Contacts of the helix formed by residues 239 - 260 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ASN* 5.6 0.4 + - - -
238A LEU* 1.3 78.1 - - - +
240A HIS* 1.3 61.7 + - - +
241A THR* 3.8 15.7 - - - +
242A ILE* 2.9 30.4 + - + +
243A ALA* 3.2 8.7 + - - +
417A PHE* 4.4 17.7 - - + -
418A GLU* 4.9 5.6 - - + -
421A ALA* 4.0 19.1 - - + -
94B PHE* 3.6 14.2 - - + -
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Residues in contact with HIS 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLY* 2.8 26.6 + - - -
231A GLY 3.3 18.7 + - - -
232A GLY 3.3 18.1 + - - -
233A LEU* 3.9 10.3 - - + -
235A ASN* 5.2 1.6 + - - +
238A LEU 3.4 15.5 - - - -
239A ALA* 1.3 73.1 - - - +
241A THR* 1.3 57.6 + - - +
243A ALA* 3.2 7.5 + - - +
244A VAL* 3.1 28.9 + - - +
298A VAL* 5.6 1.8 - - + -
364A ASP* 2.5 39.9 + - - +
365A PRO* 4.0 7.1 - - + +
366A GLN* 3.5 14.9 + - - +
418A GLU* 3.7 21.2 + - - +
15B ARG* 4.2 2.2 + - - -
94B PHE* 5.8 2.2 - + - -
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Residues in contact with THR 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ALA* 3.8 8.1 - - - +
240A HIS* 1.3 78.4 - - - +
242A ILE* 1.3 57.8 + - - +
244A VAL* 3.5 12.2 - - - +
245A ILE* 3.3 25.6 - - - +
365A PRO* 4.0 17.7 - - + -
404A ILE* 4.3 5.4 - - + -
414A LEU* 4.1 13.2 - - + -
418A GLU* 2.7 48.7 + - + +
421A ALA* 3.9 0.3 - - - +
422A LEU* 3.5 26.9 + - + +
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Residues in contact with ILE 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A VAL* 5.7 1.3 - - + -
179A ASN* 3.2 38.6 - - + +
181A ILE* 3.8 28.5 - - + -
184A LEU* 4.0 13.1 - - + +
238A LEU* 4.0 20.4 - - + -
239A ALA* 2.9 19.1 + - + +
241A THR* 1.3 76.3 + - - +
243A ALA* 1.3 66.5 + - - +
244A VAL 3.3 1.3 - - - -
245A ILE* 3.3 6.5 + - + +
246A ALA* 3.0 21.9 + - + +
421A ALA* 4.2 30.5 - - + +
425A ALA* 5.0 2.9 - - + -
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ALA 5.4 1.6 - - - +
226A ALA* 4.2 26.7 - - - +
227A MET* 4.5 0.9 - - - -
230A GLY* 5.3 2.5 - - - -
238A LEU* 4.3 9.3 - - + +
239A ALA 3.2 10.0 + - - +
240A HIS* 3.2 9.6 + - - +
242A ILE* 1.3 77.7 - - - +
244A VAL* 1.3 62.1 + - - +
246A ALA* 3.3 5.0 + - - +
247A ARG* 3.0 20.8 + - - +
366A GLN* 3.4 30.2 - - - +
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Residues in contact with VAL 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A HIS 3.1 13.5 + - - +
241A THR* 3.5 20.9 - - - +
243A ALA* 1.3 73.1 - - - +
245A ILE* 1.3 64.7 + - + +
247A ARG* 3.0 9.2 + - + +
248A ALA* 2.9 25.1 + - - +
365A PRO* 3.4 22.9 - - + +
366A GLN* 3.9 22.2 - - - +
369A MET* 3.4 32.9 - - + +
400A CYS* 3.8 12.6 - - - -
404A ILE* 4.1 14.8 - - + -
422A LEU* 5.5 0.2 - - + -
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Residues in contact with ILE 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ILE* 4.6 9.4 - - + -
184A LEU* 5.5 4.3 - - + -
241A THR 3.3 20.4 - - - +
242A ILE* 3.3 12.5 + - + +
243A ALA 3.3 0.4 - - - -
244A VAL* 1.3 77.3 - - + +
246A ALA* 1.3 64.7 + - - +
248A ALA* 3.0 13.8 + - - +
249A ILE* 3.1 34.8 + - + +
397A ALA* 4.2 14.1 - - + +
400A CYS* 4.1 15.0 - - - -
401A CYS* 3.9 24.0 - - - -
422A LEU* 4.3 5.8 - - + -
425A ALA* 3.5 32.1 - - + -
429A LEU* 4.5 7.0 - - + -
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Residues in contact with ALA 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A PHE* 4.9 1.8 - - + -
184A LEU* 4.6 14.5 - - + +
188A ILE* 3.9 22.8 - - + +
223A ALA* 4.2 7.7 - - - +
