Contacts of the helix formed by residues 269 - 287 (chain C) in PDB entry 2AXV
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 LYS 269 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C TYR* 3.2 52.0 + - + +
264C PHE* 2.9 31.2 + - + +
267C ILE* 4.3 7.2 - - + +
268C GLY* 1.3 75.5 - - - +
270C GLU* 1.3 52.4 + - - +
271C ASP* 3.2 28.9 - - - +
272C ILE* 3.1 25.0 + - + +
273C HIS* 2.9 32.0 + - - +
221D LYS* 5.9 0.9 - - - +
228D ILE* 5.9 0.6 - - - +
233D ASP* 4.3 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 270 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C LYS* 4.1 21.4 - - - +
268C GLY* 3.2 26.6 + - - +
269C LYS* 1.3 71.0 - - - +
271C ASP* 1.3 69.3 + - - +
273C HIS* 3.6 6.9 + - - +
274C ARG* 2.9 26.9 + - - +
298C TYR* 5.9 1.4 - - - -
302C TYR* 3.3 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 271 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C LYS* 3.2 35.5 + - - +
270C GLU* 1.3 81.1 + - - +
272C ILE* 1.3 85.6 + - + +
274C ARG* 3.2 12.0 + - - +
275C SER* 3.3 12.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 272 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C TYR* 4.4 13.7 - - + +
235C GLU* 4.2 17.9 - - - +
264C PHE* 3.6 31.0 - - + -
269C LYS* 3.1 31.8 + - + +
271C ASP* 1.3 92.2 - - - +
273C HIS* 1.3 65.8 + - - +
275C SER* 2.8 22.4 + - - +
276C LEU* 2.9 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 273 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C ILE* 3.1 40.6 + - + +
262C ASN* 4.5 4.8 + - - -
264C PHE* 4.2 6.1 - - - +
265C LYS* 3.7 31.4 - - + +
269C LYS 2.9 15.7 + - - +
270C GLU* 3.6 9.4 + - - +
272C ILE* 1.3 76.5 - - - +
274C ARG* 1.3 56.2 + - - +
276C LEU* 3.4 4.0 + - - +
277C VAL* 2.9 46.4 + - + +
298C TYR* 3.5 50.1 - + - -
302C TYR* 3.2 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C GLU 2.9 17.1 + - - +
271C ASP* 3.3 7.2 - - - +
273C HIS* 1.3 77.7 - - - +
275C SER* 1.3 63.6 + - - +
277C VAL* 3.7 3.4 - - - +
278C GLU* 3.2 35.6 + - - +
299C TYR* 5.7 0.2 - - - -
302C TYR* 3.3 71.0 + - + +
303C VAL* 4.2 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C GLU* 5.6 0.2 + - - -
271C ASP 3.3 8.6 + - - -
272C ILE* 2.8 18.7 + - - +
274C ARG* 1.3 80.5 - - - +
276C LEU* 1.3 65.6 + - - +
278C GLU* 3.3 13.7 - - - +
279C GLU* 2.9 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C GLU* 3.7 29.4 - - + +
238C TYR* 3.6 24.5 + - + -
239C LEU* 6.1 0.2 - - + -
261C ILE* 3.6 22.8 - - + +
264C PHE* 3.7 24.0 - - + -
272C ILE* 2.9 34.4 + - + +
273C HIS* 4.1 1.8 - - - +
275C SER* 1.3 81.2 - - - +
277C VAL* 1.3 59.8 + - - +
279C GLU* 3.2 23.0 + - - +
280C LEU* 2.8 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C ILE* 3.7 24.2 - - + +
273C HIS* 2.9 39.0 + - + +
274C ARG* 3.7 6.5 - - - +
276C LEU* 1.3 76.2 - - - +
278C GLU* 1.3 57.9 + - - +
280C LEU* 3.8 2.6 - - - +
281C THR* 3.0 29.5 + - - +
295C VAL* 3.8 21.9 - - + +
298C TYR* 4.2 10.1 - - + -
299C TYR* 3.7 39.0 - - + +
302C TYR* 5.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 278 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C ARG* 3.2 26.2 + - - +
275C SER* 3.3 16.0 - - - +
277C VAL* 1.3 78.2 - - - +
279C GLU* 1.3 69.9 + - + +
281C THR* 3.1 4.3 + - - +
282C LYS* 3.1 50.3 + - - +
299C TYR* 3.7 30.9 - - + -
303C VAL* 6.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 279 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C THR* 3.4 26.7 + - - +
