Contacts of the helix formed by residues 229 - 250 (chain C) in PDB entry 2ONK
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 ALA 229 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C ILE* 4.2 7.8 - - + +
220C ARG* 4.5 4.9 - - + -
221C TYR* 4.1 17.7 - - + +
225C GLY 4.0 7.4 - - - +
226C LEU* 2.6 17.2 + - - +
228C ALA* 1.3 72.5 - - - +
230C MET* 1.3 65.3 + - - +
231C PRO* 3.2 3.1 - - - -
232C VAL* 2.9 10.6 + - - +
233C ALA* 2.9 20.6 + - - +
104D ILE* 3.8 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 230 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C THR* 4.3 16.3 + - - +
30C LEU* 4.0 19.3 - - + -
31C GLN* 3.5 18.6 - - - +
226C LEU* 3.1 41.5 + - + +
227C SER* 4.2 13.2 - - - +
229C ALA* 1.3 75.0 - - - +
231C PRO* 1.3 71.1 - - + +
233C ALA* 2.9 10.1 + - - +
234C ALA* 2.8 23.9 + - - +
104D ILE* 4.9 2.9 - - + +
108D VAL* 3.6 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 231 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C GLN* 3.3 25.3 - - - +
34C ASN* 6.1 0.2 - - + -
37C GLU* 4.2 22.7 - - + +
38C PHE* 4.2 7.5 - - + +
41C ALA* 3.8 20.6 - - + -
227C SER 3.6 17.9 - - - +
228C ALA 4.1 4.3 - - - +
229C ALA 3.4 5.6 - - - +
230C MET* 1.3 96.1 - - + +
232C VAL* 1.3 59.3 + - + +
234C ALA* 3.2 2.6 + - - +
235C ILE* 2.8 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 232 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ALA* 4.6 6.7 - - + -
47C VAL* 4.4 18.6 - - + -
216C LEU* 3.7 23.1 - - + +
217C ILE* 3.9 19.1 - - + -
220C ARG* 3.4 40.2 - - - +
228C ALA 4.6 4.7 - - - +
229C ALA* 2.9 11.8 + - - +
231C PRO* 1.3 73.9 - - + +
233C ALA* 1.3 63.0 + - - +
235C ILE* 3.5 8.7 - - + +
236C LEU* 2.9 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 233 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C THR* 4.9 7.0 - - - +
217C ILE* 3.7 16.2 - - + +
229C ALA 2.9 11.7 + - - +
230C MET* 3.1 13.7 - - - +
232C VAL* 1.3 75.8 - - - +
234C ALA* 1.3 51.9 + - - +
236C LEU* 2.7 25.3 + - - +
237C ILE* 2.7 20.8 + - - +
101D VAL* 3.9 18.7 - - + +
104D ILE* 4.1 18.4 - - + -
105D ALA* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 234 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C THR* 4.1 6.1 + - - +
28C VAL* 4.0 20.4 - - + -
31C GLN* 3.3 35.0 - - + -
38C PHE* 4.2 7.0 - - + -
230C MET 2.8 10.4 + - - +
231C PRO 3.6 4.3 - - - +
233C ALA* 1.3 72.5 - - - +
235C ILE* 1.3 63.8 + - - +
237C ILE* 3.5 9.8 - - - +
238C LEU* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 235 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C PHE* 3.6 23.3 - - + +
41C ALA* 3.3 22.0 - - + +
42C ALA* 3.2 36.8 - - + +
47C VAL* 4.8 15.0 - - + -
48C TRP* 4.6 23.6 - - + -
231C PRO 2.8 16.9 + - - +
232C VAL* 3.5 12.1 - - + +
234C ALA* 1.3 73.8 - - - +
236C LEU* 1.3 56.5 + - + +
238C LEU* 3.7 3.7 - - - +
239C LEU* 2.6 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 236 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C VAL* 5.4 1.6 - - + -
51C VAL* 3.8 29.4 - - + -
55C TYR* 5.0 5.1 + - + +
213C ALA* 3.4 32.1 - - + +
216C LEU* 6.4 0.2 - - + -
217C ILE* 3.4 28.9 - - + -
232C VAL* 2.9 18.7 + - + +
233C ALA 2.7 14.3 + - - +
235C ILE* 1.3 71.6 - - + +
237C ILE* 1.3 68.6 + - - +
239C LEU* 3.5 12.0 - - + +
240C SER* 3.0 23.6 + - - -
98D PRO* 4.6 11.5 - - + +
101D VAL* 4.2 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 237 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C VAL* 3.5 45.1 - - + +
27C THR* 3.3 27.8 - - + +
28C VAL* 3.8 13.7 - - + -
233C ALA 2.7 17.6 + - - +
234C ALA* 3.5 8.3 - - - +
236C LEU* 1.3 71.5 - - - +
238C LEU* 1.3 57.9 + - + +
240C SER* 2.7 28.6 + - - -
241C LEU* 2.9 25.3 + - + +
97D ILE* 4.9 14.8 - - + +
98D PRO* 6.3 0.4 - - - -
101D VAL* 3.7 24.0 - - + -
