Contacts of the helix formed by residues 239 - 260 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179K ASN* 5.5 0.6 + - - -
238K LEU* 1.3 76.4 - - - +
240K HIS* 1.3 60.7 + - - +
241K THR* 3.8 8.1 - - - +
242K ILE* 2.9 28.9 + - + +
243K ALA* 3.1 9.7 + - - +
417K PHE* 4.4 16.6 - - + -
418K GLU* 5.0 4.3 - - - -
421K ALA* 3.8 29.4 - - + -
94L PHE* 3.6 14.5 - - + -
96L PRO* 5.6 0.4 - - - +
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Residues in contact with HIS 240 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230K GLY* 2.7 28.1 + - - -
231K GLY 3.2 18.8 - - - -
232K GLY 3.2 19.1 + - - -
233K LEU* 4.1 8.6 + - + -
235K ASN* 5.1 3.5 + - - +
238K LEU 3.3 15.5 - - - -
239K ALA* 1.3 71.6 - - - +
241K THR* 1.3 56.9 + - - +
243K ALA* 3.8 5.8 - - - -
244K VAL* 3.1 24.8 + - - +
298K VAL* 5.8 2.0 - - + -
364K ASP* 2.6 39.1 + - - +
365K PRO* 3.9 10.8 - - + +
366K GLN* 3.4 19.8 + - - +
418K GLU* 4.0 17.0 - - - +
15L ARG* 4.5 1.8 + - - -
94L PHE* 5.7 1.8 - + - -
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Residues in contact with THR 241 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239K ALA* 3.8 8.1 - - - +
240K HIS* 1.3 77.6 - - - +
242K ILE* 1.3 61.0 + - - +
244K VAL* 3.4 16.2 - - + +
245K ILE* 3.4 20.8 - - - +
365K PRO* 4.1 14.8 - - + +
404K ILE* 4.4 5.6 - - + -
414K LEU* 4.1 15.3 - - + -
418K GLU* 2.8 48.0 + - + +
421K ALA* 3.9 0.3 - - - +
422K LEU* 3.8 26.9 + - + +
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Residues in contact with ILE 242 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176K VAL* 6.0 1.8 - - + -
179K ASN* 3.2 41.3 - - + +
181K ILE* 4.0 27.1 - - + -
184K LEU* 4.1 15.0 - - + -
238K LEU* 4.4 16.4 - - + -
239K ALA* 2.9 17.8 + - + +
241K THR* 1.3 78.0 + - - +
243K ALA* 1.3 66.0 + - - +
244K VAL 3.2 1.6 - - - -
245K ILE* 3.0 16.6 + - + +
246K ALA* 3.0 12.5 + - + +
421K ALA* 4.0 33.4 - - + +
425K ALA* 4.9 2.7 - - + -
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Residues in contact with ALA 243 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223K ALA 5.4 1.2 - - - +
226K ALA* 4.3 18.4 - - - +
227K MET* 4.5 1.1 - - - +
230K GLY* 5.4 2.2 - - - -
238K LEU* 4.1 18.7 - - + +
239K ALA 3.1 11.4 + - - +
240K HIS* 3.7 6.3 - - + +
242K ILE* 1.3 75.1 - - - +
244K VAL* 1.3 62.7 + - - +
246K ALA* 3.1 7.0 + - - +
247K ARG* 3.0 20.1 + - - +
366K GLN* 3.3 32.3 - - - +
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Residues in contact with VAL 244 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240K HIS 3.1 16.4 + - - +
241K THR* 3.4 17.7 - - - +
242K ILE 3.2 0.4 - - - -
243K ALA* 1.3 71.4 - - - +
245K ILE* 1.3 70.0 + - + +
247K ARG* 3.1 6.1 + - + -
248K ALA 2.9 19.1 + - - -
365K PRO* 3.4 16.6 - - + +
366K GLN* 3.8 16.7 - - - +
369K MET* 3.4 44.8 - - + +
400K CYS* 3.6 14.4 - - - -
404K ILE* 4.0 17.5 - - + -
422K LEU* 5.8 0.9 - - + -
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Residues in contact with ILE 245 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181K ILE* 4.2 17.5 - - + -
184K LEU* 5.6 2.7 - - + -
241K THR 3.4 19.7 - - - +
242K ILE* 3.0 12.7 + - + +
244K VAL* 1.3 78.3 - - + +
246K ALA* 1.3 62.7 + - - +
248K ALA* 3.2 3.0 + - - +
249K ILE* 3.0 41.4 + - + +
397K ALA* 4.3 12.6 - - + +
400K CYS* 4.1 14.6 - - - -
401K CYS* 3.8 25.4 - - - -
422K LEU* 4.5 5.8 - - + -
425K ALA* 3.6 31.2 - - + -
429K LEU* 4.6 2.5 - - + -
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Residues in contact with ALA 246 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172K PHE* 5.1 1.3 - - + -
184K LEU* 4.6 14.6 - - + +
188K ILE* 4.1 22.1 - - + +
