Contacts of the helix formed by residues 274 - 281 (chain D) in PDB entry 1OL1
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 274 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLU* 3.5 29.0 - - - +
272D PRO 3.5 4.4 + - - +
273D PRO* 1.3 74.6 - - - +
275D VAL* 1.3 67.2 + - - +
276D ALA* 4.0 12.4 - - + +
277D GLU* 2.9 31.2 + - + +
278D PHE* 3.5 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 275 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLU* 3.2 44.5 + - - +
262D LEU* 3.9 21.3 - - + +
266D LYS* 5.3 0.2 - - - -
273D PRO 3.6 1.2 + - - -
274D GLU* 1.3 70.8 - - - +
276D ALA* 1.3 63.1 + - - +
278D PHE* 2.8 25.3 + - - +
279D VAL* 3.2 6.7 + - + +
288D LYS* 4.2 17.5 - - + -
291D VAL* 3.9 19.1 - - + -
292D LEU* 3.5 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 276 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLU* 4.8 2.7 + - - +
274D GLU* 3.0 11.3 + - + +
275D VAL* 1.3 81.3 - - - +
277D GLU* 1.3 57.2 + - - +
279D VAL* 2.7 32.2 + - + +
280D TYR* 3.1 11.3 + - - +
288D LYS* 4.9 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 277 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D TYR* 2.2 58.0 + - + +
273D PRO* 4.7 5.6 - - + -
274D GLU* 2.9 27.1 + - + +
276D ALA* 1.3 80.9 - - + +
278D PHE* 1.3 56.6 + - - +
280D TYR* 3.3 11.7 + - - +
281D ILE* 3.0 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 278 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D VAL* 4.5 9.9 - - + -
225D TYR* 6.3 2.0 - + - -
227D LEU* 4.9 2.5 - - + -
258D THR* 3.2 24.3 - - + +
261D MET* 3.7 34.3 - - + -
262D LEU* 3.6 37.2 - - + -
265D SER* 3.9 9.2 - - - -
273D PRO* 3.3 38.4 - - + -
274D GLU 3.5 16.8 + - - -
275D VAL* 2.8 12.2 + - - +
277D GLU* 1.3 77.7 - - - +
279D VAL* 1.3 60.3 + - - +
281D ILE* 3.0 27.7 - - + +
282D THR* 2.9 20.6 - - - +
291D VAL* 4.9 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 279 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D VAL* 3.2 11.9 + - + +
276D ALA* 2.7 14.7 + - - +
278D PHE* 1.3 79.5 - - - +
280D TYR* 1.3 57.8 + - + +
282D THR* 2.6 26.0 + - - +
284D ASP* 3.4 32.8 + - - +
286D TYR 3.6 14.1 - - - +
287D THR* 3.5 12.6 - - - +
288D LYS* 3.5 35.2 - - + +
291D VAL* 4.0 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 280 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D TYR* 4.0 16.6 - + - -
276D ALA 3.1 10.3 + - - +
277D GLU* 3.8 13.2 - - - +
279D VAL* 1.3 77.7 - - + +
281D ILE* 1.3 75.3 + - + +
282D THR 3.0 2.0 - - - -
283D ASP* 3.0 13.6 + - - +
284D ASP* 4.6 8.7 - - - +
500H CIR 5.0 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D TRP* 3.0 42.7 + - + -
221D VAL* 3.9 20.0 - - + -
224D GLU* 5.8 1.8 - - + -
225D TYR* 3.1 36.8 - - + +
258D THR* 3.7 15.5 - - + -
261D MET* 6.3 0.4 - - + -
277D GLU 3.0 14.3 + - - +
278D PHE* 3.0 37.7 - - + +
280D TYR* 1.3 84.6 - - + +
282D THR* 1.3 59.6 + - + +
283D ASP 3.2 0.2 - - - -
500H CIR 3.2 23.1 + - - +
----------------------------------------------------------
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