Contacts of the helix formed by residues 274 - 297 (chain C) in PDB entry 1WR6
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 274 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ASN 3.7 6.2 - - - +
273C ASP* 1.3 71.4 + - - +
275C SER* 1.3 64.8 + - - +
276C LEU 3.2 0.4 - - - -
277C GLY* 3.1 14.5 + - - +
278C ASP* 3.7 12.6 + - - +
45F PHE* 3.3 26.4 - - + -
46F ALA* 4.4 13.5 - - + -
59F TYR 4.2 1.6 + - - -
60F ASN* 3.4 33.1 + - - +
62F GLN* 5.4 5.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
230B GLU* 3.3 27.9 + - - +
233B LEU* 3.5 15.9 - - - +
234B HIS* 3.1 32.2 + - - -
269C THR* 4.7 4.7 - - - -
273C ASP* 2.9 9.1 + - - -
274C ASN* 1.3 78.1 - - - +
276C LEU* 1.3 64.3 + - - +
278C ASP* 2.9 16.3 + - - +
279C ILE* 3.0 16.2 + - - +
46F ALA* 4.3 3.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
266C ALA* 3.9 28.7 - - + -
269C THR* 4.2 27.6 + - + -
273C ASP 3.2 13.1 + - - +
275C SER* 1.3 78.8 - - - +
277C GLY* 1.3 58.8 + - - +
279C ILE* 3.2 10.1 + - + +
280C LEU* 2.9 55.6 + - + +
259D ARG* 3.4 42.2 - - - +
263D PHE* 4.2 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C ASP 4.6 0.2 + - - -
274C ASN* 3.1 10.4 + - - +
275C SER 3.0 0.2 + - - -
276C LEU* 1.3 78.6 - - - +
278C ASP* 1.3 58.6 + - - +
280C LEU* 3.6 7.4 + - - +
281C GLN* 3.1 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 278 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B HIS* 3.0 25.1 + - + -
218C LEU* 3.9 24.5 - - + +
274C ASN* 3.7 12.1 + - - +
275C SER* 2.9 8.1 + - - +
277C GLY* 1.3 73.2 - - - +
279C ILE* 1.3 66.7 + - + +
281C GLN* 3.2 7.8 + - - +
282C ALA* 3.0 24.9 + - - +
46F ALA* 5.7 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 279 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B LEU* 3.6 30.1 - - + -
218C LEU* 4.2 7.4 - - + -
262C LEU* 3.7 34.1 - - + +
263C PHE* 5.9 0.7 - - + -
265C LEU* 4.3 13.2 - - + +
266C ALA* 4.0 33.9 - - + +
269C THR* 5.2 4.5 - - - +
275C SER* 3.0 21.6 + - - +
276C LEU* 3.3 14.8 - - + +
278C ASP* 1.3 76.5 - - - +
280C LEU* 1.3 63.5 + - + +
282C ALA* 3.4 2.6 + - - +
283C SER* 2.9 28.1 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
263C PHE* 5.3 4.7 - - + -
266C ALA* 5.0 1.8 - - + -
276C LEU* 2.9 44.8 + - + +
277C GLY* 4.0 7.2 - - - +
279C ILE* 1.3 79.1 - - + +
281C GLN* 1.3 59.6 + - - +
283C SER* 3.6 9.4 - - - -
284C ASP* 3.0 28.8 + - - +
259D ARG* 5.1 0.9 - - - +
263D PHE* 3.7 34.3 - - + -
287D SER* 4.5 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 281 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C GLY 3.1 18.4 + - - +
278C ASP* 3.2 9.2 + - - +
280C LEU* 1.3 74.7 - - - +
282C ALA* 1.3 65.1 + - + +
284C ASP* 3.3 8.2 + - - +
285C ASN* 3.1 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 282 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C LEU* 4.1 16.4 - - + +
221C VAL* 3.8 26.0 - - + +
222C ASN* 4.6 9.2 - - - +
262C LEU* 4.1 9.4 - - + -
278C ASP 3.0 15.8 + - - +
279C ILE 3.8 3.8 - - - +
281C GLN* 1.3 74.9 - - - +
283C SER* 1.3 60.2 + - - +
285C ASN* 3.4 9.3 + - - +
286C LEU* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 283 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C ARG* 3.8 7.8 + - - +
262C LEU* 4.0 12.9 - - - +
263C PHE* 3.0 38.1 - - - -
279C ILE* 2.9 19.7 + - - -
280C LEU* 3.6 12.3 - - - -
281C GLN 3.2 0.2 - - - -
282C ALA* 1.3 78.4 - - - +
284C ASP* 1.3 57.8 + - - +
286C LEU* 3.2 7.0 + - - +
287C SER* 2.9 31.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 284 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C LEU 3.0 16.9 + - - +
281C GLN* 3.3 9.5 + - - +
283C SER* 1.3 78.7 - - - +
285C ASN* 1.3 60.5 + - - +
287C SER* 3.1 7.4 + - - +
288C ARG* 2.9 64.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 285 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C ASN* 4.5 14.2 - - - +
225C VAL* 3.9 22.8 - - + +
281C GLN* 3.1 38.1 + - - +
282C ALA* 3.7 8.3 - - - +
284C ASP* 1.3 79.2 - - - +
286C LEU* 1.3 63.0 + - - +
288C ARG* 3.4 12.2 + - - +
289C VAL* 3.2 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 286 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C VAL* 3.7 17.9 - - + +
224C ASN* 5.2 0.2 - - + -
