Contacts of the helix formed by residues 239 - 260 (chain O) in PDB entry 2I2X
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 239 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179O ASN* 5.7 0.2 + - - -
238O LEU* 1.3 75.4 - - - +
240O HIS* 1.3 59.6 + - - +
241O THR* 3.8 8.1 - - - +
242O ILE* 2.9 30.3 + - + +
243O ALA* 3.1 8.8 + - - +
417O PHE* 4.6 15.7 - - + -
418O GLU* 5.0 6.3 - - - -
421O ALA* 3.8 28.7 - - + -
94P PHE* 3.5 16.4 - - - +
96P PRO* 5.8 0.4 - - - +
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Residues in contact with HIS 240 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230O GLY* 2.7 29.4 + - - -
231O GLY 3.2 16.6 + - - -
232O GLY 3.3 18.9 + - - -
233O LEU* 4.1 9.8 + - + -
235O ASN* 5.3 0.6 + - - +
238O LEU 3.4 14.6 - - - -
239O ALA* 1.3 72.3 - - - +
241O THR* 1.3 55.9 + - - +
243O ALA* 3.2 7.1 + - - +
244O VAL* 3.0 30.0 + - - +
298O VAL* 5.5 3.1 - - + -
364O ASP* 2.4 42.3 + - - +
365O PRO* 4.1 6.2 - - + +
366O GLN* 3.4 14.2 + - - +
418O GLU* 3.9 18.0 + - - +
15P ARG* 4.3 2.6 + - - -
94P PHE* 5.4 2.2 - + - -
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Residues in contact with THR 241 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239O ALA* 3.8 1.7 - - - +
240O HIS* 1.3 77.0 - - - +
242O ILE* 1.3 61.3 + - - +
244O VAL* 3.3 21.3 - - - +
245O ILE* 3.4 17.4 - - - +
365O PRO* 4.0 17.9 - - + -
404O ILE* 4.6 4.7 - - + -
414O LEU* 4.3 11.2 - - + -
418O GLU* 2.9 48.1 + - + +
421O ALA* 3.7 16.1 - - - +
422O LEU* 3.8 19.6 + - + +
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Residues in contact with ILE 242 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176O VAL* 5.7 2.2 - - + -
179O ASN* 3.2 41.7 - - + +
181O ILE* 4.0 19.3 - - + -
184O LEU* 4.0 23.3 - - + -
226O ALA* 6.5 0.2 - - + -
238O LEU* 3.9 19.3 - - + -
239O ALA* 2.9 17.8 + - + +
241O THR* 1.3 80.2 + - - +
243O ALA* 1.3 64.9 + - - +
244O VAL 3.2 0.2 - - - -
245O ILE* 3.1 6.8 + - + +
246O ALA* 3.0 20.5 + - + +
421O ALA* 3.9 32.8 - - + +
425O ALA* 5.0 2.0 - - + -
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Residues in contact with ALA 243 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223O ALA 5.3 1.2 - - - +
226O ALA* 4.3 25.9 - - - +
227O MET* 4.5 1.7 + - + -
230O GLY* 5.4 1.1 - - - -
238O LEU* 4.3 10.4 - - + +
239O ALA 3.1 7.1 + - - +
240O HIS* 3.2 17.9 + - + +
242O ILE* 1.3 76.0 - - - +
244O VAL* 1.3 61.9 + - - +
246O ALA* 3.1 15.2 + - - +
247O ARG* 3.2 10.7 + - - +
366O GLN* 3.5 26.5 - - - +
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Residues in contact with VAL 244 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240O HIS 3.0 15.8 + - - +
241O THR* 3.3 21.1 - - - +
243O ALA* 1.3 75.8 - - - +
245O ILE* 1.3 62.2 + - + +
247O ARG* 3.2 6.7 + - + +
248O ALA 3.0 22.2 + - - -
365O PRO* 3.3 25.4 - - + +
366O GLN* 3.7 19.9 - - - +
369O MET* 3.1 40.1 - - + +
400O CYS* 3.8 13.0 - - - -
404O ILE* 4.2 14.8 - - + -
422O LEU* 5.6 0.4 - - + -
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Residues in contact with ILE 245 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181O ILE* 4.4 15.9 - - + -
184O LEU* 5.5 3.1 - - + -
241O THR 3.4 18.4 - - - +
242O ILE* 3.1 10.8 + - + +
244O VAL* 1.3 74.8 - - + +
246O ALA* 1.3 66.2 + - - +
247O ARG 3.0 1.8 - - - -
248O ALA* 3.2 2.5 + - - +
249O ILE* 3.0 32.5 + - + +
397O ALA* 4.0 23.8 - - + +
400O CYS* 4.0 20.0 - - - -
401O CYS* 3.7 21.3 - - - -
422O LEU* 4.1 6.5 - - + -
425O ALA* 3.5 31.9 - - + -
429O LEU* 4.5 2.0 - - + -
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Residues in contact with ALA 246 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172O PHE* 4.8 2.0 - - + -
