Contacts of the helix formed by residues 239 - 260 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238I LEU* 1.3 75.6 - - - +
240I HIS* 1.3 61.5 + - - +
241I THR* 3.8 17.3 - - - +
242I ILE* 2.8 32.1 + - + +
243I ALA* 3.1 9.9 + - - +
417I PHE* 4.6 10.3 - - + -
418I GLU* 5.1 4.7 - - + -
421I ALA* 3.8 20.4 - - + -
94J PHE* 3.5 20.3 - - + +
96J PRO* 5.5 1.2 - - - +
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Residues in contact with HIS 240 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230I GLY* 2.7 33.7 + - - -
231I GLY 3.3 12.6 + - - -
232I GLY 3.2 25.6 + - - -
233I LEU* 4.0 8.7 - - + -
235I ASN 5.6 1.5 + - - -
238I LEU 3.2 10.0 + - - -
239I ALA* 1.3 72.7 - - - +
241I THR* 1.3 56.4 + - - +
243I ALA* 3.4 7.1 + - + +
244I VAL* 3.1 29.1 + - - +
298I VAL* 5.8 2.7 - - + -
364I ASP* 2.6 38.1 + - - +
365I PRO* 3.8 7.3 - - + +
366I GLN* 3.7 12.7 + - - +
418I GLU* 3.8 21.1 + - - +
15J ARG* 4.2 3.2 + - - -
94J PHE* 5.1 2.4 - + - -
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Residues in contact with THR 241 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239I ALA* 3.8 8.3 - - - +
240I HIS* 1.3 77.6 - - - +
242I ILE* 1.3 61.6 + - - +
244I VAL* 3.4 17.6 - - - +
245I ILE* 3.6 17.9 - - - +
365I PRO* 4.1 19.5 - - + -
404I ILE* 4.5 5.6 - - + -
414I LEU* 4.3 11.7 - - + -
418I GLU* 2.9 48.4 + - + +
421I ALA* 3.8 0.5 - - - +
422I LEU* 3.8 26.6 + - + +
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Residues in contact with ILE 242 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176I VAL* 5.9 1.3 - - + +
179I ASN* 3.0 39.7 - - + +
181I ILE* 4.1 17.5 - - + -
184I LEU* 4.0 25.0 - - + +
238I LEU* 4.2 18.4 - - + -
239I ALA* 2.8 27.9 + - + +
241I THR* 1.3 77.5 + - - +
243I ALA* 1.3 65.3 + - - +
244I VAL 3.2 1.6 - - - -
245I ILE* 2.9 17.9 + - + +
246I ALA* 3.1 11.2 + - + +
421I ALA* 4.0 23.8 - - + +
425I ALA* 5.0 2.7 - - + -
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Residues in contact with ALA 243 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223I ALA 5.3 1.7 - - - +
226I ALA* 4.1 14.4 - - - +
227I MET* 4.4 1.6 - - - +
230I GLY* 5.4 3.1 - - - -
238I LEU* 3.9 20.8 - - + +
239I ALA 3.1 8.5 + - - +
240I HIS* 3.7 5.8 - - - +
242I ILE* 1.3 76.6 - - - +
244I VAL* 1.3 61.5 + - - +
246I ALA* 3.2 11.8 + - - +
247I ARG* 3.1 19.8 + - - +
366I GLN* 3.4 30.4 - - - +
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Residues in contact with VAL 244 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240I HIS 3.1 14.9 + - - +
241I THR* 3.4 20.4 - - - +
242I ILE 3.2 0.4 - - - -
243I ALA* 1.3 73.8 - - - +
245I ILE* 1.3 68.1 + - + +
247I ARG* 3.3 5.0 + - + -
248I ALA 3.1 17.7 + - - -
365I PRO* 3.3 31.4 - - + +
366I GLN* 3.6 19.7 - - + +
369I MET* 3.3 33.8 - - + +
400I CYS* 3.7 14.5 - - - -
404I ILE* 4.2 7.4 - - + -
422I LEU* 5.8 0.9 - - + -
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Residues in contact with ILE 245 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181I ILE* 4.5 15.0 - - + -
184I LEU* 5.5 3.4 - - + -
241I THR 3.6 17.3 - - - +
242I ILE* 2.9 13.6 + - + +
244I VAL* 1.3 77.1 - - + +
246I ALA* 1.3 64.2 + - - +
248I ALA* 3.2 3.6 + - - +
249I ILE* 3.1 37.2 + - + +
397I ALA* 4.2 16.6 - - + +
400I CYS* 4.2 15.0 - - - -
401I CYS* 3.7 26.0 - - - -
422I LEU* 4.7 7.0 - - + -
425I ALA* 3.5 31.9 - - + -
429I LEU* 4.6 1.6 - - + -
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Residues in contact with ALA 246 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172I PHE* 5.0 0.7 - - + -
184I LEU* 4.8 12.3 - - + +