202C ILE* 5.9 0.2 - - - +
203C MET* 4.6 12.8 - - + -
235C GLU* 4.8 2.4 - - - +
238C TYR* 3.5 27.0 + - - +
239C LEU* 4.3 8.5 - - - +
275C SER* 2.9 30.1 + - - +
276C LEU* 3.6 17.8 - - - +
278C GLU* 1.3 72.7 - - + +
280C LEU* 1.3 65.9 - - - +
282C LYS* 2.9 10.8 + - - +
283C ILE* 2.8 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 280 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C TYR* 3.7 10.7 + - + +
242C ILE* 4.0 19.3 - - + -
254C TYR* 3.6 30.3 - - + +
257C ALA* 5.4 2.0 - - + -
258C VAL* 4.0 24.5 - - + -
261C ILE* 3.8 18.8 - - + -
276C LEU 2.8 17.4 + - - +
277C VAL* 3.8 4.3 - - - +
279C GLU* 1.3 75.5 - - - +
281C THR* 1.3 56.7 + - - +
283C ILE* 3.4 8.2 + - + -
284C SER* 2.8 46.1 + - - +
291C PRO* 4.4 1.1 - - + -
295C VAL* 4.4 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 281 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C VAL 3.0 15.4 + - - -
278C GLU* 3.2 12.1 - - - +
280C LEU* 1.3 77.2 - - - +
282C LYS* 1.3 62.0 + - + +
284C SER* 3.4 2.4 + - - -
285C ALA* 2.9 29.0 + - + +
291C PRO* 4.0 22.1 - - + +
295C VAL* 4.5 3.3 - - - +
296C THR* 4.2 7.6 - - + +
299C TYR* 3.6 46.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 282 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C MET* 4.4 25.1 - - + -
278C GLU* 3.1 43.9 + - - +
279C GLU* 2.9 7.3 + - - +
281C THR* 1.3 79.1 - - + +
283C ILE* 1.3 60.8 + - - +
284C SER 3.1 0.2 - - - -
285C ALA* 3.2 7.9 - - - +
286C LYS* 2.9 34.9 + - + +
299C TYR* 4.6 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 283 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C ILE* 3.9 26.5 - - + +
203C MET* 4.1 20.6 - - + -
238C TYR* 4.1 10.8 - - + +
242C ILE* 4.1 19.7 - - + -
245C PHE* 5.5 4.0 - - + -
246C LEU* 4.0 27.4 - - + -
254C TYR* 6.3 0.7 - - + -
279C GLU* 2.8 39.4 + - + +
280C LEU* 3.8 9.2 - - + +
282C LYS* 1.3 77.6 - - - +
284C SER* 1.3 57.6 + - - +
286C LYS* 3.4 9.2 + - + +
287C GLU* 3.0 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 284 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C PHE* 6.1 1.3 - - - -
254C TYR* 2.8 34.4 + - - -
280C LEU* 2.8 22.9 + - - +
281C THR 3.5 5.2 - - - -
283C ILE* 1.3 74.7 - - - +
285C ALA* 1.3 66.6 + - - +
287C GLU* 3.0 10.5 + - - -
288C LYS 3.0 2.1 + - - -
289C PHE* 2.9 44.5 + - - +
291C PRO* 3.7 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 285 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C THR* 2.9 15.2 + - + +
282C LYS* 3.2 13.2 - - - +
284C SER* 1.3 73.9 - - - +
286C LYS* 1.3 58.7 + - + +
288C LYS* 2.9 29.8 + - - +
289C PHE 3.7 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 286 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C MET* 3.1 36.9 + - + +
204C ASN* 4.3 13.1 + - - +
205C ARG* 4.6 10.2 - - + +
282C LYS* 2.9 19.9 + - + +
283C ILE* 3.5 11.7 - - + +
285C ALA* 1.3 74.0 - - + +
287C GLU* 1.3 75.0 + - - +
288C LYS* 3.3 17.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 287 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LYS* 4.6 5.9 + - - -
205C ARG* 2.8 47.4 + - - +
245C PHE* 4.5 7.2 - - + -
246C LEU* 3.9 16.8 - - + +
249C LYS* 3.2 32.3 + - - +
283C ILE* 3.0 15.0 + - + +
284C SER 3.0 7.4 + - - +
286C LYS* 1.3 92.2 - - - +
288C LYS* 1.3 74.1 + - - +
289C PHE* 3.3 14.8 - - + -
----------------------------------------------------------
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