226A ALA* 4.0 22.4 - - + -
242A ILE 3.0 13.1 + - - +
243A ALA 3.3 8.7 + - - +
245A ILE* 1.3 76.5 - - - +
247A ARG* 1.3 61.8 + - - +
249A ILE* 3.4 8.7 + - - +
250A SER* 3.2 21.3 + - - -
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Residues in contact with ARG 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ASP 5.4 1.0 + - - -
223A ALA* 3.5 23.8 + - - +
224A ASN* 2.9 31.9 + - - -
227A MET* 3.5 35.4 - - - +
243A ALA 3.0 13.5 + - - +
244A VAL* 3.0 13.2 + - + +
246A ALA* 1.3 74.6 - - - +
248A ALA* 1.3 65.5 + - - +
250A SER* 2.5 25.8 + - - -
251A ALA* 3.4 3.5 + - - +
269A CYS 4.2 0.4 + - - -
271A TYR* 3.6 20.7 - - - +
272A GLU* 3.2 38.6 + - + +
275A ILE* 4.8 1.0 - - + +
299A MET* 4.8 1.4 - - - +
366A GLN* 5.2 3.0 + - + +
369A MET* 3.7 15.9 - - + -
370A LEU* 4.0 19.2 - - + +
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Residues in contact with ALA 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A VAL 2.9 9.5 + - - +
245A ILE 3.0 8.0 + - - +
247A ARG* 1.3 75.4 - - - +
249A ILE* 1.3 62.3 + - - +
251A ALA* 3.3 8.3 + - - +
252A PRO* 3.3 16.1 - - - +
275A ILE* 4.8 4.5 - - - -
369A MET* 3.4 14.5 - - + +
378A VAL* 4.6 3.7 - - + +
396A ALA* 3.6 23.2 - - + +
397A ALA* 4.3 1.3 - - - -
400A CYS* 3.5 32.1 - - + -
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Residues in contact with ILE 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ILE 4.9 1.3 - - - +
184A LEU* 4.3 8.7 - - + -
185A LEU* 3.8 33.7 - - + +
188A ILE* 3.8 12.8 - - + +
189A GLY* 3.5 30.9 - - - +
245A ILE* 3.1 24.6 + - + +
246A ALA* 3.8 6.5 - - - +
248A ALA* 1.3 72.6 - - - +
250A SER* 1.3 64.1 + - - +
251A ALA 3.1 0.2 - - - -
252A PRO* 3.1 18.4 - - - +
253A ARG* 3.6 5.9 + - - +
393A ALA* 4.2 14.4 - - + +
397A ALA* 3.8 28.3 - - + -
429A LEU* 5.0 2.0 - - + -
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Residues in contact with SER 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ILE* 3.7 10.3 - - - -
219A ASP* 3.3 34.5 - - - -
223A ALA* 3.8 4.0 - - - -
246A ALA 3.2 11.3 + - - -
247A ARG* 2.5 25.1 + - - -
249A ILE* 1.3 74.9 - - - +
251A ALA* 1.3 56.2 + - - +
253A ARG* 3.2 2.5 + - - +
254A SER* 2.8 36.9 + - - -
272A GLU* 3.2 19.3 + - - +
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Residues in contact with ALA 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ARG 4.3 0.2 - - - +
248A ALA 3.3 10.6 + - - +
249A ILE 3.1 0.4 - - - -
250A SER* 1.3 82.3 + - - +
252A PRO* 1.4 64.8 - - + +
254A SER 3.3 0.2 + - - -
255A LEU* 2.9 28.2 + - - +
272A GLU* 4.0 13.0 - - + -
275A ILE* 3.6 46.0 - - + -
276A VAL* 3.8 8.5 - - + +
279A ILE* 6.0 0.4 - - - -
382A ILE* 4.0 4.0 - - + -
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Residues in contact with PRO 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A SER* 4.0 2.8 + - - +
248A ALA 3.3 12.3 - - - +
249A ILE 3.1 20.0 - - - +
251A ALA* 1.4 82.7 - - + +
253A ARG* 1.3 65.4 + - - +
255A LEU* 3.5 14.5 + - + +
256A VAL* 3.6 2.4 - - - +
382A ILE* 3.8 22.4 - - + -
389A ILE 5.3 0.7 - - - +
392A ARG* 3.2 49.4 + - + +
393A ALA* 3.7 28.7 - - + +
396A ALA* 4.4 1.1 - - + -
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Residues in contact with ARG 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A SER* 3.2 29.1 + - - -
167A GLY 5.4 3.8 + - - +
188A ILE* 3.4 30.7 - - + +
189A GLY* 4.8 0.8 - - - -
192A GLY* 3.9 18.7 + - - -
193A SER* 3.5 11.1 + - - +
196A MET* 3.4 24.8 - - + +
217A ASP* 3.1 24.5 + - - +
218A THR 3.1 25.9 + - - +