223K ALA* 4.2 7.3 - - - +
226K ALA* 4.1 22.0 - - + -
242K ILE* 3.0 12.4 + - + +
243K ALA 3.4 9.2 - - - +
245K ILE* 1.3 76.7 - - - +
247K ARG* 1.3 61.7 + - - +
249K ILE* 3.4 7.3 + - - +
250K SER* 3.1 22.9 + - - -
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Residues in contact with ARG 247 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219K ASP 5.4 0.8 + - - -
223K ALA* 3.3 30.1 + - + +
224K ASN* 2.6 31.7 + - - -
227K MET* 3.8 20.4 - - - +
243K ALA 3.0 11.2 + - - +
244K VAL* 3.1 13.0 + - + +
246K ALA* 1.3 74.1 - - - +
248K ALA* 1.3 66.1 + - - +
250K SER* 2.6 23.0 + - - -
251K ALA* 3.4 3.8 + - - -
269K CYS 4.4 0.4 + - - -
271K TYR* 3.4 27.7 - - - +
272K GLU* 2.9 47.0 + - + +
275K ILE* 5.3 0.4 - - + -
299K MET* 5.4 2.0 - - - +
366K GLN* 5.5 2.3 + - + -
369K MET* 3.8 14.6 - - + -
370K LEU* 4.0 20.2 - - + +
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Residues in contact with ALA 248 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244K VAL 2.9 7.4 + - - +
245K ILE 3.2 6.0 + - - +
247K ARG* 1.3 75.0 - - - +
249K ILE* 1.3 61.3 + - - +
251K ALA* 3.3 6.4 + - - +
252K PRO* 3.2 17.8 - - - +
275K ILE* 4.7 5.6 - - - -
369K MET* 3.4 18.1 - - + +
378K VAL* 4.5 4.4 - - + +
396K ALA* 3.5 23.1 - - + +
397K ALA* 4.6 0.4 - - - +
400K CYS* 3.6 31.9 - - + -
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Residues in contact with ILE 249 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181K ILE* 5.0 3.8 - - + +
184K LEU* 4.1 12.8 - - + +
185K LEU* 4.0 28.7 - - + +
188K ILE* 3.8 12.8 - - + +
189K GLY* 3.6 30.6 - - - +
245K ILE* 3.0 33.2 + - + +
246K ALA* 3.8 5.4 - - - +
248K ALA* 1.3 76.8 - - - +
250K SER* 1.3 61.8 + - - +
252K PRO* 3.3 17.2 - - - +
253K ARG* 3.8 4.2 + - - +
393K ALA* 4.1 14.8 - - + +
397K ALA* 3.8 24.5 - - + -
429K LEU* 5.4 0.2 - - + -
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Residues in contact with SER 250 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188K ILE* 3.6 10.1 - - - -
219K ASP* 3.2 33.2 - - - -
223K ALA* 3.8 4.4 - - - +
246K ALA 3.1 11.5 + - - -
247K ARG* 2.6 22.9 + - - -
249K ILE* 1.3 76.4 - - - +
251K ALA* 1.3 60.5 + - - +
253K ARG* 3.4 2.0 + - - +
254K SER* 2.9 32.4 + - - -
272K GLU* 3.4 20.5 + - - +
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Residues in contact with ALA 251 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247K ARG 3.4 0.8 + - - +
248K ALA 3.3 7.9 + - - +
249K ILE 3.1 1.2 - - - -
250K SER* 1.3 80.2 + - - +
252K PRO* 1.3 65.9 - - + +
254K SER* 3.0 4.7 + - - -
255K LEU* 2.8 28.6 + - - +
272K GLU* 4.0 14.6 - - + +
275K ILE* 3.8 45.1 - - + -
276K VAL* 4.1 6.4 - - + +
279K ILE* 6.3 0.2 - - - -
382K ILE* 3.9 4.0 - - + -
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Residues in contact with PRO 252 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189K GLY* 6.1 0.2 - - - -
193K SER* 4.2 3.4 + - - +
248K ALA 3.2 15.0 - - - +
249K ILE 3.3 11.9 - - - +
251K ALA* 1.3 92.5 - - + +
253K ARG* 1.3 59.7 + - - +
255K LEU* 3.5 14.4 - - + +
256K VAL* 3.5 1.9 - - - +
382K ILE* 3.7 20.6 - - + -
389K ILE 5.4 0.7 - - - +
392K ARG* 2.9 52.8 + - + +
393K ALA* 3.9 26.7 - - + +
396K ALA* 4.4 0.7 - - + -
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Residues in contact with ARG 253 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165K SER* 3.2 36.8 + - - -
167K GLY 5.4 4.2 + - - +
188K ILE* 3.3 38.8 - - + +
189K GLY* 4.9 0.6 - - - -
192K GLY* 3.9 18.3 + - - -
193K SER* 3.7 10.9 + - - +
196K MET* 3.5 23.1 - - + +
217K ASP* 3.3 7.1 + - - +
218K THR 3.0 34.7 + - - +
219K ASP* 3.2 22.7 + - - +
222K GLN* 4.3 2.2 + - - -
