Contacts of the helix formed by residues 247 - 271 (chain C) in PDB entry 4COF
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 SER 247 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ILE* 5.3 0.4 - - - -
246B ALA* 3.4 35.4 - - - +
248B ALA* 6.0 0.2 - - - +
249B ALA* 4.0 6.8 + - - +
245C ASP 3.0 12.2 + - - -
246C ALA* 1.3 72.0 - - - +
248C ALA* 1.4 65.8 + - - +
250C ARG 3.8 0.3 - - - -
251C VAL* 2.9 34.4 + - - +
299C TYR* 3.1 22.1 - - - -
303C ASN* 4.3 7.2 - - - -
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Residues in contact with ALA 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ALA* 3.8 28.0 - - + -
249B ALA* 4.1 12.9 - - - +
246C ALA 3.5 0.4 - - - -
247C SER* 1.4 79.1 + - - +
249C ALA* 1.3 52.9 + - - +
251C VAL* 3.2 1.6 + - - +
252C ALA* 2.6 39.4 + - - +
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Residues in contact with ALA 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C ILE* 4.5 12.1 - - + -
246C ALA* 3.6 22.1 + - + +
247C SER 3.5 0.4 - - - -
248C ALA* 1.3 75.8 - - - +
250C ARG* 1.3 59.2 + - - +
252C ALA* 3.3 7.4 + - - +
253C LEU* 3.0 36.4 + - + +
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Residues in contact with ARG 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C SER* 2.9 42.8 + - - +
240C PHE* 3.8 6.1 - - - +
242C ILE* 2.8 42.1 + - + -
243C ASN 3.6 11.0 - - - -
244C TYR* 3.6 13.9 - - - +
246C ALA 3.0 15.2 + - - +
249C ALA* 1.3 74.7 - - - +
251C VAL* 1.3 61.3 + - - +
253C LEU* 3.4 6.2 + - + +
254C GLY* 3.1 18.4 + - - -
296C LEU* 4.5 2.4 - - - +
298C GLU* 3.3 16.6 + - - -
299C TYR* 3.3 38.8 - - + +
302C VAL* 4.7 0.8 - - - +
424C ASP* 2.7 41.0 + - - -
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Residues in contact with VAL 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ILE* 3.9 22.4 - - + -
249B ALA* 3.7 27.6 - - + +
252B ALA* 5.2 0.7 - - + -
253B LEU* 3.9 21.1 - - + -
247C SER 2.9 24.1 + - - +
248C ALA 4.0 0.9 - - - +
250C ARG* 1.3 69.3 - - - +
252C ALA* 1.4 54.4 + - - +
254C GLY* 3.0 1.9 + - - -
255C ILE* 2.7 56.0 + - + +
296C LEU* 4.3 11.2 - - + +
299C TYR* 3.9 15.9 - - + -
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Residues in contact with ALA 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ALA* 6.1 3.6 - - + +
248C ALA 2.6 23.0 + - - +
249C ALA* 3.3 7.6 + - - +
251C VAL* 1.4 71.9 - - - +
253C LEU* 1.4 60.5 + - - +
255C ILE* 4.0 8.1 - - - +
256C THR* 3.0 32.9 + - - +
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Residues in contact with LEU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C LEU* 3.5 48.2 - - + +
236C SER* 5.4 2.7 - - - +
238C VAL* 4.4 12.6 - - + -
239C SER* 3.8 36.6 - - - +
242C ILE* 5.1 7.4 - - + -
249C ALA* 3.0 21.9 + - + +
250C ARG* 3.8 7.4 - - + +
252C ALA* 1.4 73.1 - - - +
254C GLY* 1.3 58.3 + - - +
256C THR* 3.8 4.0 - - + -
257C THR* 2.9 38.4 + - + +
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Residues in contact with GLY 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C SER* 5.9 0.4 - - - -
250C ARG 3.1 8.2 + - - -
251C VAL 3.0 6.6 + - - -
253C LEU* 1.3 74.9 - - - +
255C ILE* 1.3 63.2 + - - +
257C THR* 3.5 4.0 + - - -
258C VAL* 3.2 32.3 + - - +
292C VAL 5.5 0.4 - - - -
295C ALA* 6.4 0.9 - - - -
296C LEU* 3.7 32.5 - - - +
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Residues in contact with ILE 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B LEU* 5.0 4.7 - - + -
