Contacts of the strand formed by residues 1847 - 1855 (chain B) in PDB entry 2IWP
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 ILE1847 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1926A SER* 3.6 3.3 - - - -
1927A VAL* 2.9 43.4 + - + +
1837B MET* 5.6 0.2 - - + -
1845B LEU* 4.2 12.6 - - + -
1846B GLY* 1.3 78.6 - - - +
1848B SER* 1.3 63.0 + - - +
1849B ILE* 4.2 18.6 - - + -
1864B ILE* 4.4 17.7 - - + -
1866B MET 3.5 8.5 - - - +
1867B MET* 4.2 16.2 - - + +
1868B HIS 4.8 0.2 - - - +
1873B ALA* 3.1 33.0 - - + -
1879B LEU* 4.8 5.6 - - + -
1905B LEU* 5.2 0.2 - - + -
1914B MET* 4.4 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1848 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1924A GLU* 3.5 23.6 + - - -
1925A THR 3.2 13.5 - - - -
1926A SER* 3.5 16.6 + - - -
1847B ILE* 1.3 75.5 - - - +
1849B ILE* 1.3 62.7 + - - +
1864B ILE* 3.6 4.7 - - - +
1865B ALA* 2.8 25.4 + - - -
1866B MET* 3.0 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1849 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1924A GLU* 3.4 1.8 - - - -
1925A THR 2.9 33.5 + - - +
1927A VAL* 4.6 4.9 - - + +
1847B ILE* 4.2 19.1 - - + -
1848B SER* 1.3 77.0 - - - +
1850B ALA* 1.3 61.0 + - - +
1862B ILE* 4.4 10.8 - - + -
1863B PHE 3.3 7.6 - - - +
1864B ILE* 4.6 1.8 - - + -
1885B ILE* 3.5 27.6 - - + -
1898B HIS* 3.4 11.0 - - + +
1901B ALA* 3.7 30.3 - - + -
1902B VAL* 3.8 24.2 - - + +
1905B LEU* 4.2 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1850 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1923A SER 3.5 22.0 - - - +
1924A GLU* 4.2 0.7 - - + -
1849B ILE* 1.3 75.5 - - - +
1851B GLY* 1.3 68.2 + - - +
1857B LEU* 4.3 2.5 - - + -
1862B ILE* 3.3 4.3 - - - +
1863B PHE* 2.9 58.2 + - + -
1865B ALA* 4.1 11.9 - - + -
1898B HIS* 4.0 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1851 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1923A SER 4.9 0.6 + - - -
1850B ALA* 1.3 72.6 - - - +
1852B GLY* 1.3 56.5 + - - -
1855B SER* 3.5 13.4 + - - -
1856B PRO* 6.0 0.4 - - - +
1857B LEU* 4.3 5.8 - - - +
1860B VAL* 3.4 26.0 - - - -
1861B PRO 3.6 3.8 - - - -
1862B ILE* 2.8 18.3 - - - +
1863B PHE* 4.5 0.7 - - - -
1898B HIS* 2.8 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1852 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1851B GLY* 1.3 73.1 - - - -
1853B VAL* 1.3 68.5 + - - -
1855B SER* 3.2 5.7 + - - -
1858B GLY 3.0 20.3 - - - +
1860B VAL 2.7 21.7 + - - +
1862B ILE* 2.9 23.7 - - - +
1896B MET 3.7 4.9 - - - -
1898B HIS 3.9 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1853 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1852B GLY* 1.3 71.0 - - - -
1854B GLY* 1.3 64.8 + - - +
1859B ASP* 3.7 25.1 - - + +
1860B VAL 4.2 0.4 + - - -
1895B GLY* 4.0 23.6 - - - +
1896B MET 3.0 17.6 + - - +
1897B THR* 3.2 24.8 - - + -
1898B HIS 3.0 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1854 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1852B GLY 3.3 0.2 + - - -
1853B VAL* 1.3 75.4 - - - +
1855B SER* 1.3 65.8 + - - +
1856B PRO* 3.8 1.4 - - - +
1858B GLY* 5.0 0.9 - - - -
1859B ASP* 2.9 18.7 + - - -
1897B THR* 5.5 1.1 - - - -
1898B HIS* 4.7 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1855 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1851B GLY* 3.5 28.5 - - - -
1852B GLY 3.2 12.9 + - - -
1853B VAL 3.2 0.8 - - - -
1854B GLY* 1.3 82.2 - - - +
1856B PRO* 1.3 70.6 - - - +
1857B LEU* 3.0 16.4 + - - +
1858B GLY* 2.6 41.0 + - - -
1898B HIS* 3.8 9.4 - - - -
----------------------------------------------------------
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