249K ILE 4.1 1.3 - - - +
250K SER 3.4 5.8 + - - +
251K ALA 3.1 0.6 - - - -
252K PRO* 1.3 80.4 - - - +
254K SER* 1.3 86.4 + - - +
256K VAL* 3.2 21.7 + - - +
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Residues in contact with SER 254 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196K MET* 3.9 5.6 - - - +
217K ASP* 5.4 3.9 - - - +
218K THR* 4.0 4.4 - - - -
219K ASP* 3.5 2.1 + - - +
250K SER 2.9 15.9 + - - -
251K ALA 3.9 2.2 - - - -
253K ARG* 1.3 95.7 + - - +
255K LEU* 1.3 63.4 + - - +
256K VAL 3.1 3.7 + - - -
257K ALA* 3.3 10.4 + - - +
258K TYR* 3.3 20.7 - - - -
272K GLU* 2.9 30.8 + - - -
273K ASN* 5.3 3.6 - - - -
276K VAL* 4.4 7.6 - - - -
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Residues in contact with LEU 255 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K TYR* 3.7 17.9 - - + +
251K ALA 2.8 16.2 + - - +
252K PRO* 3.5 7.6 - - + +
254K SER* 1.3 77.9 - - - +
256K VAL* 1.3 62.2 + - - +
258K TYR* 3.1 19.1 + - - +
259K GLU* 3.2 33.3 + - - +
276K VAL* 4.2 10.7 - - + +
279K ILE* 3.8 19.5 - - + -
280K THR* 3.5 32.1 - - + -
382K ILE* 4.1 21.3 - - + -
392K ARG* 3.8 15.0 - - - +
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Residues in contact with VAL 256 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K ALA 5.7 0.4 - - - +
5K ARG* 4.1 12.3 - - - +
193K SER* 3.7 26.9 - - - +
196K MET* 3.7 8.7 - - + +
197K GLU* 3.5 38.8 - - + +
252K PRO 3.5 3.6 - - - +
253K ARG 3.3 16.4 - - - +
254K SER 3.1 0.8 - - - -
255K LEU* 1.3 74.2 - - - +
257K ALA* 1.3 66.4 + - - +
258K TYR 3.0 0.2 + - - -
259K GLU* 3.0 9.2 + - + +
260K ALA* 2.8 24.6 + - + +
392K ARG* 3.5 20.9 - - - +
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Residues in contact with ALA 257 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196K MET* 3.4 20.9 - - + +
200K TRP* 3.7 35.7 - - + +
217K ASP 4.3 8.1 - - - +
254K SER 3.3 9.2 + - - +
255K LEU 3.3 0.4 - - - -
256K VAL* 1.3 77.6 - - - +
258K TYR* 1.3 59.1 + - + +
260K ALA* 3.5 3.3 + - - +
261K GLY 3.2 8.5 + - - -
262K ALA* 2.8 36.8 + - + +
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Residues in contact with TYR 258 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K TYR* 4.3 8.1 + - + -
215K ALA 3.4 19.1 - - - -
216K GLY* 3.7 11.3 - - - -
217K ASP 4.1 5.7 + - - -
254K SER* 3.3 25.4 - - - -
255K LEU 3.1 6.9 + - - +
256K VAL 3.0 0.8 - - - -
257K ALA* 1.3 76.6 - - + +
259K GLU* 1.3 65.9 + - - +
260K ALA 3.1 1.9 + - - -
261K GLY* 3.3 9.0 + - - -
262K ALA* 3.5 27.7 - - + +
264K GLY* 3.8 7.4 - - - -
266K GLY* 3.1 28.4 - - - -
273K ASN* 4.7 2.5 + - - -
276K VAL* 3.5 27.1 - - + -
280K THR* 4.0 13.5 - - + -
282K MET* 3.6 28.7 - - - +
284K MET* 3.8 15.8 - - + -
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Residues in contact with GLU 259 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K ALA* 4.3 6.4 - - - +
4K LYS* 3.0 50.2 + - - +
5K ARG* 3.2 22.6 + - - +
6K TYR* 2.8 37.1 + - + -
255K LEU* 3.2 17.0 + - - +
256K VAL* 3.0 9.2 + - - +
258K TYR* 1.3 76.2 - - - +
260K ALA* 1.3 59.0 + - - +
261K GLY 3.4 0.7 + - - -
392K ARG* 2.6 47.5 + - - -
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Residues in contact with ALA 260 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K ALA* 4.3 15.7 - - - +
197K GLU* 4.5 9.6 - - - +
200K TRP* 3.5 26.4 - - + +
201K THR* 3.8 23.9 + - - +
204K SER* 3.4 12.4 + - - -
256K VAL* 2.8 16.6 + - + +
257K ALA 3.6 2.7 - - - -
259K GLU* 1.3 77.1 - - - +
261K GLY* 1.3 53.7 + - - +
262K ALA 3.8 0.2 - - - -
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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