188I ILE* 4.1 23.3 - - + +
223I ALA* 4.6 6.7 - - - -
226I ALA* 4.1 23.1 - - + -
242I ILE* 3.1 9.6 + - + +
243I ALA 3.2 10.3 + - - +
245I ILE* 1.3 75.9 - - - +
247I ARG* 1.3 64.5 + - - +
249I ILE* 3.2 10.0 + - - +
250I SER* 3.0 22.3 + - - -
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Residues in contact with ARG 247 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219I ASP* 5.5 0.6 - - - +
223I ALA* 3.3 30.6 + - + +
224I ASN* 2.7 30.7 + - - -
227I MET* 3.6 26.3 - - - +
243I ALA 3.1 12.4 + - - +
244I VAL* 3.4 12.8 - - + +
246I ALA* 1.3 77.3 - - - +
248I ALA* 1.3 63.4 + - - +
250I SER* 2.7 23.0 + - - -
251I ALA* 3.3 5.2 + - - +
269I CYS 4.3 0.2 + - - -
271I TYR* 3.4 21.8 - - - +
272I GLU* 3.0 43.4 + - + +
275I ILE* 5.0 1.2 - - + +
299I MET* 5.6 2.4 - - - +
366I GLN* 5.3 4.7 + - + +
369I MET* 3.9 4.9 - - + -
370I LEU* 3.7 29.0 - - + +
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Residues in contact with ALA 248 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244I VAL 3.1 6.6 + - - +
245I ILE 3.2 8.7 + - - +
247I ARG* 1.3 76.1 - - - +
249I ILE* 1.3 60.9 + - - +
250I SER 3.3 0.5 + - - -
251I ALA* 3.5 5.4 + - - +
252I PRO* 3.3 15.9 - - - +
275I ILE* 5.0 2.9 - - - -
369I MET* 3.4 13.6 - - + +
378I VAL* 4.7 7.4 - - + +
396I ALA* 3.6 25.1 - - + +
397I ALA* 4.3 1.6 - - - +
400I CYS* 3.6 31.4 - - + -
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Residues in contact with ILE 249 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181I ILE* 4.9 2.9 - - + +
184I LEU* 3.8 18.6 - - + +
185I LEU* 3.7 30.5 - - + +
188I ILE* 3.5 12.8 - - + +
189I GLY* 3.5 32.4 - - - +
245I ILE* 3.1 28.7 + - + +
246I ALA* 3.7 7.2 - - - +
248I ALA* 1.3 75.1 - - - +
250I SER* 1.3 58.2 + - - +
252I PRO* 3.1 22.5 - - - +
253I ARG* 3.8 3.5 + - - +
393I ALA* 4.1 14.8 - - + +
397I ALA* 4.0 19.7 - - + -
429I LEU* 5.8 0.4 - - + -
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Residues in contact with SER 250 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188I ILE* 3.6 8.5 - - - -
219I ASP* 3.0 35.4 - - - -
223I ALA* 3.8 4.6 - - - +
246I ALA 3.0 9.8 + - - -
247I ARG* 2.7 23.6 + - - -
249I ILE* 1.3 76.3 - - - +
251I ALA* 1.3 65.8 + - - +
253I ARG* 3.0 4.5 + - - +
254I SER* 2.9 24.3 + - - -
272I GLU* 3.3 20.9 + - - +
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Residues in contact with ALA 251 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247I ARG 3.3 2.0 + - - -
248I ALA 3.7 7.4 - - - +
250I SER* 1.3 80.9 + - - +
252I PRO* 1.4 65.4 - - + +
254I SER* 3.1 2.4 + - - -
255I LEU* 2.8 28.0 + - - +
272I GLU* 3.9 14.3 - - + +
275I ILE* 3.4 46.9 - - + -
276I VAL* 3.8 7.5 - - + +
279I ILE* 6.1 0.7 - - - -
382I ILE* 4.1 2.9 - - + -
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Residues in contact with PRO 252 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189I GLY* 5.8 0.4 - - - -
193I SER* 4.0 3.5 + - - +
248I ALA 3.3 8.7 - - - +
249I ILE 3.1 22.0 - - - +
251I ALA* 1.4 88.2 - - + +
253I ARG* 1.3 61.2 + - - +
255I LEU* 3.4 15.5 - - + +
256I VAL* 3.5 2.8 - - - +
382I ILE* 4.0 20.1 - - + -
389I ILE 5.5 0.7 - - - +
392I ARG* 2.9 50.8 + - + +
393I ALA* 3.9 26.7 - - + -
396I ALA* 4.6 0.2 - - + -
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Residues in contact with ARG 253 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165I SER* 2.9 42.4 + - - -
167I GLY 5.2 5.1 + - - +
188I ILE* 3.5 29.6 - - + +
189I GLY* 4.9 1.0 - - - -
192I GLY* 3.8 18.0 + - - -
193I SER* 3.7 10.3 - - - +
196I MET* 3.5 26.1 - - + +
217I ASP* 3.3 11.5 + - - -
218I THR 3.0 34.6 + - - +
