Contacts of the strand formed by residues 228 - 232 (chain C) in PDB entry 2BHT
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 GLU 228 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C THR* 3.9 18.2 - - - +
195C ILE 3.1 3.5 + - - +
196C VAL* 3.2 30.4 - - + +
197C GLY 2.8 25.1 + - - -
226C VAL* 4.0 2.4 - - - +
227C ASP* 1.3 81.0 - - - +
229C VAL* 1.3 64.8 + - - +
230C LEU* 3.9 20.6 - - + +
266C VAL* 4.5 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C MET* 4.0 22.0 - - + -
197C GLY 3.9 1.8 - - - -
199C GLN* 3.4 24.9 - - + +
221C PHE* 5.5 8.3 - - + -
226C VAL* 4.1 16.6 - - + -
228C GLU* 1.3 76.9 - - - +
230C LEU* 1.3 75.0 + - - +
231C ASP 4.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C VAL* 4.1 9.0 - - + -
197C GLY 3.0 6.6 + - - +
198C LEU* 3.2 31.1 - - + -
199C GLN 2.9 26.2 + - - +
228C GLU* 3.9 33.9 - - + +
229C VAL* 1.3 84.9 - - - +
231C ASP* 1.3 63.3 + - - +
262C GLY 4.6 12.3 - - - +
265C ARG* 4.6 19.1 - - + +
266C VAL* 4.7 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 231 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C LEU* 5.0 0.2 - - - +
199C GLN 3.0 7.9 - - - +
200C PRO 3.4 1.9 - - - +
201C GLU* 2.8 48.8 + - + +
202C GLU* 4.4 7.0 + - - +
229C VAL 4.4 0.4 + - - -
230C LEU* 1.3 76.7 - - - +
232C ILE* 1.3 54.4 + - - +
265C ARG* 2.7 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 232 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C LEU* 4.4 13.9 - - + -
199C GLN 3.2 8.5 + - - +
200C PRO* 3.0 19.6 - - + +
201C GLU* 3.0 21.0 + - - +
204C SER* 3.8 0.2 + - - -
206C ILE* 4.3 3.1 - - + +
209C ILE* 4.1 20.0 - - + -
231C ASP* 1.3 74.9 - - - +
233C HIS* 1.3 82.2 + - - +
234C GLN 3.8 0.7 + - - -
236C ASP* 4.9 2.0 - - + -
237C ALA* 3.9 21.5 - - + +
258C GLY* 3.8 31.4 - - - +
261C ALA* 4.6 4.7 - - + -
265C ARG* 3.8 27.6 - - - +
----------------------------------------------------------
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