Contacts of the helix formed by residues 1785 - 1803 (chain A) in PDB entry 5G04
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 GLU1785 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941A LEU* 4.0 32.0 - - + +
944A LEU* 4.8 1.9 - - - +
945A GLU* 3.7 14.7 - - - +
956A ARG* 2.8 54.5 + - - +
959A ILE* 6.1 1.0 - - - +
963A ARG* 5.9 6.3 - - - +
1783A THR* 3.3 6.5 - - - +
1784A PRO* 1.3 79.3 - - + +
1786A MET* 1.3 69.3 + - - +
1787A LEU 3.3 0.2 - - - -
1788A PRO* 3.2 24.1 - - - +
602O PRO* 6.4 0.9 - - - -
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Residues in contact with MET1786 (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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949A PHE* 6.1 1.1 - - + -
952A ALA* 6.5 0.2 - - + -
953A LEU* 3.7 32.3 - - + -
956A ARG* 3.6 29.6 - - - +
1778A CYS* 3.8 2.5 - - - -
1783A THR* 3.3 29.2 + - + +
1784A PRO 3.2 1.4 - - - -
1785A GLU* 1.3 88.8 - - - +
1787A LEU* 1.3 65.2 + - - +
1788A PRO 3.4 0.2 - - - -
1789A ALA* 3.2 22.6 + - + +
1790A TYR* 2.9 45.1 + - + +
1839A PHE* 3.6 26.0 - - + -
1840A MET* 4.6 7.4 - - - +
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Residues in contact with LEU1787 (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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1747A LEU* 4.6 22.2 - - + -
1750A PHE* 3.9 54.7 - - + -
1774A VAL* 5.3 2.5 - - + -
1775A LEU* 5.2 7.2 - - + -
1778A CYS* 3.4 21.5 - - + -
1784A PRO* 3.3 13.2 + - + +
1785A GLU 3.3 0.2 - - - -
1786A MET* 1.3 75.9 - - - +
1788A PRO* 1.4 75.6 - - + +
1790A TYR* 3.3 3.2 + - - +
1791A ILE* 3.0 29.7 + - + +
601O LEU* 4.4 20.9 - - + -
602O PRO* 5.2 7.2 - - + -
605O LEU* 5.5 1.3 - - + -
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Residues in contact with PRO1788 (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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945A GLU* 4.1 17.0 - - - +
949A PHE* 6.0 0.2 - - - -
956A ARG* 5.2 3.8 - - - +
1784A PRO 4.0 2.9 - - - +
1785A GLU* 3.2 23.8 - - - +
1787A LEU* 1.4 97.6 - - + +
1789A ALA* 1.3 58.9 + - + +
1791A ILE 3.0 0.3 + - - -
1792A ALA* 2.9 27.5 + - - +
598O THR* 3.0 40.4 - - + +
599O ILE* 4.1 15.3 - - + -
602O PRO* 4.6 13.2 - - + -
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Residues in contact with ALA1789 (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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949A PHE* 4.0 33.0 - - + +
953A LEU* 5.0 3.4 - - + -
1785A GLU 5.0 0.4 - - - +
1786A MET* 3.2 34.2 + - + +
1788A PRO* 1.3 80.6 - - + +
1790A TYR* 1.3 58.1 + - + +
1792A ALA* 3.5 7.7 + - - +
1793A MET* 2.9 38.1 + - - +
1840A MET* 6.6 0.2 - - + -
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Residues in contact with TYR1790 (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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1774A VAL* 3.3 27.6 - - + -
1777A GLU* 3.9 29.0 + - + +
1778A CYS* 3.4 33.7 - - - -
1781A GLN* 5.0 8.5 + - - +
1783A THR* 5.5 3.0 - - + +
1786A MET* 2.9 26.5 + - + +
1787A LEU 3.6 2.5 - - - +
1789A ALA* 1.3 77.4 - - + +
1791A ILE* 1.3 63.2 + - - +
1793A MET* 3.1 25.5 - - - +
1794A ASP* 3.2 14.3 + - - +
