Contacts of the helix formed by residues 278 - 289 (chain B) in PDB entry 2ONL
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 ASN 278 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASP* 2.9 34.0 + - - +
128B GLN* 4.1 6.7 - - - +
217B LEU* 5.3 0.6 - - - +
277B ALA* 1.3 73.0 - - - +
279B PRO* 1.3 95.5 - - - +
280B LEU* 3.1 20.4 + - - +
281B ALA* 2.8 31.7 + - + +
282B VAL* 3.0 6.4 + - - +
307B TYR* 3.9 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ALA 3.1 7.9 - - - +
278B ASN* 1.3 92.3 - - - +
280B LEU* 1.3 66.0 + - + +
281B ALA 3.1 0.2 + - - -
282B VAL* 3.2 8.3 + - + +
283B ASP* 2.8 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ASN* 3.1 14.4 + - - +
279B PRO* 1.3 85.5 - - + +
281B ALA* 1.3 62.4 + - - +
283B ASP* 3.3 9.3 + - + +
284B LEU* 3.0 17.8 + - - +
305B HIS* 3.2 23.1 - - + -
306B ALA* 4.2 25.8 - - + +
307B TYR* 3.8 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B MET* 4.1 3.0 - - + +
217B LEU* 4.4 22.2 - - + -
277B ALA* 5.3 0.2 - - + -
278B ASN* 2.8 20.4 + - + +
280B LEU* 1.3 75.5 - - - +
282B VAL* 1.3 59.0 + - + +
284B LEU* 2.7 28.1 + - - +
285B LEU* 2.9 15.1 + - - +
307B TYR* 3.5 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B PHE* 3.4 39.7 - - + +
271B ALA* 4.0 7.4 - - + +
274B PHE* 3.8 35.0 - - + +
277B ALA* 4.3 11.2 - - + +
278B ASN 3.0 11.5 + - - +
279B PRO* 3.7 8.5 - - + +
281B ALA* 1.3 74.7 - - + +
283B ASP* 1.3 62.0 + - - +
285B LEU* 3.1 20.3 + - + +
286B GLU* 3.2 17.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B PRO 2.8 13.2 + - - +
280B LEU* 3.3 19.1 - - + +
282B VAL* 1.3 77.4 - - - +
284B LEU* 1.3 60.6 + - - +
286B GLU* 3.4 21.8 + - - +
287B LYS* 2.9 49.8 + - - +
305B HIS* 2.9 22.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ILE* 5.5 0.2 - - + -
135B LEU* 5.3 1.1 - - + -
213B MET* 3.9 16.4 - - + -
280B LEU 3.0 11.1 + - - +
281B ALA* 2.7 18.6 + - - +
283B ASP* 1.3 73.4 - - - +
285B LEU* 1.3 58.3 + - - +
287B LYS* 3.3 4.2 + - + +
288B MET* 3.1 28.0 + - + +
297B ILE* 4.2 20.2 - - + -
302B ALA* 4.7 5.4 - - + -
305B HIS* 3.3 30.2 + - + +
307B TYR* 3.6 20.0 - - + -
308B PHE* 3.2 40.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B GLY* 3.5 24.2 - - - +
213B MET* 3.0 33.9 - - + -
214B ALA* 3.9 10.5 - - + +
217B LEU* 4.2 20.6 - - + -
270B PHE* 3.3 15.0 - - + -
274B PHE* 4.3 28.0 - - + -
281B ALA 2.9 6.3 + - - +
282B VAL* 3.1 20.4 + - + +
284B LEU* 1.3 75.6 - - - +
286B GLU* 1.3 60.2 + - - +
288B MET* 4.4 0.2 - - - -
289B LEU* 2.9 49.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LYS* 3.8 19.3 + - - +
269B ASN* 5.2 1.0 - - - -
270B PHE* 3.4 39.7 + - + +
271B ALA 4.9 1.9 + - - -
282B VAL* 3.2 18.2 + - - +
283B ASP* 3.6 22.5 - - - +
284B LEU 3.2 0.2 - - - -
285B LEU* 1.3 77.4 - - - +
287B LYS* 1.3 71.6 + - - +
288B MET 3.4 0.3 + - - -
289B LEU 3.7 7.1 + - - +
290B VAL* 3.2 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ASP* 2.9 55.3 + - - +
284B LEU* 3.3 8.8 + - - +
286B GLU* 1.3 89.3 + - - +
288B MET* 1.3 58.5 + - - +
290B VAL* 3.4 15.2 - - - +
295B LYS 4.3 0.7 - - - +
296B ARG* 3.6 0.5 - - - -
297B ILE* 3.1 47.8 + - + +
305B HIS* 4.4 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ILE* 5.7 0.9 - - - -
135B LEU* 4.9 8.7 - - - -
206B ILE* 3.0 29.3 - - + +
207B TRP* 4.2 5.6 - - - -
209B VAL* 3.2 33.7 - - + -
210B GLY* 3.5 17.0 - - - +
213B MET* 3.0 43.1 - - + -
284B LEU* 3.1 19.8 + - + +
285B LEU* 4.2 0.9 - - + -
287B LYS* 1.3 76.0 - - - +
289B LEU* 1.3 63.2 + - + +
290B VAL 3.0 11.4 + - - -
296B ARG* 3.3 22.3 - - - +
297B ILE* 3.7 13.2 - - + -
302B ALA* 5.7 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B TRP* 3.8 23.1 - - + +
210B GLY* 3.4 30.3 - - - -
211B CYS* 4.6 3.8 - - - +
222B LEU* 3.1 35.7 - - + -
223B PHE* 3.9 15.5 - - + -
238B LEU* 5.4 3.1 - - + -
239B VAL* 2.8 23.8 - - + +
270B PHE* 4.1 17.3 - - + -
274B PHE* 6.2 1.3 - - + -
285B LEU* 2.9 44.8 + - + +
286B GLU 3.8 7.4 - - - +
288B MET* 1.3 73.4 - - + +
290B VAL* 1.3 59.2 + - - +
----------------------------------------------------------
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