Contacts of the helix formed by residues 1777 - 1799 (chain D) in PDB entry 6AH0
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1775D GLY* 3.3 4.4 - - - -
1776D ILE* 1.3 85.3 - - - +
1778D HIS* 1.3 64.4 + - - +
1779D ARG 3.7 1.6 - - - +
1780D HIS* 3.8 6.8 - - - +
1781D LEU* 3.4 13.9 + - - -
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Residues in contact with HIS1778 (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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1777D SER* 1.3 68.7 - - - +
1779D ARG* 1.3 57.7 + - - +
1780D HIS 3.0 4.3 + - - -
1781D LEU* 3.2 2.8 + - - -
1782D SER* 2.9 25.5 + - - -
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Residues in contact with ARG1779 (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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1777D SER* 4.7 0.2 - - - +
1778D HIS* 1.3 74.0 - - - +
1780D HIS* 1.3 56.9 + - - +
1782D SER* 3.8 3.4 - - - +
1783D ASP* 2.9 25.7 + - - +
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Residues in contact with HIS1780 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1775D GLY* 4.8 16.4 - - - +
1777D SER* 3.8 10.9 + - - +
1778D HIS 3.0 1.6 - - - -
1779D ARG* 1.3 76.6 - - - +
1781D LEU* 1.3 58.3 + - - +
1783D ASP* 3.9 0.5 - - - -
1784D HIS* 3.0 24.1 + - - -
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Residues in contact with LEU1781 (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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1775D GLY 4.9 1.6 + - - -
1777D SER 3.4 10.9 + - - -
1778D HIS 3.2 5.2 + - - -
1780D HIS* 1.3 75.5 - - - +
1782D SER* 1.3 58.5 + - - +
1784D HIS* 3.1 2.8 + - - +
1785D LEU* 2.9 26.3 + - - -
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Residues in contact with SER1782 (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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1778D HIS 2.9 15.3 + - - -
1779D ARG* 4.1 2.7 - - - +
1781D LEU* 1.3 76.7 - - - +
1783D ASP* 1.3 61.8 + - - +
1784D HIS 3.2 0.2 + - - -
1785D LEU* 3.3 1.1 + - - +
1786D SER* 2.9 21.1 + - - -
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Residues in contact with ASP1783 (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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1779D ARG* 2.9 18.9 + - - +
1780D HIS 3.9 0.9 - - - -
1782D SER* 1.3 74.8 - - - +
1784D HIS* 1.3 56.8 + - - +
1786D SER* 3.8 1.5 - - - +
1787D GLU* 2.9 25.1 + - - -
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Residues in contact with HIS1784 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1780D HIS 3.0 16.7 + - - -
1781D LEU* 3.1 4.4 + - - +
1783D ASP* 1.3 74.4 - - - +
1785D LEU* 1.3 65.2 + - - +
1787D GLU* 3.3 1.3 + - - +
1788D LEU* 2.9 19.6 + - - -
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Residues in contact with LEU1785 (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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1752D VAL* 5.9 5.0 - - - -
1781D LEU 2.9 13.9 + - - -
1782D SER* 3.9 2.2 - - - +
1784D HIS* 1.3 73.8 - - - +
1786D SER* 1.3 63.0 + - - +
1788D LEU* 3.1 2.7 + - - +
1789D VAL* 3.0 21.3 + - - -
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Residues in contact with SER1786 (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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1782D SER 2.9 16.5 + - - -
1783D ASP* 3.8 2.5 - - - +
1784D HIS 3.2 0.2 - - - -
1785D LEU* 1.3 74.8 - - - +
1787D GLU* 1.3 64.7 + - - +
1788D LEU 3.0 0.5 + - - -
1789D VAL* 3.3 0.5 + - - -
1790D GLU* 2.9 21.0 + - - -
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Residues in contact with GLU1787 (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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1783D ASP 2.9 16.6 + - - -
1784D HIS 3.8 1.6 - - - -
1786D SER* 1.3 73.9 - - - +
1788D LEU* 1.3 57.3 + - - +
1790D GLU* 3.7 2.1 - - - +
1791D GLN* 3.0 25.5 + - - -
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Residues in contact with LEU1788 (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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1784D HIS 2.9 15.1 + - - -
1785D LEU* 3.4 5.2 - - - +
1786D SER 3.0 1.8 - - - -
1787D GLU* 1.3 74.2 - - - +
1789D VAL* 1.3 64.9 + - - +
1790D GLU 3.1 0.3 + - - -
1791D GLN* 3.2 1.9 + - - -
1792D THR* 2.9 20.8 + - - -
