Contacts of the strand formed by residues 1884 - 1888 (chain A) in PDB entry 2IWO
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 ARG1884 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1861A PRO* 3.7 29.5 + - + +
1862A ILE 3.4 6.7 - - - +
1863A PHE* 3.6 31.2 - - + +
1882A GLY* 2.8 32.0 + - - -
1883A ASP* 1.3 72.5 - - - +
1885A ILE* 1.3 61.9 + - - +
1886A VAL 3.7 0.5 + - - -
1916A VAL* 3.1 6.0 - - - -
1917A VAL* 2.8 42.1 + - + +
1919A GLY* 3.6 8.4 - - - -
1923A SER* 3.1 12.5 + - - -
1924A GLU* 2.9 43.4 + - - -
1827B PHE* 4.3 2.9 - - + -
1830B MET* 3.6 38.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1885 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1849A ILE* 3.8 28.5 - - + -
1862A ILE* 2.8 34.7 + - + +
1863A PHE 4.8 0.9 - - - -
1864A ILE* 4.2 17.0 - - + -
1883A ASP 4.6 0.4 - - - +
1884A ARG* 1.3 72.1 - - - +
1886A VAL* 1.3 52.9 + - - +
1887A THR 3.4 24.7 - - - +
1888A ILE* 3.4 22.7 - - + -
1893A THR* 2.6 29.8 + - + +
1905A LEU* 5.1 0.7 - - + -
1914A MET* 3.8 28.7 - - + -
1915A GLN 3.7 2.5 - - - -
1916A VAL* 4.1 12.1 - - + -
1827B PHE* 3.8 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1886 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1832A LEU* 4.3 4.0 - - + -
1884A ARG 4.1 1.6 - - - +
1885A ILE* 1.3 75.2 - - - +
1887A THR* 1.3 73.8 + - + +
1892A SER* 3.6 4.2 + - - -
1893A THR* 3.0 24.1 + - - -
1894A GLU 4.7 0.2 + - - -
1915A GLN* 2.8 17.5 + - + +
1917A VAL* 3.9 33.4 - - + +
1827B PHE* 4.0 18.6 - - + -
1832B LEU* 3.7 23.8 - - + -
1886B VAL* 4.1 17.9 - - + -
1915B GLN* 4.3 9.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1887 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1885A ILE* 3.4 8.8 - - - +
1886A VAL* 1.3 91.4 - - + +
1888A ILE* 1.3 63.5 + - - +
1891A THR 3.2 19.3 - - - +
1893A THR* 4.2 1.1 - - - -
1913A GLU* 2.9 16.5 + - - -
1914A MET* 3.3 4.7 - - - -
1915A GLN* 2.7 54.5 + - - +
1886B VAL* 4.7 0.4 - - + -
1887B THR* 3.5 29.2 - - + -
1892B SER* 4.1 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1888 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1862A ILE* 5.0 1.1 - - + -
1885A ILE* 3.4 27.6 - - + -
1887A THR* 1.3 72.4 - - - +
1889A CYS* 1.3 85.5 + - - +
1890A GLY 3.0 1.3 - - - -
1891A THR* 2.9 27.1 + - - +
1893A THR* 3.8 19.2 - - + +
1896A MET* 4.5 5.2 - - + -
1901A ALA* 4.1 22.0 - - + +
1904A LEU* 3.8 17.9 - - + +
1905A LEU* 3.4 44.9 - - + -
1913A GLU 3.6 5.8 - - - +
1914A MET* 4.5 6.1 - - + -
----------------------------------------------------------
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