219I ASP* 3.2 27.0 + - - +
222I GLN* 4.3 3.6 + - - +
249I ILE 3.8 4.9 + - - +
250I SER 3.0 10.5 + - - +
252I PRO* 1.3 79.9 - - - +
254I SER* 1.3 73.6 + - - +
256I VAL* 3.3 21.1 + - - +
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Residues in contact with SER 254 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196I MET* 3.9 9.3 - - - +
217I ASP* 5.5 3.0 - - - +
218I THR* 4.1 4.4 - - - -
219I ASP* 3.5 1.6 + - - +
250I SER 2.9 13.5 + - - -
251I ALA 3.7 3.4 - - - -
253I ARG* 1.3 90.9 + - - +
255I LEU* 1.3 65.2 + - - +
257I ALA* 3.2 15.1 + - - +
258I TYR* 3.4 20.3 - - - -
272I GLU* 2.7 32.6 + - - -
273I ASN* 5.2 4.3 - - - -
276I VAL* 4.3 6.7 - - - -
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Residues in contact with LEU 255 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I TYR* 3.8 18.6 - - + -
251I ALA 2.8 16.4 + - - +
252I PRO* 3.4 10.3 - - + +
254I SER* 1.3 73.6 - - - +
256I VAL* 1.3 65.6 + - - +
258I TYR* 2.9 17.3 + - - +
259I GLU* 3.1 30.8 + - - +
276I VAL* 4.2 11.4 - - + +
279I ILE* 3.9 29.4 - - + -
280I THR* 3.6 30.5 - - + -
382I ILE* 3.9 19.3 - - + -
392I ARG* 4.0 6.5 - - - +
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Residues in contact with VAL 256 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I ALA 5.3 0.2 - - - +
5I ARG* 4.1 12.3 - - - +
193I SER* 3.6 26.7 - - - +
196I MET* 3.5 7.9 - - + +
197I GLU* 3.3 40.6 - - + +
252I PRO 3.5 4.0 - - - +
253I ARG 3.4 16.4 - - - +
254I SER 3.1 0.4 - - - -
255I LEU* 1.3 78.3 - - - +
257I ALA* 1.3 51.0 - - - +
259I GLU* 3.0 11.3 + - + +
260I ALA* 2.7 33.9 + - + +
392I ARG* 3.5 20.0 - - - +
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Residues in contact with ALA 257 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196I MET* 3.7 18.3 - - + +
200I TRP* 3.9 34.0 - - + +
217I ASP 4.5 5.2 - - - +
254I SER 3.2 13.4 + - - +
255I LEU 3.1 0.6 + - - -
256I VAL* 1.3 77.5 - - - +
258I TYR* 1.3 68.2 - - + +
260I ALA* 3.2 12.1 + - - +
261I GLY 3.2 1.9 + - - -
262I ALA* 3.1 28.0 + - + +
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Residues in contact with TYR 258 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I TYR* 4.4 8.4 + - + +
215I ALA 3.1 21.1 - - - -
216I GLY* 3.5 12.7 - - - -
217I ASP 4.1 6.2 + - - -
254I SER* 3.4 24.5 - - - -
255I LEU* 2.9 7.3 + - - +
257I ALA* 1.3 75.1 - - + +
259I GLU* 1.3 67.4 + - - +
260I ALA 3.1 1.1 - - - -
261I GLY* 3.3 10.2 + - - -
262I ALA* 3.4 33.1 - - + +
264I GLY* 3.7 8.3 - - - -
266I GLY* 3.3 27.0 - - - -
273I ASN* 4.8 3.3 + - - -
276I VAL* 3.6 28.9 - - + -
280I THR* 4.0 12.6 - - + -
282I MET* 3.8 25.9 - - + +
284I MET* 3.8 10.1 - - + +
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Residues in contact with GLU 259 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I ALA* 3.5 10.6 - - - +
4I LYS* 3.3 45.9 + - - +
5I ARG* 3.3 16.6 + - - -
6I TYR* 3.1 37.6 + - + -
255I LEU* 3.1 15.1 + - - +
256I VAL* 3.0 15.7 + - - +
258I TYR* 1.3 76.8 - - - +
260I ALA* 1.3 58.8 + - - +
261I GLY 3.6 0.5 + - - -
392I ARG* 2.4 49.2 + - - -
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Residues in contact with ALA 260 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I ALA* 4.0 15.6 - - + +
197I GLU* 4.3 12.1 - - - +
200I TRP* 3.4 22.4 - - + +
201I THR* 4.0 22.6 + - - +
204I SER* 3.2 13.4 + - - -
256I VAL 2.7 15.0 + - - +
257I ALA 3.2 6.7 + - - +
258I TYR 3.1 0.2 - - - -
259I GLU* 1.3 77.4 - - - +
261I GLY* 1.3 55.7 + - - +
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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