Contacts of the strand formed by residues 274 - 279 (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 VAL 274 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLU* 3.3 28.0 - - + +
28C TRP* 3.7 15.5 - - + +
162C THR* 4.3 20.2 - - + +
165C ARG* 3.1 55.4 - - + +
166C ILE* 3.6 4.9 - - - +
167C THR* 3.1 30.7 + - + +
168C HIS 3.8 1.6 + - - +
273C ALA* 1.3 73.8 - - - +
275C VAL* 1.3 61.3 + - - +
276C VAL* 3.7 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C SER* 4.8 1.1 - - - +
26C GLU 2.6 27.6 + - - +
27C VAL* 3.8 17.5 - - + -
28C TRP* 3.0 27.2 + - - -
168C HIS* 3.9 18.4 - - + +
170C VAL* 4.3 14.1 - - + -
263C ALA* 4.0 28.5 - - + +
266C VAL* 4.9 7.0 - - + +
267C ALA* 4.1 18.2 - - + -
273C ALA* 4.3 10.8 - - + +
274C VAL* 1.3 74.7 - - - +
276C VAL* 1.3 67.5 + - - +
277C ALA 4.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 4.3 6.1 - - + -
28C TRP* 3.6 11.2 - - + +
30C LYS* 4.9 0.2 - - + -
158C ILE* 3.3 44.6 - - + -
162C THR* 4.0 18.8 - - + -
166C ILE* 3.9 28.9 - - + -
168C HIS 3.2 7.3 + - - -
169C PHE* 3.3 9.6 - - + -
170C VAL* 3.0 24.9 + - - +
274C VAL* 4.3 1.8 - - + +
275C VAL* 1.3 83.7 - - - +
277C ALA* 1.3 68.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C VAL* 5.2 2.4 - - + +
28C TRP 2.9 13.2 + - - +
29C LEU* 3.7 16.0 - - + -
30C LYS* 3.1 24.4 + - - +
170C VAL* 3.9 11.7 - - + -
259C ALA* 4.2 27.6 - - + +
260C VAL* 4.8 1.6 - - + -
263C ALA* 4.5 8.3 - - + -
275C VAL* 4.2 1.4 - - - +
276C VAL* 1.3 75.3 - - - +
278C ILE* 1.3 69.3 + - - +
279C ILE* 5.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 278 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LYS* 4.1 12.1 - - + +
32C GLU* 4.8 6.5 - - + -
40C VAL* 4.7 9.9 - - + -
154C THR* 4.8 5.6 - - + -
158C ILE* 3.6 20.4 - - + -
169C PHE* 3.2 40.6 - - + -
170C VAL 3.7 8.3 + - - +
171C SER* 5.1 7.0 - - - +
172C SER 6.0 0.2 - - - +
178C THR* 4.1 20.6 - - + +
256C SER* 4.6 0.3 + - - -
259C ALA* 3.7 17.1 - - - +
276C VAL* 4.4 0.2 - - + -
277C ALA* 1.3 78.7 - - - +
279C ILE* 1.3 77.4 + - - +
280C CYS* 3.6 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 279 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU* 3.3 52.7 - - + -
30C LYS 2.9 16.2 + - - +
31C LEU* 4.1 16.8 - - + -
32C GLU* 2.8 30.8 + - - +
33C GLY 5.4 0.7 - - - +
250C ILE* 5.0 3.6 - - + -
252C CYS* 3.8 30.5 - - + -
256C SER* 3.9 17.0 - - - +
259C ALA* 5.1 0.9 - - + -
260C VAL* 4.0 13.9 - - + -
277C ALA* 5.1 0.7 - - + -
278C ILE* 1.3 80.1 - - - +
280C CYS* 1.3 61.9 + - - +
281C ASP 4.1 4.7 - - - +
----------------------------------------------------------
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