1840A MET* 3.3 48.6 - - + +
1842A SER* 5.4 1.4 - - - -
1844A PHE* 3.7 28.0 - + - -
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Residues in contact with ILE1791 (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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1750A PHE* 4.2 15.3 - - + -
1771A PHE* 3.6 48.7 - - + +
1774A VAL* 3.5 29.8 - - + -
1787A LEU* 3.0 18.8 + - + +
1788A PRO 3.0 2.2 + - - -
1790A TYR* 1.3 71.2 - - - +
1792A ALA* 1.3 53.4 + - - +
1794A ASP* 2.9 14.4 + - + +
1795A GLN* 2.7 35.3 + - + +
598O THR* 3.2 21.8 - - + -
601O LEU* 4.9 1.1 - - + -
634O LEU* 4.3 13.9 - - + -
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Residues in contact with ALA1792 (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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949A PHE* 3.6 33.0 - - + -
1788A PRO 2.9 15.1 + - - +
1789A ALA* 3.5 5.6 - - - +
1791A ILE* 1.3 76.3 - - - +
1793A MET* 1.3 60.3 + - - +
1795A GLN* 3.1 7.8 + - - +
1796A ALA* 3.0 25.6 + - - +
1799A ARG* 5.1 0.2 + - - -
1814A ILE* 4.9 0.2 - - - +
596O SER* 5.9 4.3 - - - -
598O THR* 3.4 21.5 + - - +
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Residues in contact with MET1793 (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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949A PHE* 4.4 15.2 - - + -
1789A ALA* 2.9 23.2 + - - +
1790A TYR* 3.1 31.4 - - - +
1792A ALA* 1.3 74.4 - - - +
1794A ASP* 1.3 63.8 + - - +
1796A ALA 3.6 0.3 + - - -
1797A ILE* 3.3 30.4 + - - +
1814A ILE* 4.1 19.2 - - + +
1817A VAL* 4.7 11.4 - - + -
1818A LEU* 5.2 1.3 - - + -
1840A MET* 4.3 7.4 - - - -
1844A PHE* 3.9 19.1 - - + -
1845A LEU* 3.7 29.2 - - + -
1848A VAL* 3.9 22.9 - - + -
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Residues in contact with ASP1794 (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 LEU* 3.3 40.9 - - + +
1771A PHE* 6.1 0.2 - - + -
1774A VAL* 3.2 23.3 - - - +
1790A TYR 3.2 8.2 + - - +
1791A ILE* 2.9 20.2 + - + +
1793A MET* 1.3 74.7 - - - +
1795A GLN* 1.3 66.5 + - - +
1797A ILE* 3.2 10.4 - - - +
1798A ARG* 3.2 27.4 + - - +
1844A PHE* 3.0 29.3 - - - -
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Residues in contact with GLN1795 (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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1771A PHE* 5.3 1.0 - - - -
1791A ILE* 2.7 23.3 + - + +
1792A ALA* 3.1 13.9 + - - +
1794A ASP* 1.3 74.3 - - - +
1796A ALA* 1.3 57.1 + - - +
1798A ARG* 3.9 3.7 - - - +
1799A ARG* 3.0 60.4 + - - +
597O PRO* 5.8 9.6 - - + +
598O THR* 4.5 5.6 - - - +
633O ILE* 3.9 15.4 + - - +
634O LEU* 3.4 48.6 - - + +
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Residues in contact with ALA1796 (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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949A PHE* 6.3 0.4 - - + -
1792A ALA 3.0 11.7 + - - +
1795A GLN* 1.3 75.3 - - - +
1797A ILE* 1.3 59.2 + - - +
1799A ARG* 3.2 17.4 + - - +
1800A LEU* 3.0 36.3 + - + +
1810A GLU* 4.8 17.9 - - + +
1811A LEU* 5.4 4.0 - - + +
1814A ILE* 3.6 27.8 - - + -
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Residues in contact with ILE1797 (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 LEU* 3.9 26.7 - - + -