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Residues in contact with VAL1789 (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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1751D ALA* 6.2 4.7 - - - +
1785D LEU 3.0 16.0 + - - -
1786D SER 4.0 1.1 - - - -
1788D LEU* 1.3 71.9 - - - +
1790D GLU* 1.3 61.3 + - - +
1792D THR* 4.4 1.8 - - - +
1793D LEU* 2.9 22.3 + - - +
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Residues in contact with GLU1790 (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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1786D SER 2.9 15.2 + - - -
1787D GLU* 3.7 4.0 - - - +
1788D LEU 3.0 0.2 - - - -
1789D VAL* 1.3 77.5 - - - +
1791D GLN* 1.3 56.8 + - - +
1793D LEU* 3.9 0.3 - - - -
1794D SER* 3.0 24.8 + - - -
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Residues in contact with GLN1791 (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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1787D GLU 3.0 14.4 + - - -
1788D LEU 3.9 1.6 - - - -
1790D GLU* 1.3 75.4 - - - +
1792D THR* 1.3 59.7 + - - +
1794D SER* 4.3 1.8 - - - +
1795D ASP* 2.9 25.8 + - - -
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Residues in contact with THR1792 (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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1733D HIS* 5.5 11.2 - - - +
1788D LEU 2.9 15.4 + - - -
1789D VAL* 4.0 1.6 - - - +
1791D GLN* 1.3 79.4 - - - +
1793D LEU* 1.3 56.5 + - - +
1795D ASP* 3.8 0.7 - - - +
1796D LEU* 2.9 24.8 + - - -
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Residues in contact with LEU1793 (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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1789D VAL* 2.9 17.4 + - - +
1790D GLU 4.0 0.4 - - - -
1792D THR* 1.3 72.6 - - - +
1794D SER* 1.3 60.4 + - - +
1796D LEU* 3.3 2.2 + - - +
1797D GLU* 2.9 25.8 + - - -
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Residues in contact with SER1794 (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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1790D GLU 3.0 17.1 + - - -
1791D GLN* 3.9 2.2 - - - +
1792D THR 3.3 0.2 - - - -
1793D LEU* 1.3 75.5 - - - +
1795D ASP* 1.3 56.0 + - - +
1797D GLU* 3.0 2.9 + - - +
1798D GLN* 2.9 27.4 + - - -
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Residues in contact with ASP1795 (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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1791D GLN 2.9 16.3 + - - -
1792D THR 3.8 1.3 - - - -
1794D SER* 1.3 74.2 - - - +
1796D LEU* 1.3 60.1 + - - +
1798D GLN* 3.6 2.0 + - - +
1799D SER* 3.4 16.1 + - - -
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Residues in contact with LEU1796 (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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1792D THR 2.9 16.7 + - - -
1793D LEU* 3.3 3.3 + - - +
1794D SER 3.1 0.2 - - - -
1795D ASP* 1.3 78.4 - - - +
1797D GLU* 1.3 57.8 + - - +
1798D GLN 3.4 0.2 - - - -
1799D SER* 3.5 4.7 + - - +
1801D CYS* 3.1 27.3 + - - -
1802D ILE* 3.6 6.5 + - - -
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Residues in contact with GLU1797 (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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1793D LEU 2.9 14.2 + - - -
1794D SER* 3.5 3.4 - - - +
1796D LEU* 1.3 74.7 - - - +
1798D GLN* 1.3 63.2 + - - +
1799D SER 3.1 1.6 - - - -
1800D LYS* 3.1 12.8 + - - -
1802D ILE 3.6 20.4 - - - +
1803D SER* 5.7 0.4 - - - +
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Residues in contact with GLN1798 (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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1794D SER 2.9 14.8 + - - -
1795D ASP* 3.6 3.1 + - - +
1796D LEU 3.4 0.2 - - - -
1797D GLU* 1.3 76.1 - - - +
1799D SER* 1.3 59.6 + - - +
1800D LYS 3.1 1.1 + - - -
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Residues in contact with SER1799 (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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1795D ASP 3.4 13.2 + - - -
1796D LEU 3.5 4.2 + - - -
1797D GLU 3.1 0.8 - - - -
1798D GLN* 1.3 76.2 - - - +
1800D LYS* 1.3 63.0 + - - +
1801D CYS* 3.2 4.0 + - - -
1830D GLU* 5.2 9.9 - - - +
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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