + - + +
1823F GLY* 3.3 1.9 + - - +
1824F GLY* 2.9 25.5 + - - -
1839F PHE* 5.0 4.3 - - - -
1866F MET* 4.1 31.8 - - + +
1925F GLU* 4.0 28.5 - - + +
1926F GLY 5.8 0.4 - - - -
1927F LEU* 5.3 15.3 - - + +
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Residues in contact with ARG1821 (chain F).
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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1817F GLY 2.9 17.7 + - - +
1818F GLU* 3.7 7.0 - - - +
1820F VAL* 1.3 79.5 - - + +
1822F ASP* 1.3 57.1 + - - +
1824F GLY* 3.3 1.5 + - - -
1825F GLN* 2.9 29.5 + - - +
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Residues in contact with ASP1822 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1232F ARG* 5.7 7.4 - - - +
1818F GLU 2.9 17.4 + - - +
1819F ALA* 3.8 5.4 - - - +
1821F ARG* 1.3 77.1 - - - +
1823F GLY* 1.3 61.9 + - - +
1825F GLN* 3.4 7.4 + - - +
1826F HIS* 3.2 17.2 + - - -
1827F ALA* 4.0 12.3 + - + +
1830F PRO* 6.5 1.1 - - + -
1831F VAL* 6.0 4.3 - - + -
1839F PHE* 5.7 3.4 - - + -
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Residues in contact with GLY1823 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1819F ALA 2.9 16.8 + - - -
1820F VAL* 3.8 2.2 - - - -
1822F ASP* 1.3 77.7 - - - +
1824F GLY* 1.3 60.2 + - - +
1826F HIS* 3.4 16.6 + - - +
1835F VAL* 6.5 0.4 - - - -
1839F PHE* 4.5 10.9 - - - -
1930F MET* 4.3 30.7 - - - +
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Residues in contact with GLY1824 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1820F VAL 2.9 16.6 + - - -
1821F ARG* 3.8 1.8 - - - -
1823F GLY* 1.3 76.6 - - - +
1825F GLN* 1.3 61.7 + - - +
1826F HIS* 3.4 3.6 + - - +
1925F GLU* 4.4 18.1 - - - +
1930F MET* 5.9 0.9 - - - -
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Residues in contact with GLN1825 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1231F GLN* 5.1 13.5 - - + +
1821F ARG 2.9 17.2 + - - +
1822F ASP* 3.8 8.1 - - - +
1823F GLY 3.3 0.4 - - - -
1824F GLY* 1.3 75.1 - - - +
1826F HIS* 1.3 70.7 + - - +
1827F ALA* 4.5 7.8 - - + +
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Residues in contact with HIS1826 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1229F ASN* 5.0 4.0 - - - +
1822F ASP 3.2 7.7 + - - -
1823F GLY* 3.4 11.8 + - - +
1824F GLY 3.2 5.8 - - - +
1825F GLN* 1.3 80.1 - - - +
1827F ALA* 1.3 66.3 + - - +
1828F ARG 4.0 0.2 + - - -
1930F MET* 6.3 2.7 - - + -
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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