252B ALA* 3.9 15.3 - - + -
253B LEU* 3.8 39.9 - - + +
256B THR* 3.3 35.2 - - + +
251C VAL* 2.7 44.6 + - + +
252C ALA* 4.0 5.6 - - - +
254C GLY* 1.3 70.7 - - - +
256C THR* 1.3 62.8 + - - +
258C VAL* 3.4 2.9 + - - +
259C LEU* 2.9 38.0 + - + +
296C LEU* 4.9 4.3 - - + -
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Residues in contact with THR 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C ILE* 6.3 0.4 - - + -
235C LEU* 4.5 19.3 - - + -
252C ALA* 3.0 20.9 + - - +
253C LEU* 3.8 5.8 - - + +
255C ILE* 1.3 79.2 - - - +
257C THR* 1.3 52.9 + - - +
259C LEU* 4.1 3.0 - - - +
260C THR* 2.6 50.6 + - + +
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Residues in contact with THR 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C ILE* 3.6 30.4 - - + +
235C LEU* 3.8 22.9 - - + +
236C SER* 3.7 32.3 - - - +
253C LEU* 2.9 23.2 + - + +
254C GLY* 3.5 6.8 + - - -
256C THR* 1.3 73.4 - - + +
258C VAL* 1.4 65.2 + - - +
260C THR* 3.2 7.1 + - - -
261C MET* 3.0 25.5 + - - +
292C VAL* 3.9 12.9 + - - +
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Residues in contact with VAL 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ILE* 5.9 1.8 - - + -
235B LEU* 4.6 20.4 - - + -
254C GLY 3.2 19.9 + - - +
255C ILE* 3.9 3.4 - - - +
257C THR* 1.4 81.0 + - - +
259C LEU* 1.4 63.7 + - + +
261C MET* 3.4 4.2 + - - +
262C THR* 3.2 27.1 + - + +
289C PHE* 3.9 20.2 - - + -
292C VAL* 3.9 14.8 - - + +
293C PHE* 3.8 44.4 - - + +
296C LEU* 4.4 8.5 - - + -
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Residues in contact with LEU 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ILE* 3.7 30.7 - - + -
235B LEU* 4.1 15.9 - - + -
256B THR* 3.4 28.5 - - + +
260B THR* 3.9 17.7 - - + +
255C ILE* 2.9 28.7 + - + +
256C THR* 4.3 2.9 - - - +
258C VAL* 1.4 68.5 - - + +
260C THR* 1.4 66.7 + - + +
261C MET 3.1 1.6 - - - -
262C THR* 2.9 20.1 + - + +
263C THR* 3.0 19.7 + - + +
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Residues in contact with THR 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C ILE* 3.5 27.3 - - + +
256C THR* 2.6 34.8 + - + +
257C THR* 3.2 7.8 + - - -
259C LEU* 1.4 74.7 - - + +
261C MET* 1.3 54.3 + - - +
263C THR* 3.3 13.9 + - + +
264C ILE* 3.0 36.8 + - - +
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Residues in contact with MET 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C SER* 3.5 31.9 - - - +
232C ILE* 3.7 23.5 - - + +
233C THR* 3.6 14.1 - - - +
257C THR 3.0 18.8 + - - +
258C VAL 3.4 5.8 - - - +
259C LEU 3.1 0.2 - - - -
260C THR* 1.3 76.9 + - - +
262C THR* 1.4 63.1 + - - +
264C ILE* 3.3 26.3 + - - +
265C ASN* 3.3 12.6 + - - +
285C LEU* 4.2 11.2 - - - +
288C CYS* 3.8 15.3 - - + -
289C PHE* 3.8 29.8 - - + +
292C VAL* 4.0 13.0 - - + -
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Residues in contact with THR 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B PRO* 5.6 9.9 - - + +
231B LEU* 5.3 5.6 - - + -
232B ILE* 4.9 18.6 - - + +
258C VAL* 3.2 20.3 + - + +
259C LEU* 2.9 12.7 + - - +
261C MET* 1.4 74.6 - - - +
263C THR* 1.4 62.7 + - - +
265C ASN* 3.2 7.2 + - - +
266C THR* 2.9 36.6 + - - +
289C PHE* 3.3 28.5 - - + -
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Residues in contact with THR 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C LEU* 3.0 20.3 + - + +
260C THR* 3.3 14.3 + - + +
262C THR* 1.4 76.3 - - - +
264C ILE* 1.4 60.6 + - - +
266C THR* 3.4 10.0 + - - +
267C HIS* 2.8 38.6 + - - +