219A ASP* 3.1 27.7 + - - +
222A GLN* 4.4 2.2 + - - +
249A ILE 3.6 10.7 + - - +
250A SER 3.2 7.2 + - - +
252A PRO* 1.3 81.6 - - - +
254A SER* 1.3 82.4 + - - +
256A VAL* 3.2 18.2 + - - +
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Residues in contact with SER 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A MET* 3.9 2.0 - - - +
217A ASP* 5.2 3.4 - - - +
218A THR* 4.0 4.6 - - - -
219A ASP 3.4 1.7 + - - -
250A SER 2.8 18.0 + - - -
251A ALA 4.0 2.2 - - - -
253A ARG* 1.3 96.1 + - - +
255A LEU* 1.3 64.6 + - - +
256A VAL 3.0 1.0 + - - -
257A ALA* 3.3 14.0 + - - +
258A TYR* 3.5 17.8 - - - -
272A GLU* 2.7 33.2 + - - -
273A ASN* 5.2 4.0 - - - -
276A VAL* 4.4 6.5 - - - -
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Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A TYR* 3.9 11.7 - - + -
251A ALA 2.9 17.9 + - - +
252A PRO* 3.5 7.0 - - + +
253A ARG 3.2 0.2 - - - -
254A SER* 1.3 76.9 - - - +
256A VAL* 1.3 60.9 + - - +
258A TYR* 3.1 17.8 + - - +
259A GLU* 3.2 31.1 + - - +
276A VAL* 4.2 10.2 - - + +
279A ILE* 3.9 37.7 - - + -
280A THR* 3.5 31.9 - - + -
382A ILE* 4.2 11.2 - - + -
392A ARG* 3.8 14.4 - - - +
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Residues in contact with VAL 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ARG* 3.8 15.7 - - - +
193A SER* 3.8 21.8 - - - +
196A MET* 3.6 8.1 - - + +
197A GLU* 3.4 44.0 - - + +
252A PRO 3.6 3.1 - - - +
253A ARG 3.4 15.5 - - - +
254A SER 3.0 1.6 + - - -
255A LEU* 1.3 74.9 - - - +
257A ALA* 1.3 55.2 + - - +
259A GLU* 3.1 8.7 + - + +
260A ALA* 2.8 34.8 + - + +
392A ARG* 3.5 22.2 - - - +
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Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A MET* 3.6 22.6 - - + +
200A TRP* 3.7 34.2 - - + +
217A ASP 4.4 7.9 - - - +
254A SER 3.3 8.8 + - - +
255A LEU 3.3 0.4 - - - -
256A VAL* 1.3 76.0 - - - +
258A TYR* 1.3 65.6 + - + +
260A ALA* 3.3 4.2 + - - +
261A GLY 3.1 9.2 + - - -
262A ALA* 2.8 29.4 + - + +
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Residues in contact with TYR 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A TYR* 4.5 7.8 + - + -
215A ALA 3.3 21.1 - - - -
216A GLY* 3.5 12.4 - - - -
217A ASP 4.1 5.9 + - - -
254A SER* 3.5 24.0 - - - -
255A LEU* 3.1 8.8 + - - +
257A ALA* 1.3 73.9 - - + +
259A GLU* 1.3 68.1 + - - +
260A ALA 3.0 1.1 - - - -
261A GLY* 3.0 12.0 + - - -
262A ALA* 3.5 22.5 - - + +
264A GLY* 3.7 9.6 - - - -
266A GLY* 3.1 28.4 - - - -
273A ASN* 4.6 2.8 + - - -
276A VAL* 3.6 25.6 - - + -
280A THR* 4.0 14.1 - - + -
282A MET* 3.6 33.7 - - + +
284A MET* 3.8 12.7 - - + -
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Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ALA* 3.8 7.5 - - - +
4A LYS* 3.3 48.6 + - - +
5A ARG* 3.3 20.8 + - - +
6A TYR* 2.9 35.5 + - + -
255A LEU* 3.2 15.8 + - - +
256A VAL* 3.1 12.1 + - - +
258A TYR* 1.3 76.3 - - - +
260A ALA* 1.3 57.7 + - - +
261A GLY 3.4 2.1 + - - -
392A ARG* 2.6 46.6 + - - -
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Residues in contact with ALA 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA* 4.1 19.7 - - + +
197A GLU* 4.4 10.3 - - + +
200A TRP* 3.4 21.6 - - + +
201A THR* 4.0 22.3 + - - +
204A SER* 3.4 13.3 + - - -
256A VAL 2.8 16.7 + - - +
257A ALA 3.4 6.7 - - - +
258A TYR 3.0 0.2 - - - -
259A GLU* 1.3 76.0 - - - +
261A GLY* 1.3 56.2 + - - +
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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