1793A MET 3.3 14.1 + - - +
1794A ASP* 3.2 20.2 - - - +
1796A ALA* 1.3 75.7 - - - +
1798A ARG* 1.3 67.9 + - - +
1800A LEU* 3.5 10.7 + - - +
1801A GLY* 3.4 16.6 + - - -
1814A ILE* 4.8 3.1 - - + -
1844A PHE* 5.5 1.8 - - + -
1848A VAL* 3.9 22.7 - - + -
1851A THR* 3.8 29.7 - - + +
1852A ILE* 3.5 26.0 - - + -
1855A THR* 5.1 2.4 + - - -
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Residues in contact with ARG1798 (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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1766A GLU* 3.9 7.1 + - - +
1767A ILE* 3.2 54.2 - - + +
1770A LEU* 3.4 36.2 - - - +
1794A ASP 3.2 15.3 + - - +
1795A GLN* 4.0 2.9 - - - +
1797A ILE* 1.3 85.0 - - - +
1799A ARG* 1.3 59.9 + - - +
1801A GLY* 3.5 2.3 + - - +
1802A ARG* 3.0 36.4 + - + +
1804A GLU* 5.2 0.4 - - - -
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Residues in contact with ARG1799 (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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1795A GLN* 3.0 69.2 + - - +
1796A ALA* 3.3 15.9 - - - +
1798A ARG* 1.3 75.5 - - - +
1800A LEU* 1.3 53.6 + - + +
1802A ARG 3.5 0.9 + - - -
1803A ARG* 2.8 27.9 + - - -
1804A GLU* 3.3 28.0 + - + +
1805A MET* 3.5 51.3 - - + +
1810A GLU* 3.4 38.6 + - - +
597O PRO* 5.8 7.7 - - - +
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Residues in contact with LEU1800 (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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1796A ALA* 3.0 20.6 + - + +
1797A ILE* 3.6 8.3 - - - +
1798A ARG 3.3 0.2 - - - -
1799A ARG* 1.3 74.9 - - + +
1801A GLY* 1.3 61.0 + - - +
1803A ARG* 2.9 22.6 + - - +
1805A MET 6.0 0.4 - - - -
1811A LEU* 4.9 15.5 - - + -
1814A ILE* 6.3 0.2 - - + -
1852A ILE* 3.5 42.0 - - + -
1855A THR* 3.8 19.8 - - + +
1856A LEU* 3.9 24.7 - - + -
1884A MET* 5.2 6.0 - - - +
1887A CYS* 4.0 22.9 - - + -
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Residues in contact with GLY1801 (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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1797A ILE 3.4 10.4 + - - -
1798A ARG* 3.5 4.0 + - - -
1799A ARG 3.4 0.2 - - - -
1800A LEU* 1.3 78.8 - - - +
1802A ARG* 1.3 61.1 + - - +
1803A ARG* 3.4 2.1 + - - +
1855A THR* 4.1 13.9 + - - +
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Residues in contact with ARG1802 (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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1798A ARG* 3.0 26.1 + - + +
1799A ARG 3.7 0.4 - - - +
1801A GLY* 1.3 75.3 + - - +
1803A ARG* 1.3 64.8 + - - +
1804A GLU* 3.0 45.3 + - + +
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Residues in contact with ARG1803 (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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1799A ARG 2.8 8.7 + - - -
1800A LEU* 2.9 17.2 + - - +
1801A GLY 4.6 2.0 - - - +
1802A ARG* 1.3 76.6 - - - +
1804A GLU* 1.3 64.8 + - - +
1805A MET 3.7 7.5 - - - +
1883A SER* 4.4 10.9 + - - -
1884A MET* 3.8 32.5 - - + +
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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