176O VAL* 6.2 0.2 - - + -
184O LEU* 4.6 14.0 - - + +
188O ILE* 3.8 25.7 - - + +
223O ALA* 4.3 9.4 - - - +
226O ALA* 4.0 21.1 - - + -
242O ILE* 3.0 11.7 + - + +
243O ALA 3.1 9.6 + - - +
245O ILE* 1.3 76.2 - - - +
247O ARG* 1.3 62.1 + - - +
249O ILE* 3.4 7.2 + - - +
250O SER* 3.1 21.8 + - - -
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Residues in contact with ARG 247 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219O ASP 5.6 0.4 + - - -
223O ALA* 3.6 28.4 + - - +
224O ASN* 3.0 29.9 + - - -
227O MET* 3.5 29.1 - - - +
243O ALA 3.2 10.6 + - - +
244O VAL* 3.3 13.7 - - + +
245O ILE 3.0 0.4 - - - -
246O ALA* 1.3 74.2 - - - +
248O ALA* 1.3 66.9 + - - +
250O SER* 2.6 24.8 + - - -
251O ALA* 3.4 3.3 + - - +
271O TYR* 3.4 22.1 - - - +
272O GLU* 3.1 43.6 + - + +
275O ILE* 5.0 0.8 - - + +
299O MET* 5.1 1.6 - - - +
366O GLN* 5.2 2.6 + - + +
369O MET* 4.0 4.3 - - + -
370O LEU* 3.9 28.7 - - + +
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Residues in contact with ALA 248 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244O VAL 3.0 5.6 + - - +
245O ILE 3.2 6.5 + - - +
247O ARG* 1.3 75.4 - - - +
249O ILE* 1.3 63.5 + - - +
250O SER 3.2 0.9 + - - -
251O ALA* 3.3 5.4 + - - +
252O PRO* 3.3 17.0 - - - +
275O ILE* 4.8 3.1 - - - -
369O MET* 3.5 25.5 - - + +
378O VAL* 4.5 8.6 - - + +
396O ALA* 3.6 22.9 - - - +
397O ALA* 4.4 1.6 - - - +
400O CYS* 3.5 23.3 - - + -
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Residues in contact with ILE 249 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181O ILE* 5.0 2.0 - - + +
184O LEU* 4.1 11.2 - - + +
185O LEU* 3.8 37.0 - - + +
188O ILE* 3.6 12.5 - - + +
189O GLY* 3.5 32.5 - - - +
245O ILE* 3.0 34.2 + - + +
246O ALA* 3.7 5.8 - - - +
248O ALA* 1.3 74.6 - - - +
250O SER* 1.3 63.0 + - - +
252O PRO* 3.1 17.2 - - - +
253O ARG* 3.8 4.3 + - - +
393O ALA* 4.3 11.4 - - + +
397O ALA* 3.8 22.2 - - + -
429O LEU* 5.3 1.8 - - + -
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Residues in contact with SER 250 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188O ILE* 3.6 10.1 - - - +
219O ASP* 3.3 35.4 - - - -
223O ALA* 3.9 4.0 - - - +
246O ALA 3.1 10.3 + - - -
247O ARG* 2.6 23.6 + - - -
249O ILE* 1.3 76.6 - - - +
251O ALA* 1.3 52.7 + - - +
253O ARG* 3.0 4.6 + - - +
254O SER* 2.7 36.2 + - - -
272O GLU* 3.3 21.4 + - - +
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Residues in contact with ALA 251 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247O ARG 3.4 0.2 + - - -
248O ALA 3.3 7.9 + - - +
249O ILE 3.3 0.2 - - - -
250O SER* 1.3 79.6 + - - +
252O PRO* 1.4 65.7 - - + +
254O SER 3.3 0.7 + - - -
255O LEU* 2.8 30.1 + - - +
272O GLU* 4.1 15.9 - - + +
275O ILE* 3.6 46.7 - - + -
276O VAL* 3.8 6.5 - - + +
279O ILE* 5.9 0.7 - - - -
382O ILE* 4.1 3.1 - - + -
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Residues in contact with PRO 252 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189O GLY* 5.8 0.7 - - - -
193O SER* 4.0 4.0 + - - +
248O ALA 3.3 11.2 - - - +
249O ILE 3.1 22.9 - - - +
251O ALA* 1.4 84.9 - - + +
253O ARG* 1.3 60.5 + - - +
255O LEU* 3.4 12.7 - - + +
256O VAL* 3.4 4.2 - - - +
382O ILE* 3.7 21.3 - - + -
389O ILE 5.2 0.9 - - - +
392O ARG* 3.0 49.2 + - + +
393O ALA* 3.7 28.0 - - + +
396O ALA* 4.3 0.7 - - + -
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Residues in contact with ARG 253 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165O SER* 3.1 40.2 + - - -
167O GLY* 5.2 5.1 + - - +
188O ILE* 3.5 32.3 - - + +
189O GLY* 4.9 0.4 - - - -
192O GLY* 3.9 8.1 - - - -
193O SER* 3.7 21.7 + - - +
196O MET* 3.6 23.3 - - + +
217O ASP* 3.4 14.5 + - - -
