Contacts of the strand formed by residues 1814 - 1822 (chain A) in PDB entry 4ASI
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 GLU1814 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1810A GLU* 3.8 2.0 - - - -
1811A ASP 2.9 33.1 + - - +
1812A GLU 3.2 4.5 + - - +
1813A GLY* 1.3 75.0 - - - +
1815A SER* 1.3 63.3 + - - +
1816A ARG* 3.7 21.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1815 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1791A THR* 4.9 0.7 - - - -
1792A PRO* 3.3 35.5 - - - +
1808A HIS* 2.8 33.0 + - - -
1809A VAL 3.7 4.5 - - - -
1810A GLU* 4.8 3.4 - - - +
1813A GLY 4.0 0.2 + - - -
1814A GLU* 1.3 74.9 - - - +
1816A ARG* 1.3 60.1 + - - +
1817A TYR* 4.6 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1816 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1773A VAL 5.1 1.2 + - - -
1774A ALA* 4.6 5.9 - - - +
1787A TYR* 3.2 23.9 + - - -
1789A TYR* 3.2 57.7 + - + -
1790A LEU 4.1 4.0 - - - -
1791A THR* 5.4 0.2 - - - +
1792A PRO* 5.1 0.2 - - - -
1808A HIS* 3.5 4.5 - - - -
1809A VAL* 2.9 42.4 + - + +
1811A ASP* 3.1 31.5 + - - -
1812A GLU* 3.0 30.0 + - - +
1814A GLU* 3.7 19.2 - - + +
1815A SER* 1.3 79.0 + - - +
1817A TYR* 1.3 67.1 + - - +
1818A LYS 3.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1817 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1789A TYR* 3.2 2.8 - - - +
1790A LEU* 3.0 36.3 + - + +
1792A PRO* 3.9 39.8 - - + +
1795A TYR* 3.1 49.4 - + + -
1806A CYS* 3.5 23.7 - - + -
1807A GLU 3.6 2.5 - - - -
1808A HIS* 3.6 41.9 - + + +
1816A ARG* 1.3 75.0 - - - +
1818A LYS* 1.3 66.8 + - - +
1819A ILE 3.2 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1818 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1787A TYR* 3.6 46.9 - - + -
1788A LEU 3.8 4.5 - - - -
1789A TYR* 4.0 4.6 - - - +
1806A CYS* 3.0 23.0 - - - -
1807A GLU* 2.9 44.7 + - + +
1809A VAL* 4.3 19.8 - - + +
1816A ARG 3.8 2.6 + - - -
1817A TYR* 1.3 69.3 - - - +
1819A ILE* 1.3 69.5 + - - +
1820A THR* 3.4 7.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1819 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1767A ILE* 4.7 6.5 - - + -
1771A PHE* 4.0 15.3 - - + -
1787A TYR* 5.9 0.5 - - - +
1788A LEU* 2.9 29.3 + - + +
1789A TYR* 3.4 38.1 - - - +
1790A LEU* 4.3 10.5 - - + -
1804A VAL* 4.8 4.9 - - + -
1805A HIS 3.9 4.7 - - - +
1806A CYS* 4.0 9.6 - - - -
1817A TYR 3.9 4.9 - - - +
1818A LYS* 1.3 75.1 - - - +
1820A THR* 1.3 63.3 + - - +
1821A ASP 4.0 10.8 - - - +
1822A ILE* 3.7 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1820 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1805A HIS* 2.9 21.0 + - - +
1806A CYS 4.5 1.8 - - - -
1807A GLU* 4.1 29.8 - - + +
1818A LYS* 3.7 18.8 - - + +
1819A ILE* 1.3 75.1 - - - +
1821A ASP* 1.3 86.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1821 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1804A VAL* 3.5 4.0 - - - +
1805A HIS* 2.8 43.4 + - - +
1819A ILE* 4.0 2.1 - - - +
1820A THR* 1.3 101.4 + - - +
1822A ILE* 1.3 64.0 + - - +
1823A ILE* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1822 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1764A ALA* 3.7 31.2 - - + +
1767A ILE* 4.3 25.8 - - + -
1788A LEU* 6.5 0.4 - - + -
1803A SER 3.9 7.4 - - - +
1804A VAL* 4.5 2.5 - - + +
1819A ILE* 3.7 24.2 - - + -
1821A ASP* 1.3 71.6 - - - +
1823A ILE* 1.3 66.1 + - - +
1824A GLY 4.2 0.7 - - - +
----------------------------------------------------------
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