Contacts of the helix formed by residues 1777 - 1799 (chain r) in PDB entry 6FF7
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 SER1777 (chain r).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1775r GLY* 3.3 3.4 - - - -
1776r ILE* 1.3 84.3 - - - +
1778r HIS* 1.3 65.4 + - - +
1779r ARG* 4.4 2.2 - - - -
1780r HIS* 3.7 16.8 - - - +
1781r LEU* 3.4 18.5 + - - +
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Residues in contact with HIS1778 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1777r SER* 1.3 72.0 - - - +
1779r ARG* 1.3 57.7 + - - +
1780r HIS 3.0 3.8 + - - -
1781r LEU* 3.2 5.8 + - - +
1782r SER* 2.9 28.8 + - - -
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Residues in contact with ARG1779 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1777r SER* 4.4 2.3 - - - -
1778r HIS* 1.3 77.6 - - - +
1780r HIS* 1.3 58.0 + - - +
1782r SER* 3.8 9.9 - - - -
1783r ASP* 2.9 31.5 + - - +
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Residues in contact with HIS1780 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1773r LEU* 5.9 1.5 - - - +
1775r GLY* 3.5 34.1 - - - +
1777r SER* 3.7 22.6 + - - +
1778r HIS 3.0 0.2 - - - -
1779r ARG* 1.3 77.6 - - - +
1781r LEU* 1.3 60.9 + - - +
1783r ASP* 3.9 3.0 - - - +
1784r HIS* 3.0 27.9 + - - +
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Residues in contact with LEU1781 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1764r MET* 5.9 7.2 - - + -
1765r THR* 5.5 12.1 - - - -
1775r GLY 4.9 1.1 + - - -
1776r ILE 5.6 0.4 - - - +
1777r SER 3.4 9.9 + - - +
1778r HIS* 3.2 7.5 + - - +
1780r HIS* 1.3 79.2 - - - +
1782r SER* 1.3 57.9 + - - +
1784r HIS* 3.1 7.7 + - - +
1785r LEU* 2.9 30.2 + - - +
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Residues in contact with SER1782 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1778r HIS 2.9 16.8 + - - -
1779r ARG* 4.0 9.0 - - - -
1781r LEU* 1.3 77.7 - - - +
1783r ASP* 1.3 63.1 + - - +
1784r HIS 3.2 0.2 + - - -
1785r LEU* 3.3 4.9 + - - +
1786r SER* 2.9 24.6 + - - -
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Residues in contact with ASP1783 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1779r ARG 2.9 20.6 + - - +
1780r HIS* 3.9 4.5 - - - +
1782r SER* 1.3 75.8 - - - +
1784r HIS* 1.3 56.3 + - - +
1786r SER* 3.6 6.9 - - - -
1787r GLU* 2.9 29.5 + - - +
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Residues in contact with HIS1784 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1773r LEU* 5.0 16.6 - - + -
1780r HIS 3.0 16.7 + - - +
1781r LEU* 3.1 12.8 + - - +
1783r ASP* 1.3 76.5 - - - +
1785r LEU* 1.3 65.9 + - - +
1787r GLU* 3.3 5.9 + - - +
1788r LEU* 2.9 22.1 + - - +
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Residues in contact with LEU1785 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1752r VAL* 5.5 13.3 - - + +
1755r LEU* 5.3 12.8 - - + -
1781r LEU 2.9 14.7 + - - +
1782r SER* 3.9 4.9 - - - +
1784r HIS* 1.3 76.0 - - - +
1786r SER* 1.3 63.5 + - - +
1788r LEU* 3.1 8.8 + - - +
1789r VAL* 3.0 24.1 + - - +
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Residues in contact with SER1786 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1752r VAL* 6.0 2.9 - - - +
1782r SER 2.9 17.3 + - - -
1783r ASP* 3.6 8.7 - - - -
1784r HIS 3.2 0.2 - - - -
1785r LEU* 1.3 74.8 - - - +
1787r GLU* 1.3 67.8 + - - +
1788r LEU 3.0 0.5 + - - -
1789r VAL* 3.3 2.7 + - - +
1790r GLU* 2.9 24.2 + - - +
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Residues in contact with GLU1787 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1783r ASP 2.9 17.3 + - - +
1784r HIS* 3.7 5.6 - - - +
1786r SER* 1.3 75.7 - - - +
1788r LEU* 1.3 56.8 + - - +
1790r GLU* 3.3 8.2 - - - +
1791r GLN* 3.0 30.7 + - - +
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Residues in contact with LEU1788 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1784r HIS 2.9 15.0 + - - +
1785r LEU* 3.2 12.6 - - - +
1786r SER 2.9 1.4 - - - -
1787r GLU* 1.3 74.5 - - - +
1789r VAL* 1.3 65.7 + - - +
1790r GLU 3.0 1.5 + - - -
1791r GLN* 3.2 3.3 + - - +
1792r THR* 2.9 24.2 + - - -