218O THR 3.1 31.0 + - - +
219O ASP* 2.9 28.9 + - - +
222O GLN* 4.4 2.8 + - - +
249O ILE 3.8 1.5 + - - +
250O SER 3.0 10.8 + - - +
252O PRO* 1.3 82.3 - - - +
254O SER* 1.3 74.2 + - - +
256O VAL* 3.1 20.3 + - - +
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Residues in contact with SER 254 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196O MET* 4.0 2.0 - - - +
217O ASP* 5.4 3.1 - - - +
218O THR* 4.0 5.0 - - - -
219O ASP* 3.5 1.4 + - - +
250O SER 2.7 17.9 + - - -
251O ALA 4.0 1.1 - - - -
253O ARG* 1.3 94.3 + - - +
255O LEU* 1.3 65.8 + - - +
256O VAL 3.1 1.2 + - - -
257O ALA* 3.2 14.6 + - - +
258O TYR* 3.4 18.6 - - - -
272O GLU* 2.8 35.5 + - - -
273O ASN* 5.2 4.3 - - - -
276O VAL* 4.4 7.0 - - - -
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Residues in contact with LEU 255 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6O TYR* 3.9 11.0 - - + +
251O ALA 2.8 19.2 + - - +
252O PRO* 3.4 7.9 - - + +
254O SER* 1.3 76.9 - - - +
256O VAL* 1.3 62.7 + - - +
258O TYR* 3.0 17.7 + - - -
259O GLU* 3.2 33.6 + - - +
276O VAL* 4.1 9.3 - - + +
279O ILE* 3.8 35.9 - - + -
280O THR* 3.6 30.7 - - + -
382O ILE* 4.2 10.8 - - + -
383O VAL* 5.6 0.4 - - + -
392O ARG* 3.6 15.5 - - - +
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Residues in contact with VAL 256 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3O ALA 5.4 0.4 - - - +
5O ARG* 3.9 14.8 - - - +
193O SER* 3.7 22.2 - - - +
196O MET* 3.6 7.2 - - + -
197O GLU* 3.3 43.5 - - + +
252O PRO 3.4 17.3 - - - +
253O ARG 3.4 9.9 - - - +
254O SER 3.1 1.4 + - - -
255O LEU* 1.3 73.9 - - - +
257O ALA* 1.3 65.6 - - - +
259O GLU* 3.2 10.6 + - + +
260O ALA* 2.8 23.3 + - + +
389O ILE* 5.2 0.2 - - + -
392O ARG* 3.5 12.8 - - - +
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Residues in contact with ALA 257 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196O MET* 3.6 17.9 - - + +
200O TRP* 3.7 32.9 - - + +
217O ASP 4.3 8.1 - - - +
254O SER 3.2 13.9 + - - +
255O LEU 3.2 0.4 - - - -
256O VAL* 1.3 79.2 - - - +
258O TYR* 1.3 66.6 + - + +
260O ALA* 3.2 4.0 + - - +
261O GLY 3.2 8.1 + - - -
262O ALA* 3.0 27.6 + - + +
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Residues in contact with TYR 258 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6O TYR* 4.5 8.4 + - - +
215O ALA 3.2 21.1 - - - -
216O GLY* 3.7 11.4 - - - -
217O ASP 4.2 6.1 + - - -
254O SER* 3.4 24.7 - - - -
255O LEU 3.0 8.3 + - - +
257O ALA* 1.3 77.0 - - + +
259O GLU* 1.3 62.8 - - - +
260O ALA 3.1 1.6 - - - -
261O GLY* 3.2 10.7 + - - -
262O ALA* 3.6 24.6 - - + +
264O GLY* 3.6 11.2 - - - -
266O GLY* 3.1 27.2 - - - -
273O ASN* 4.6 3.4 + - - -
276O VAL* 3.7 27.4 - - + -
280O THR* 4.2 10.5 - - + -
282O MET* 3.5 33.5 - - + +
284O MET* 3.8 13.7 - - + -
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Residues in contact with GLU 259 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3O ALA* 3.7 11.0 + - - +
4O LYS* 3.1 44.9 + - - +
5O ARG* 3.4 21.4 + - - +
6O TYR* 3.2 33.9 + - + -
255O LEU* 3.2 16.4 + - - +
256O VAL* 3.5 11.5 - - - +
258O TYR* 1.3 75.4 - - - +
260O ALA* 1.3 58.8 + - - +
261O GLY 3.4 0.7 + - - -
392O ARG* 2.5 46.6 + - - -
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Residues in contact with ALA 260 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3O ALA* 4.2 14.4 - - - +
197O GLU* 4.4 9.9 - - - +
200O TRP* 3.5 24.1 - - + +
201O THR* 3.8 24.8 - - - +
204O SER* 3.1 14.9 + - - -
256O VAL* 2.8 17.2 + - + +
257O ALA 3.5 2.7 - - - -
258O TYR 3.1 0.4 - - - -
259O GLU* 1.3 77.7 - - - +
261O GLY* 1.3 54.5 + - - +
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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