Contacts of the helix formed by residues 1772 - 1783 (chain B) in PDB entry 1GZH
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 ASN1772 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1738B MET* 5.5 0.2 - - - -
1770B PRO 3.4 6.9 + - - +
1771B PHE* 1.3 80.6 + - - +
1773B LYS* 1.3 68.4 + - - +
1774B GLN* 3.1 23.5 + - - +
1775B TYR* 2.8 43.6 + - + +
1776B THR* 2.9 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1773 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1736B LEU* 3.5 44.6 + - + +
1737B THR* 4.1 1.3 - - - +
1738B MET* 4.0 25.8 - - + -
1771B PHE* 4.1 18.0 - - + -
1772B ASN* 1.3 71.9 + - - +
1774B GLN* 1.3 75.5 + - - +
1776B THR* 3.5 1.7 + - - -
1777B GLU* 3.0 45.9 + - - +
1789B GLU* 5.5 4.4 + - - -
1814B LYS* 3.7 11.9 - - - +
2972B SO4 3.4 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1774 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1772B ASN* 3.1 19.3 + - - +
1773B LYS* 1.3 97.4 - - - +
1775B TYR* 1.3 61.6 + - - +
1777B GLU* 3.5 16.0 + - - +
1778B SER* 3.1 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1775 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1769B PRO* 5.8 9.0 - - + -
1772B ASN* 2.8 30.9 + - + +
1774B GLN* 1.3 70.6 - - - +
1776B THR* 1.3 64.2 + - - +
1778B SER* 2.4 42.1 + - - -
1779B GLN* 3.0 41.5 + - + +
1832B HIS* 6.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1776 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1736B LEU* 4.0 12.8 - - + -
1771B PHE* 3.5 23.4 - - - -
1772B ASN 2.9 14.8 + - - -
1773B LYS 3.9 2.9 - - - -
1775B TYR* 1.3 77.9 - - - +
1777B GLU* 1.3 57.9 + - - +
1779B GLN* 3.1 17.2 + - - +
1780B LEU* 2.8 53.7 + - + +
1805B ILE* 4.2 5.4 - - + -
1828B HIS* 4.4 5.6 + - + +
1831B VAL* 3.8 24.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1777 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1736B LEU* 4.0 17.9 - - + -
1773B LYS* 3.0 50.2 + - - +
1774B GLN* 3.6 16.0 - - - +
1775B TYR 3.2 0.2 - - - -
1776B THR* 1.3 75.3 - - - +
1778B SER* 1.3 57.9 + - - +
1780B LEU* 3.1 3.5 + - - +
1781B ARG* 2.8 63.2 + - - +
1787B ILE* 4.1 26.6 - - + +
1789B GLU* 4.3 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1778 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1774B GLN 3.1 12.4 + - - -
1775B TYR* 2.4 39.6 + - - -
1777B GLU* 1.3 77.9 - - - +
1779B GLN* 1.3 62.1 + - - +
1781B ARG* 3.4 8.7 + - - +
1782B ALA* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1779 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1724B LEU* 4.2 7.7 - - + +
1729B PHE* 3.8 10.5 - - - -
1775B TYR* 3.0 50.2 + - + +
1776B THR* 3.5 11.7 + - - +
1778B SER* 1.3 83.0 + - - +
1780B LEU* 1.3 65.7 + - - +
1782B ALA* 3.4 15.4 + - - +
1783B GLY 3.4 7.3 + - - -
1831B VAL* 4.0 17.7 - - + +
1832B HIS* 4.9 12.8 + - - +
1835B CYS* 3.4 33.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1780 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1729B PHE* 3.8 25.9 - - + -
1734B PHE* 3.5 56.3 - - + -
1736B LEU* 4.5 7.4 - - + -
1776B THR* 2.8 41.9 + - + +
1777B GLU* 3.5 5.2 - - - +
1779B GLN* 1.3 77.2 - - - +
1781B ARG* 1.3 61.7 + - - +
1783B GLY* 3.0 9.4 + - - -
1785B GLY* 2.8 24.5 + - - -
1787B ILE* 4.0 18.4 - - + -
1805B ILE* 4.8 0.9 - - + -
1831B VAL* 4.2 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1781 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1777B GLU* 2.8 49.9 + - - +
1778B SER* 3.9 7.1 - - - +
1780B LEU* 1.3 68.1 - - - +
1782B ALA* 1.3 58.1 + - - +
1783B GLY 2.9 4.5 - - - -
1784B ALA* 2.8 22.2 + - - -
1785B GLY 3.9 12.8 - - - +
1787B ILE* 3.5 35.3 - - + +
1789B GLU* 4.1 7.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1782 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1724B LEU* 3.9 19.7 - - + +
1725B ASN 4.1 1.2 - - - +
1726B LYS* 3.4 29.1 + - - +
1778B SER 3.0 17.3 + - - +
1779B GLN* 3.5 8.5 - - - +
1781B ARG* 1.3 76.0 - - - +
1783B GLY* 1.3 56.4 + - - +
1784B ALA 3.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1783 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1724B LEU* 5.3 1.1 - - - -
1725B ASN 3.9 8.3 - - - -
1726B LYS 3.2 12.6 - - - -
1728B LEU 3.5 3.2 + - - -
1729B PHE* 2.8 37.9 + - - -
1730B LEU 3.1 4.7 + - - -
1779B GLN 3.4 3.4 + - - -
1780B LEU 3.0 6.5 + - - -
1781B ARG 2.9 1.4 - - - -
1782B ALA* 1.3 80.1 - - - +
1784B ALA* 1.3 66.9 + - - +
1785B GLY 3.1 2.9 + - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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