Contacts of the helix formed by residues 241 - 269 (chain D) in PDB entry 1WR6
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 241 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D SER* 1.3 77.3 - - - +
242D ASP* 1.3 62.7 + - - +
243D GLY* 3.0 7.2 + - - -
244D ASP* 2.8 38.8 + - - +
245D ARG* 3.3 23.9 + - - -
49H GLN* 5.5 1.6 - - - +
51H GLU* 5.8 3.8 - - - -
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Residues in contact with ASP 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D SER* 1.3 72.8 - - - +
243D GLY* 1.3 57.6 + - - +
245D ARG* 3.4 26.3 + - - +
246D GLU* 3.1 28.1 + - - +
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Residues in contact with GLY 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D SER* 3.0 8.4 + - - -
242D ASP* 1.3 77.9 - - - +
244D ASP* 1.3 58.3 + - - +
246D GLU* 3.3 7.8 - - - +
247D LEU 3.0 18.5 + - - -
49H GLN* 2.8 27.6 + - - -
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Residues in contact with ASP 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231D MSE 3.9 12.2 - - + +
240D SER* 4.6 3.4 - - - -
241D SER* 2.8 29.9 + - - +
242D ASP 3.4 0.2 - - - -
243D GLY* 1.3 71.2 - - - +
245D ARG* 1.3 58.3 + - - +
246D GLU 2.9 1.8 - - - -
247D LEU* 2.9 3.3 + - - +
248D MSE 2.7 59.3 + - + +
47H GLY 4.9 0.7 - - - -
48H LYS* 4.4 23.0 + - - +
49H GLN* 3.1 38.2 + - - +
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Residues in contact with ARG 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D TYR* 3.4 32.3 + - + -
237D GLN 4.7 8.7 + - - -
238D GLU 5.6 0.4 + - - -
240D SER* 2.7 39.1 + - - +
241D SER 3.3 21.0 + - - +
242D ASP* 3.4 28.8 + - - +
244D ASP* 1.3 78.9 - - - +
246D GLU* 1.3 57.9 + - - +
248D MSE 3.6 13.5 + - - +
249D LYS* 3.1 26.0 + - - +
293D TYR* 4.3 4.4 + - - +
297D ILE* 4.7 18.8 - - + -
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Residues in contact with GLU 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D ASP 3.1 19.9 + - - +
243D GLY* 3.3 9.3 - - - +
244D ASP 2.9 0.8 - - - -
245D ARG* 1.3 75.5 - - - +
247D LEU* 1.3 63.8 + - - +
248D MSE 3.1 0.2 - - - -
249D LYS* 3.2 9.1 + - - +
250D GLU* 2.6 51.7 + - - +
42H ARG* 2.8 16.8 + - - -
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Residues in contact with LEU 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231D MSE 3.8 12.6 - - + -
243D GLY 3.0 12.6 + - - +
244D ASP 2.9 7.0 + - - +
246D GLU* 1.3 75.5 + - - +
248D MSE 1.3 62.7 + - - +
250D GLU* 3.3 5.2 + - + +
251D LEU* 3.1 43.9 + - + +
42H ARG* 3.4 31.4 - - + +
44H ILE* 3.5 38.4 - - + -
49H GLN* 3.7 18.8 - - + +
70H VAL* 4.0 17.3 - - + -
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Residues in contact with MSE 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D LEU* 4.4 9.7 - - + +
231D MSE 3.8 51.8 - - + +
232D LEU* 4.1 16.2 - - - -
235D TYR* 3.8 26.0 - - + -
240D SER* 5.2 2.0 - - - +
244D ASP* 2.7 43.4 + - + +
245D ARG* 3.7 8.3 - - - +
247D LEU* 1.3 75.3 - - - +
249D LYS* 1.3 55.4 + - - +
251D LEU* 3.3 9.3 + - - +
252D PHE* 2.8 35.0 + - - +
293D TYR* 3.9 14.8 - - + -
297D ILE* 4.3 7.6 - - - -
47H GLY 5.0 1.8 - - - +
48H LYS* 6.0 2.0 - - - +
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Residues in contact with LYS 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D ARG 3.1 15.0 + - - +
246D GLU* 3.2 15.0 + - - +
248D MSE 1.3 74.1 - - - +
250D GLU* 1.3 58.2 + - + +
252D PHE* 3.3 16.0 + - + +
253D ASP* 2.6 70.9 + - - +
293D TYR* 3.5 24.6 + - - +
298D GLU* 5.3 5.8 + - - -
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Residues in contact with GLU 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D GLU* 2.6 41.7 + - - +
247D LEU* 3.4 9.6 - - + +
249D LYS* 1.3 81.4 - - + +
251D LEU* 1.3 57.0 + - + +
253D ASP* 3.4 7.0 + - - +
254D GLN* 2.8 34.8 + - - +
42H ARG* 2.8 30.2 + - - +
70H VAL* 5.1 2.4 - - - +
71H LEU 4.9 0.3 - - - +
73H LEU* 3.5 38.3 - - + +
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Residues in contact with LEU 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D ASN* 4.4 15.4 - - - +
