Contacts of the strand formed by residues 270 - 274 (chain A) in PDB entry 1OBA
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 270 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU* 3.2 6.5 - - - +
267A VAL* 2.9 32.7 + - - +
269A SER* 1.3 88.6 - - - +
271A TRP* 1.3 61.3 - - - +
272A TYR* 2.6 41.1 + - + -
301A MET* 3.8 10.8 - - - +
302A VAL* 4.4 2.1 - - - +
303A SER* 3.8 25.3 + - - +
318A THR* 4.6 17.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A TRP* 4.0 27.1 - + + -
265A VAL* 3.7 23.3 - - - -
266A LEU* 3.9 40.8 - - + +
269A SER 5.1 3.1 + - - -
270A GLU* 1.3 75.6 - - - +
272A TYR* 1.3 62.1 + - - +
287A TYR* 5.0 18.8 - + - -
292A TYR* 3.6 43.4 + + + -
294A MET* 3.6 6.4 - - - +
303A SER* 2.5 32.2 + - - -
305A GLU* 3.8 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A TRP* 3.7 34.3 - + + -
264A TRP* 3.3 8.7 - - - -
265A VAL* 2.9 42.9 + - + +
267A VAL* 4.0 18.6 - - + -
270A GLU* 2.6 44.9 + - + -
271A TRP* 1.3 77.0 - - - +
273A TYR* 1.3 61.5 + - - +
274A MET* 4.6 3.8 - - - -
280A MET* 4.2 20.9 - - + -
294A MET* 3.8 9.6 - - + -
301A MET* 3.1 32.8 - - + +
302A VAL 3.3 25.2 + - - -
303A SER* 4.0 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS 4.6 2.3 + - - -
5A ASN* 3.2 31.6 + - - +
263A GLY* 3.2 29.7 - - - -
264A TRP* 3.4 46.2 - + + -
272A TYR* 1.3 75.3 - - - +
274A MET* 1.3 74.3 + - - +
275A ASP* 5.5 1.3 - - - -
276A ASP* 5.5 2.6 + - - -
280A MET* 3.6 4.8 - - - +
281A VAL* 2.8 44.6 + - + +
285A VAL* 4.0 13.9 - - + -
294A MET* 3.9 11.2 - - + -
335A LEU* 3.8 20.7 - - + +
337A THR* 3.7 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A TRP* 4.1 11.7 - - + -
251A TRP 3.5 17.0 - - - +
252A TYR* 3.6 1.6 - - - -
253A TYR* 3.5 25.1 - - + +
261A ALA* 3.7 23.3 - - + +
263A GLY* 2.7 35.5 + - - +
265A VAL* 4.1 20.4 - - + -
272A TYR* 4.6 2.2 - - - -
273A TYR* 1.3 90.3 - - - +
275A ASP* 1.3 69.5 + - - +
276A ASP* 5.2 0.7 - - - +
278A GLY 3.0 30.3 - - - +
279A ALA 3.3 4.3 - - - -
280A MET* 3.7 20.0 - - + +
281A VAL* 4.4 3.6 - - - -
----------------------------------------------------------
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