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Residues in contact with VAL1789 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1748r LYS* 4.8 8.1 - - + +
1751r ALA* 3.9 28.9 - - + -
1752r VAL* 4.8 8.7 - - + +
1785r LEU 3.0 16.5 + - - +
1786r SER* 4.3 2.7 - - - +
1788r LEU* 1.3 73.3 - - - +
1790r GLU* 1.3 63.4 + - - +
1792r THR* 4.4 6.3 - - - -
1793r LEU* 2.9 28.2 + - + +
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Residues in contact with GLU1790 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1786r SER 2.9 14.1 + - - +
1787r GLU* 3.3 15.3 - - - +
1789r VAL* 1.3 78.5 - - - +
1791r GLN* 1.3 59.2 + - + +
1793r LEU* 3.9 2.2 - - - +
1794r SER* 3.0 28.3 + - - -
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Residues in contact with GLN1791 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1787r GLU 3.0 12.3 + - - +
1788r LEU* 4.3 2.0 - - - +
1790r GLU* 1.3 78.6 - - + +
1792r THR* 1.3 61.0 + - - +
1794r SER* 3.7 6.9 - - - -
1795r ASP* 2.9 31.2 + - - +
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Residues in contact with THR1792 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1732r MET* 5.2 8.7 - - - -
1733r HIS* 5.2 17.5 - - - +
1736r PHE* 5.2 14.6 - - - -
1788r LEU 2.9 16.8 + - - -
1789r VAL* 4.1 5.8 - - - -
1791r GLN* 1.3 78.0 - - - +
1793r LEU* 1.3 57.5 + - - +
1795r ASP* 3.5 5.0 + - - +
1796r LEU* 2.9 29.3 + - - +
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Residues in contact with LEU1793 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1736r PHE* 6.2 0.9 - - - +
1748r LYS* 6.4 1.8 - - + -
1789r VAL* 2.9 18.4 + - + +
1790r GLU* 4.1 2.0 - - - +
1792r THR* 1.3 74.4 - - - +
1794r SER* 1.3 60.5 + - - +
1796r LEU* 3.7 6.5 - - - +
1797r GLU* 2.9 30.3 + - - +
1802r ILE* 5.6 1.2 - - - +
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Residues in contact with SER1794 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1790r GLU 3.0 18.9 + - - -
1791r GLN* 3.7 7.9 - - - -
1792r THR 3.3 0.2 - - - -
1793r LEU* 1.3 76.6 - - - +
1795r ASP* 1.3 57.5 + - - +
1797r GLU* 3.0 7.5 + - - +
1798r GLN* 2.9 30.9 + - - +
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Residues in contact with ASP1795 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1733r HIS* 6.2 3.1 - - + -
1791r GLN 2.9 18.7 + - - +
1792r THR* 3.9 5.2 - - - +
1794r SER* 1.3 75.5 - - - +
1796r LEU* 1.3 61.6 + - - +
1798r GLN* 3.6 9.1 + - - +
1799r SER* 3.4 21.7 + - - -
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Residues in contact with LEU1796 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1733r HIS* 5.6 12.8 - - + +
1736r PHE* 6.2 3.6 - - + -
1737r ASN* 5.7 7.6 - - + +
1792r THR 2.9 18.7 + - - +
1793r LEU* 3.7 8.3 - - - +
1794r SER 3.1 0.4 - - - -
1795r ASP* 1.3 79.8 - - - +
1797r GLU* 1.3 57.4 + - - +
1799r SER* 3.5 7.2 + - - -
1801r CYS* 3.1 35.9 + - + +
1802r ILE* 3.6 12.9 + - + -
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Residues in contact with GLU1797 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1793r LEU 2.9 17.4 + - - +
1794r SER* 3.0 6.9 + - - +
1796r LEU* 1.3 74.6 - - - +
1798r GLN* 1.3 64.4 + - - +
1799r SER 3.1 1.6 - - - -
1800r LYS* 3.1 13.0 + - - +
1802r ILE* 3.6 23.4 - - + +
1803r SER* 5.4 0.4 - - - -
1804r ILE* 4.9 16.6 - - + +
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Residues in contact with GLN1798 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1794r SER 2.9 14.4 + - - +
1795r ASP* 3.8 10.3 - - - +
1796r LEU 3.4 0.2 - - - -
1797r GLU* 1.3 77.6 - - - +
1799r SER* 1.3 59.1 + - - +
1800r LYS* 3.1 2.5 + - - +
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Residues in contact with SER1799 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1795r ASP 3.4 14.6 + - - -
1796r LEU* 3.8 7.2 - - - -
1797r GLU 3.1 1.0 - - - -
1798r GLN* 1.3 77.7 - - - +
1800r LYS* 1.3 69.5 + - - +
1801r CYS* 3.2 7.0 + - - +
1815r LEU* 4.6 6.2 - - - +
1826r TYR* 5.7 6.5 - - - -
1830r GLU* 4.5 25.6 - - - +
1833r SER* 5.8 2.6 - - - -
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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