227D LEU* 4.2 18.2 - - + -
228D LEU* 3.7 24.0 - - + -
231D MSE 3.9 20.9 - - - -
247D LEU* 3.1 41.3 + - + +
248D MSE 3.3 6.5 + - - +
250D GLU* 1.3 76.3 - - + +
252D PHE* 1.3 57.1 + - - +
254D GLN* 3.2 6.9 + - + +
255D CYS* 2.7 39.2 + - - -
8H LEU* 4.4 22.4 - - + -
70H VAL* 5.2 4.3 - - + -
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Residues in contact with PHE 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ASN* 5.8 2.0 - - - -
228D LEU* 4.0 10.5 - - + +
248D MSE 2.8 17.3 + - - +
249D LYS* 3.4 13.2 - - - +
251D LEU* 1.3 74.4 - - - +
253D ASP* 1.3 76.1 + - - +
255D CYS* 3.2 3.4 + - - +
256D GLU* 3.0 57.0 + - - +
290D ILE* 3.5 44.2 - - + -
293D TYR* 3.3 51.6 - + + -
294D LYS* 4.3 11.9 - - + -
298D GLU* 5.0 6.3 - - - -
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Residues in contact with ASP 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C ASP* 4.9 3.6 - - - +
249D LYS* 2.6 58.2 + - - +
250D GLU* 3.7 6.9 - - - +
252D PHE* 1.3 79.2 - - - +
254D GLN* 1.3 65.6 + - - +
256D GLU* 3.1 21.8 + - - +
257D ASN* 3.3 22.2 + - - +
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Residues in contact with GLN 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D GLU* 5.2 1.7 - - - +
224D ASN* 3.7 20.4 - - - +
250D GLU 2.8 19.9 + - - +
251D LEU* 3.3 12.8 - - + +
253D ASP* 1.3 80.6 - - - +
255D CYS* 1.3 56.5 + - - +
257D ASN* 3.4 12.3 + - - +
258D LYS* 3.1 49.6 + - - +
8H LEU* 6.2 0.4 - - + -
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Residues in contact with CYS 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D ASN* 4.2 26.7 - - - -
228D LEU* 4.0 17.9 - - + -
251D LEU* 2.7 26.0 + - - +
252D PHE* 3.6 7.0 - - - +
254D GLN* 1.3 71.7 - - - +
256D GLU* 1.3 66.4 + - - +
258D LYS* 3.3 5.3 + - - +
259D ARG* 2.9 23.9 + - - +
286D LEU* 3.6 29.6 - - + +
289D VAL* 4.5 6.5 - - + -
290D ILE* 4.1 16.5 - - + +
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Residues in contact with GLU 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C ASP* 3.2 36.7 - - - +
272C ASN* 5.6 0.5 + - - +
252D PHE* 3.0 51.4 + - - +
253D ASP* 3.1 14.0 + - - +
255D CYS* 1.3 75.6 - - - +
257D ASN* 1.3 61.9 + - - +
259D ARG* 3.3 12.1 + - - +
260D ARG* 3.2 40.9 + - - +
290D ILE* 3.4 32.5 - - + +
294D LYS* 4.2 9.0 + - - -
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Residues in contact with ASN 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D ASP* 3.3 19.5 + - - +
254D GLN* 3.8 14.3 + - - +
255D CYS 3.2 0.2 - - - -
256D GLU* 1.3 74.6 - - - +
258D LYS* 1.3 68.2 + - + +
260D ARG* 2.8 37.6 + - - +
261D THR* 2.9 27.1 + - + +
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Residues in contact with LYS 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D GLU* 2.8 38.4 + - - +
221D VAL* 4.6 18.8 - - + +
224D ASN* 3.5 34.8 - - + +
254D GLN* 3.1 46.1 + - + +
255D CYS* 3.3 8.0 + - - +
257D ASN* 1.3 76.2 - - + +
259D ARG* 1.3 63.2 + - - +
261D THR* 3.1 13.8 + - + +
262D LEU* 2.9 25.2 + - + +
286D LEU* 4.1 11.9 - - + -
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Residues in contact with ARG 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C THR* 6.1 0.4 - - - +
276C LEU* 3.4 31.2 - - - +
280C LEU* 5.1 2.2 - - - +
255D CYS 2.9 16.5 + - - +
256D GLU* 3.6 13.9 + - - +
257D ASN 3.1 0.2 - - - -
258D LYS* 1.3 76.3 - - - +
260D ARG* 1.3 65.6 + - + +
262D LEU* 3.1 5.8 + - - +
263D PHE* 2.9 47.4 + - + -
283D SER* 4.1 12.8 - - - +
286D LEU* 3.7 15.4 - - + +
287D SER* 3.0 41.2 + - - +
290D ILE* 3.5 33.3 - - + +
291D ASN* 4.9 3.8 + - - -
294D LYS* 4.9 6.1 - - - +
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Residues in contact with ARG 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C ALA 4.1 7.2 - - - +
267C SER* 3.1 43.1 - - - +
268C GLU* 5.2 0.4 - - - +
269C THR* 3.2 28.3 + - + +
270C GLU* 4.3 2.0 - - - +
271C ASP* 2.8 35.8 + - - +
256D GLU* 3.2 28.7 + - - +
257D ASN* 2.8 36.8 + - - +