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Residues in contact with ILE 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C GLN 5.9 0.7 - - - +
225C THR* 3.8 15.9 - - + +
228C PRO* 4.3 24.5 - - + +
229C SER* 3.9 2.9 - - - +
232C ILE* 4.1 24.0 - - + -
260C THR* 3.0 21.1 + - - +
261C MET* 3.3 21.3 + - - +
263C THR* 1.4 75.8 + - - +
265C ASN* 1.4 61.7 + - - +
267C HIS* 4.1 3.9 - - - +
268C LEU* 3.3 24.1 + - - +
285C LEU* 3.8 30.5 - - + +
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Residues in contact with ASN 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B GLN* 4.8 0.4 - - - -
261C MET 3.3 7.8 + - - +
262C THR* 3.2 10.1 + - - +
264C ILE* 1.4 76.9 - - - +
266C THR* 1.3 66.6 + - + +
267C HIS 3.4 0.2 + - - -
268C LEU* 3.5 3.6 + - - +
269C ARG* 3.0 49.6 + - - +
282C ASP* 3.0 17.7 + - - +
285C LEU* 3.7 31.8 - - + +
286C MET* 3.5 25.3 - - - +
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Residues in contact with THR 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B LEU 5.0 1.8 - - - +
224B GLN* 3.3 37.9 + - - +
228B PRO* 4.2 25.8 - - + -
262C THR* 2.9 28.9 + - - +
263C THR* 3.4 11.4 + - - +
265C ASN* 1.3 71.0 - - + +
267C HIS* 1.3 68.7 + - - +
269C ARG* 3.5 1.9 + - - +
270C GLU* 3.3 21.6 + - - -
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Residues in contact with HIS 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C THR* 2.8 25.7 + - - +
264C ILE* 4.1 3.8 - - - +
266C THR* 1.3 73.0 + - - +
268C LEU* 1.4 62.6 + - - +
270C GLU* 2.9 32.5 + - + +
271C THR* 3.3 25.8 + - - +
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Residues in contact with LEU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C TYR* 4.3 24.2 - - + +
221C PHE* 5.5 3.8 - - + -
225C THR* 4.5 17.7 - - + +
264C ILE 3.3 15.4 + - - +
265C ASN 3.8 2.5 - - - +
266C THR 3.5 0.2 - - - -
267C HIS* 1.4 80.3 - - + +
269C ARG* 1.3 61.7 + - - +
271C THR* 3.1 29.4 + - + +
272C LEU* 3.7 9.0 + - + +
279C LYS* 3.6 13.0 - - - +
281C ILE* 3.4 40.8 - - + -
282C ASP* 3.9 9.2 - - - +
285C LEU* 3.9 11.9 - - + -
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Residues in contact with ARG 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TYR* 4.2 23.1 + - + -
223B LEU* 3.5 49.5 + - - +
224B GLN* 3.2 40.9 + - + +
265C ASN* 3.0 35.2 + - - +
266C THR* 3.6 3.1 - - - +
267C HIS 3.2 0.8 - - - -
268C LEU* 1.3 78.1 - - - +
270C GLU* 1.3 59.1 + - - +
272C LEU* 3.4 21.5 + - - +
273C PRO 4.8 0.9 - - - +
275C ILE* 5.9 1.6 - - + -
277C TYR 4.7 2.2 + - - -
278C VAL* 5.2 0.4 - - - +
279C LYS* 4.3 18.5 - - - +
282C ASP* 3.1 25.6 + - - +
286C MET* 3.4 23.4 - - - +
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Residues in contact with GLU 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TYR* 4.1 11.0 - - - +
224B GLN* 3.1 26.3 + - - +
267B HIS* 3.3 34.2 + - - -
271B THR* 6.5 0.2 - - + -
53C VAL* 5.6 0.3 - - - +
266C THR* 3.3 10.2 + - - +
267C HIS* 2.9 21.3 + - + +
269C ARG* 1.3 74.8 - - - +
271C THR* 1.4 58.2 + - - +
272C LEU 3.2 9.5 + - - +
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Residues in contact with THR 271 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C VAL* 3.3 20.1 - - - +
143C TYR* 5.6 3.8 - - - +
267C HIS* 3.3 27.4 + - - -
268C LEU* 3.1 20.3 + - + +
270C GLU* 1.4 74.4 - - - +
272C LEU* 1.4 65.7 + - + +
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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