105D ALA* 5.0 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 238 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C VAL* 3.3 36.3 - - + -
38C PHE* 3.8 29.4 - - + -
234C ALA 2.9 20.8 + - - +
235C ILE* 3.8 3.1 - - - +
237C ILE* 1.3 74.3 - - - +
239C LEU* 1.3 64.4 + - - +
240C SER 2.9 1.4 + - - -
241C LEU* 3.1 20.1 + - + +
242C ALA* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C TRP* 3.7 24.9 - - + -
51C VAL* 3.6 41.1 - - + -
55C TYR* 3.3 26.2 - - + +
235C ILE* 2.6 24.9 + - + +
236C LEU* 3.5 16.6 - - + +
237C ILE 3.1 0.2 + - - -
238C LEU* 1.3 74.0 - - - +
240C SER* 1.3 59.1 + - - +
242C ALA* 3.9 4.2 - - + +
243C VAL* 3.1 24.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 240 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C TYR* 3.7 12.9 + - - -
197C ILE* 4.9 5.5 - - - +
236C LEU 3.0 12.7 + - - -
237C ILE* 2.7 17.9 + - - -
239C LEU* 1.3 68.8 - - - +
241C LEU* 1.3 67.3 + - - -
242C ALA 3.0 1.9 + - - -
243C VAL* 3.0 2.2 + - - +
244C PHE* 2.9 34.4 + - - -
96D VAL* 3.2 39.8 + - - +
97D ILE* 5.7 2.2 - - - -
98D PRO* 4.9 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C VAL* 5.9 1.1 - - + -
28C VAL* 6.3 0.2 - - + -
237C ILE* 2.9 30.8 + - + +
238C LEU* 3.1 19.9 + - + +
240C SER* 1.3 75.7 - - - +
242C ALA* 1.3 58.4 + - - +
244C PHE* 5.1 2.0 - - - -
245C VAL* 2.8 44.4 + - + +
93D LEU* 3.8 29.2 - - + -
96D VAL* 5.6 4.5 - - + -
97D ILE* 6.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C LEU 3.0 14.9 + - - +
239C LEU* 3.9 6.5 - - + +
240C SER 3.0 0.6 + - - -
241C LEU* 1.3 77.2 - - - +
243C VAL* 1.3 57.0 + - + +
245C VAL* 4.2 1.5 - - - +
246C ALA* 2.8 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C TYR* 3.9 20.6 - - + -
193C TRP* 3.5 35.2 - - + -
239C LEU* 3.1 24.4 + - + +
240C SER* 3.0 4.4 + - - +
242C ALA* 1.3 80.6 - - + +
244C PHE* 1.3 63.0 + - + +
246C ALA* 3.6 5.7 - - - +
247C LEU* 3.2 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C TYR* 5.5 0.2 - - - -
190C ILE* 4.0 25.6 - - + -
193C TRP* 3.2 42.8 - + - -
194C ALA* 3.7 32.1 - - + -
197C ILE* 4.6 5.2 - - + -
240C SER* 2.9 23.6 + - - +
241C LEU* 4.3 2.2 - - - +
243C VAL* 1.3 78.9 - - + +
245C VAL* 1.3 68.0 + - + +
246C ALA 3.0 1.1 - - - -
247C LEU* 3.0 8.0 + - + +
248C ARG* 2.8 25.9 + - + +
96D VAL* 3.2 40.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C LEU* 2.8 33.0 + - + +
242C ALA* 4.2 2.0 - - - +
244C PHE* 1.3 71.8 - - - +
246C ALA* 1.3 62.4 + - - +
248C ARG* 3.3 10.2 + - + +
249C ILE* 2.9 44.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C ALA 2.8 21.1 + - - +
243C VAL* 3.6 7.9 - - - +
245C VAL* 1.3 77.7 - - - +
247C LEU* 1.3 64.3 + - + +
249C ILE* 3.1 15.0 + - - +
250C ILE* 2.9 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C ILE* 3.6 46.4 - - + -
193C TRP* 5.0 6.3 - - + -
243C VAL* 3.2 24.8 + - + +
244C PHE* 3.0 17.8 + - + +
246C ALA* 1.3 78.5 - - + +
248C ARG* 1.3 61.6 + - + +
250C ILE* 3.1 24.4 + - + +
251C VAL* 3.4 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C PHE* 2.8 17.4 + - + +
245C VAL* 3.6 13.7 - - + +
247C LEU* 1.3 68.4 - - - +
249C ILE* 1.3 59.8 + - + +
250C ILE 3.0 4.7 - - - -
251C VAL* 3.1 5.1 + - - +
252C GLY* 2.8 31.9 + - - -
85D SER* 4.2 10.9 + - - +
88D GLU* 4.6 9.3 + - - +
89D GLY* 4.1 20.0 - - - +
92D ASP* 3.4 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C VAL* 2.9 35.5 + - + +
246C ALA* 3.1 7.4 + - - +
248C ARG* 1.3 77.6 - - + +
250C ILE* 1.3 58.9 + - + +
251C VAL 3.3 2.8 + - - -
252C GLY 4.4 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C ALA* 2.9 30.2 + - + +
247C LEU* 3.6 18.8 - - + +
248C ARG 3.0 1.0 - - - -
249C ILE* 1.3 82.0 - - + +
251C VAL* 1.3 69.4 + - + +
----------------------------------------------------------
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