259D ARG* 1.3 83.8 - - + +
261D THR* 1.3 56.9 + - + +
263D PHE* 3.4 4.3 + - + -
264D LYS* 3.0 22.2 + - - +
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Residues in contact with THR 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D ASN* 2.9 22.8 + - + +
258D LYS* 3.1 11.6 + - + +
260D ARG* 1.3 75.6 - - + +
262D LEU* 1.3 68.9 + - - +
264D LYS* 3.1 20.1 + - - +
265D LEU* 2.8 36.4 + - - +
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Residues in contact with LEU 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D THR* 5.3 5.4 - - - +
218D LEU* 4.7 9.4 - - + -
221D VAL* 4.1 18.4 - - + -
258D LYS 2.9 13.6 + - - +
259D ARG 3.5 8.5 - - - +
261D THR* 1.3 87.4 + - - +
263D PHE* 1.3 57.5 + - - +
265D LEU* 3.3 11.5 + - + +
266D ALA* 2.8 25.3 + - - +
279D ILE* 3.3 29.7 - - + +
282D ALA* 3.4 31.9 - - + -
283D SER* 3.5 18.4 - - - +
286D LEU* 3.7 20.9 - - + -
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Residues in contact with PHE 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C PHE* 3.4 45.3 - + - +
266C ALA* 3.6 26.5 - - + -
267C SER 3.8 3.4 - - - +
276C LEU* 4.2 10.8 - - + -
280C LEU* 3.7 32.8 - - + -
259D ARG* 2.9 52.6 + - + -
260D ARG* 3.7 7.9 - - + +
262D LEU* 1.3 73.6 - - - +
264D LYS* 1.3 61.3 + - - +
266D ALA* 3.2 5.5 + - + +
267D SER* 2.9 25.6 + - - -
280D LEU* 5.8 2.5 - - + -
283D SER* 3.9 23.8 - - - -
287D SER* 5.0 2.0 - - - -
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Residues in contact with LYS 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C LYS* 6.2 0.9 - - + -
267C SER* 3.5 18.1 - - - +
260D ARG 3.0 14.9 + - - +
261D THR* 3.4 21.6 - - - +
263D PHE* 1.3 76.7 - - - +
265D LEU* 1.3 76.4 + - + +
267D SER* 2.6 26.1 + - - +
268D GLU* 3.3 32.7 + - - +
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Residues in contact with LEU 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D LEU* 3.9 36.8 - - + +
217D THR* 5.3 5.4 - - - +
218D LEU* 6.0 1.6 - - + -
261D THR* 2.8 20.6 + - - +
262D LEU* 3.5 20.6 - - + +
264D LYS* 1.3 102.5 - - - +
266D ALA* 1.3 54.7 + - - +
268D GLU* 2.8 37.1 + - - +
269D THR* 3.0 14.1 + - - -
279D ILE* 4.4 10.8 - - + -
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Residues in contact with ALA 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C ARG* 4.0 5.9 - - - +
263C PHE* 3.7 21.0 - - + -
262D LEU 2.8 21.2 + - - +
263D PHE* 3.5 9.0 - - + +
265D LEU* 1.3 74.1 - - - +
267D SER* 1.3 60.8 + - - +
268D GLU 3.1 0.9 + - - -
269D THR* 3.3 16.6 + - - +
276D LEU* 3.4 33.2 - - + +
279D ILE* 4.3 4.4 - - + +
280D LEU* 3.9 11.9 - - + -
----------------------------------------------------------
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Residues in contact with SER 267 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C ARG* 3.1 54.0 - - - +
263C PHE* 3.6 3.1 - - - +
264C LYS* 3.5 31.7 - - - +
263D PHE 2.9 8.9 + - - -
264D LYS* 2.6 27.2 + - - +
266D ALA* 1.3 76.3 - - - +
268D GLU* 1.3 60.2 + - - +
269D THR 3.6 0.2 - - - -
----------------------------------------------------------
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Residues in contact with GLU 268 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C ARG* 4.9 0.9 - - - -
264D LYS* 3.3 32.4 + - + +
265D LEU* 2.8 26.2 + - - +
267D SER* 1.3 83.4 - - - +
269D THR* 1.3 57.2 + - - -
270D GLU* 2.8 15.2 + - - +
----------------------------------------------------------
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Residues in contact with THR 269 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C ARG* 3.7 17.8 + - - +
215D LEU* 5.4 0.3 - - - +
265D LEU 3.0 12.2 + - - -
266D ALA 3.3 9.9 + - - +
268D GLU* 1.3 72.8 - - - +
270D GLU* 1.3 73.0 + - - +
273D ASP* 3.7 6.3 - - + +
274D ASN* 3.3 44.6 + - - +
276D LEU* 3.7 28.5 - - + +
279D ILE* 3.6 21.7 - - - +
----------------------------------------------------------
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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