225C VAL* 3.4 26.5 - - + +
255C CYS* 3.7 33.7 - - + +
258C LYS* 3.9 8.5 - - + -
259C ARG* 3.4 39.0 - - + +
262C LEU* 3.7 22.4 - - + -
282C ALA 2.9 6.3 + - - +
283C SER* 3.3 9.4 - - - +
284C ASP 3.1 0.2 - - - -
285C ASN* 1.3 78.6 - - - +
287C SER* 1.3 58.0 + - - +
289C VAL* 3.3 4.6 - - - +
290C ILE* 3.0 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 287 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C ARG* 2.9 34.8 + - - +
263C PHE* 5.4 0.5 - - - -
283C SER* 2.9 17.1 + - - -
284C ASP* 3.1 12.8 + - - -
286C LEU* 1.3 74.4 - - - +
288C ARG* 1.3 62.6 + - - +
290C ILE* 3.5 1.5 - - - +
291C ASN* 2.9 40.7 + - - +
280D LEU* 5.0 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 288 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C ASP* 2.9 48.3 + - - +
285C ASN* 3.6 14.7 + - - +
287C SER* 1.3 78.8 - - - +
289C VAL* 1.3 57.9 + - - +
291C ASN* 3.9 4.1 - - - +
292C SER* 3.0 28.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 289 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C VAL* 4.0 19.1 - - + +
228C LEU* 3.6 25.9 - - + +
229C SER* 3.8 20.6 - - - +
232C LEU* 4.1 12.3 - - + -
255C CYS* 4.1 22.7 - - - -
285C ASN 3.2 10.4 + - - +
286C LEU* 3.3 17.3 - - - +
288C ARG* 1.3 76.9 - - - +
290C ILE* 1.3 59.6 + - - +
292C SER* 3.9 6.3 - - - -
293C TYR* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 290 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C LEU* 5.4 0.2 - - - -
252C PHE* 3.5 23.8 - - + -
255C CYS* 3.8 20.9 - - + +
256C GLU* 3.4 39.3 - - - +
259C ARG* 3.5 30.3 - - - +
286C LEU 3.0 24.4 + - - +
287C SER* 3.1 4.7 + - - +
289C VAL* 1.3 76.7 - - - +
291C ASN* 1.3 64.2 + - - +
293C TYR* 3.2 5.7 + - - +
294C LYS* 3.0 45.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 291 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C ARG* 5.6 2.6 - - - +
287C SER* 2.9 22.5 + - - +
288C ARG* 4.0 4.8 - - - +
290C ILE* 1.3 78.1 - - - +
292C SER* 1.3 65.8 + - - +
294C LYS* 3.2 27.9 + - - +
295C THR* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 292 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C LEU* 3.8 15.0 - - - +
288C ARG 3.0 19.7 + - - -
289C VAL* 3.6 11.4 - - - +
291C ASN* 1.3 75.7 - - - +
293C TYR* 1.3 63.5 + - - +
295C THR* 3.3 4.8 + - - -
296C ILE* 3.0 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 293 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C LEU* 4.3 9.4 - - + -
232C LEU* 4.2 22.8 - - + +
245C ARG 4.5 3.3 + - - -
248C MSE 4.0 24.2 - - + -
249C LYS* 3.8 24.9 + - + +
252C PHE* 3.3 45.3 - + + -
289C VAL 2.9 13.6 + - - +
290C ILE 3.4 8.3 - - - +
291C ASN 3.2 0.2 - - - -
292C SER* 1.3 74.6 + - - +
294C LYS* 1.3 63.4 + - - +
296C ILE 4.6 0.2 - - - +
297C ILE* 2.8 74.2 + - + +
298C GLU* 3.9 20.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 294 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C PHE* 4.2 17.3 - - + -
256C GLU* 4.8 5.4 + - - -
259C ARG* 5.3 4.2 - - - +
290C ILE* 3.0 31.0 + - - +
291C ASN* 3.5 31.4 - - - +
293C TYR* 1.3 78.2 - - - +
295C THR* 1.3 58.2 + - - +
298C GLU* 3.0 18.0 + - - +
299C GLY 2.9 23.7 + - - -
300C GLN* 3.0 44.7 + - + +
273D ASP* 5.0 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 295 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C ASN* 2.9 18.7 + - - +
292C SER* 3.8 5.8 - - - -
293C TYR 3.1 0.2 - - - -
294C LYS* 1.3 78.3 - - - +
296C ILE* 1.3 64.8 + - + +
299C GLY* 3.6 14.4 - - - -
300C GLN* 3.5 24.8 + - - +
301C VAL* 4.5 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 296 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C LEU* 3.8 27.4 - - + +
235C TYR* 3.5 37.1 + - + -
292C SER* 3.0 30.9 + - - +
293C TYR 4.3 0.9 - - - +
295C THR* 1.3 81.8 - - + +
297C ILE* 1.3 70.5 + - + +
299C GLY* 4.5 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 297 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C LEU* 4.4 7.2 - - + -
235C TYR* 3.7 47.5 + - + +
245C ARG* 5.9 7.6 - - + -
248C MSE 4.3 11.4 - - + -
293C TYR* 2.8 61.5 + - + +
296C ILE* 1.3 79.8 - - + +
298C GLU* 1.3 63.6 + - + +
299C GLY 3.3 4.6 + - - -
----------------------------------------------------------
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