Contacts of the strand formed by residues 1803 - 1808 (chain D) in PDB entry 3SUA
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 LEU1803 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1755D LEU* 5.0 3.4 - - + -
1757D VAL* 3.8 29.8 - - + -
1781D LYS* 4.0 19.6 + - + -
1785D LEU* 3.8 29.4 - - + -
1798D PRO* 4.5 15.5 - - + -
1799D ASP 4.0 11.9 - - - +
1800D PRO* 3.0 22.9 + - + +
1801D ARG 4.3 3.5 - - - +
1802D THR* 1.3 86.7 - - - +
1804D ASP* 1.3 59.2 + - - +
1849D LEU* 3.9 20.6 - - + -
1850D VAL 3.5 16.2 - - - +
1851D PRO* 4.3 2.0 - - + -
1852D CYS* 4.7 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1804 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1781D LYS* 5.3 2.0 - - - +
1803D LEU* 1.3 74.2 - - - +
1805D VAL* 1.4 84.4 + - - +
1816D ILE* 3.3 39.7 - - - +
1817D LEU 3.3 12.3 - - - +
1818D SER* 5.4 1.4 - - - -
1848D ALA 3.4 2.1 - - - +
1849D LEU* 3.4 3.6 - - - -
1850D VAL* 2.7 45.5 + - + +
1851D PRO 3.8 12.5 - - - +
1852D CYS* 4.6 9.8 - - - -
1853D LEU* 4.1 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1805 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1777D ILE* 3.8 33.7 - - + +
1780D ALA* 5.3 1.8 - - + -
1781D LYS* 3.8 22.6 - - + +
1784D MET* 4.2 13.0 - - - -
1804D ASP* 1.4 81.1 + - - +
1806D GLU* 1.4 57.2 + - - +
1816D ILE* 3.4 1.4 - - - -
1817D LEU* 3.1 41.1 + - + +
1847D VAL* 3.5 22.9 - - + -
1848D ALA 3.6 3.4 - - - -
1849D LEU* 3.5 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1806 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1805D VAL* 1.4 72.7 - - - +
1807D TRP* 1.3 69.5 + - - +
1808D ARG* 3.1 33.0 + - - -
1814D HIS* 3.9 27.9 + - - +
1815D LEU 3.4 11.7 - - - +
1816D ILE* 3.6 26.4 - - + +
1846D THR 3.7 1.0 - - - +
1847D VAL* 3.4 3.2 - - - -
1848D ALA* 2.8 43.9 + - + +
1850D VAL* 3.6 23.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1807 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 4.4 11.2 - - + -
37A PHE* 3.4 24.5 - + + -
64A TYR* 4.9 1.3 - + - -
67A LEU* 3.6 28.3 - - + -
1805D VAL 4.3 0.6 - - - -
1806D GLU* 1.3 75.0 - - - +
1808D ARG* 1.3 95.0 + - - +
1809D SER* 5.3 2.3 - - - -
1814D HIS 3.5 1.7 + - - -
1815D LEU* 2.8 32.7 + - + +
1817D LEU* 3.8 27.2 - - + +
1839D TYR* 3.6 11.4 - - + -
1840D LYS 3.8 6.1 - - - -
1841D VAL* 3.6 39.0 - - + -
1842D PRO* 3.2 28.3 - - + +
1845D ALA* 3.5 26.4 - - + +
1846D THR 3.3 6.3 - - - -
1847D VAL* 4.4 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1808 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.9 4.0 - - - -
1754D LEU* 4.5 7.7 - - - +
1756D ALA* 4.5 6.9 - - - +
1806D GLU* 3.1 27.5 + - - -
1807D TRP* 1.3 91.1 + - - +
1809D SER* 1.4 59.9 + - - +
1813D GLY* 3.7 9.2 - - - +
1814D HIS 3.7 14.3 - - - +
1845D ALA* 5.2 0.5 - - - -
1846D THR* 2.7 54.6 + - - +
1848D ALA* 3.2 36.3 - - - +
1850D VAL* 4.2 7.3 - - - +
----------------------------------------------------------
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