Contacts of the helix formed by residues 251 - 275 (chain D) in PDB entry 6D6U
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 251 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C SER* 4.4 13.7 + - - -
248C ALA* 6.2 2.7 - - - -
247D LEU* 6.5 0.2 - - - -
248D ASN* 3.5 20.2 + - - +
249D ARG 3.5 1.3 - - - -
250D GLU* 1.3 73.2 - - - +
252D VAL* 1.3 66.1 + - - +
253D PRO* 3.6 4.9 - - - -
254D ALA* 3.7 15.7 + - - -
255D ARG* 3.4 24.8 + - - +
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Residues in contact with VAL 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D ARG 4.1 12.3 - - - +
250D GLU* 2.8 19.3 + - - +
251D SER* 1.3 70.4 - - - +
253D PRO* 1.3 77.4 - - + +
255D ARG* 3.1 5.1 + - - +
256D THR* 3.0 36.7 + - + +
304D PHE* 4.3 8.7 - - + -
308D ASN* 3.6 32.3 - - - +
409D Y01 5.2 4.7 - - + +
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Residues in contact with PRO 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C ALA* 6.5 0.7 - - + -
250D GLU 5.0 0.2 - - - +
251D SER* 3.8 3.1 - - - -
252D VAL* 1.3 96.0 - - + +
254D ALA* 1.3 62.2 + - - +
256D THR* 2.5 25.4 + - + +
257D VAL* 2.9 17.1 + - - +
257E ILE* 3.8 24.9 - - + -
258E ASN* 5.4 11.0 - - + +
261E ALA* 4.0 24.5 - - + -
264E ALA* 4.1 9.4 - - + -
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Residues in contact with ALA 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C SER* 6.1 0.4 - - - +
248C ALA* 4.8 17.8 - - + +
251C VAL* 4.3 30.1 - - + +
247D LEU* 5.0 4.3 - - + -
251D SER* 3.9 20.4 - - - +
252D VAL 3.2 0.8 - - - -
253D PRO* 1.3 81.6 - - - +
255D ARG* 1.3 59.9 + - + +
257D VAL* 3.4 4.6 + - - +
258D PHE* 2.9 30.2 + - - +
264E ALA* 5.1 2.6 - - - +
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Residues in contact with ARG 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D SER* 2.4 48.6 + - - +
245D PHE* 4.0 13.5 + - - +
247D LEU* 3.1 40.2 + - + +
248D ASN 3.3 21.2 + - - +
249D ARG* 4.3 12.9 - - - +
251D SER 3.4 10.9 + - - +
252D VAL 3.1 3.8 + - - +
254D ALA* 1.3 76.4 - - + +
256D THR* 1.3 58.2 + - - +
258D PHE* 3.3 7.0 + - - +
259D GLY* 2.9 27.0 + - - -
303D GLU* 5.0 1.6 + - - -
304D PHE* 3.1 50.2 - - + +
307D VAL* 5.9 1.4 - - - +
322D ASP* 4.5 18.3 + - - -
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Residues in contact with THR 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D VAL* 3.0 24.8 + - + +
253D PRO* 2.5 27.5 + - + +
255D ARG* 1.3 76.1 - - - +
257D VAL* 1.3 67.0 + - - +
259D GLY* 3.2 2.1 + - - -
260D VAL* 3.0 30.1 + - - +
301D LEU* 5.1 2.3 - - - +
304D PHE* 3.5 25.8 - - + -
409D Y01 4.1 28.0 - - + -
253E VAL* 5.2 4.0 - - - -
257E ILE* 4.1 16.7 - - + +
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Residues in contact with VAL 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C ALA* 5.6 4.0 - - + -
255C ILE* 4.5 13.7 - - + -
253D PRO 2.9 16.4 + - - +
254D ALA* 3.9 4.3 - - - +
256D THR* 1.3 84.3 + - - +
258D PHE* 1.3 63.5 + - - +
260D VAL* 3.9 5.5 - - - +
261D THR* 2.8 41.2 + - - +
257E ILE* 4.8 7.9 - - + -
264E ALA* 3.6 38.8 - - + +
267E SER* 4.8 13.5 - - - -
268E LEU* 4.7 17.9 - - + +
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Residues in contact with PHE 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C VAL* 4.8 3.8 - - + -
255C ILE* 3.4 37.5 - - + +
296C LEU* 4.3 9.6 - - + -
240D LEU* 3.0 48.9 - - + -
241D SER* 4.3 5.4 - - - -
243D VAL* 3.7 17.0 - - + -
244D SER* 3.3 39.3 - - - -
247D LEU* 4.3 12.8 - - + -
254D ALA 2.9 18.4 + - - +
255D ARG* 3.5 7.4 - - - +
257D VAL* 1.3 80.1 - - - +
259D GLY* 1.3 62.7 + - - +
261D THR* 4.3 1.8 - - - -
262D THR* 3.3 27.8 + - + +
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Residues in contact with GLY 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D SER* 5.8 2.5 - - - -
255D ARG 2.9 16.1 + - - -
256D THR 3.8 2.5 - - - -
258D PHE* 1.3 80.0 - - - +
260D VAL* 1.3 60.7 + - - +
262D THR* 2.5 24.8 + - - -
263D VAL* 3.6 10.0 + - - +
297D VAL 5.5 0.5 - - - +
301D LEU* 4.3 20.1 - - - +
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Residues in contact with VAL 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D THR 3.0 23.2 + - - +
257D VAL* 3.3 3.3 + - - +
259D GLY* 1.3 76.6 - - - +
261D THR* 1.3 63.3 + - - +
263D VAL* 3.1 10.2 + - - +
264D LEU* 3.0 24.1 + - + +
301D LEU* 4.8 5.4 - - + -
409D Y01 4.7 10.8 - - + -
250E LEU* 3.6 42.0 - - + +
253E VAL* 4.4 19.7 - - + -
268E LEU* 3.7 28.0 - - + -
272E THR* 6.0 0.2 - - + -
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Residues in contact with THR 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C ILE* 3.4 33.0 - - + +
259C LEU* 3.6 29.2 - - + -
257D VAL* 2.8 26.1 + - - +
258D PHE 4.3 1.8 - - - -
260D VAL* 1.3 77.2 - - - +
262D THR* 1.3 58.0 + - - +
264D LEU* 3.2 9.8 + - - +
265D THR* 2.9 33.4 + - - +
268E LEU* 4.9 3.1 - - - +
271E THR* 3.8 18.9 + - + +
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Residues in contact with THR 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D THR* 3.9 7.9 - - + +
240D LEU* 4.6 15.3 - - + +
241D SER* 3.7 41.0 - - - +
258D PHE* 3.3 18.6 + - + +
259D GLY* 2.5 26.0 + - - -
261D THR* 1.3 78.5 - - - +
263D VAL* 1.3 58.6 + - - +
265D THR* 3.3 8.3 + - - -
266D MET* 2.9 33.2 + - - +
297D VAL* 4.3 8.2 + - - +
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Residues in contact with VAL 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259D GLY 3.8 11.9 - - - +
260D VAL* 3.1 9.3 + - - +
262D THR* 1.3 76.6 + - - +
264D LEU* 1.3 58.8 + - - +
266D MET* 3.2 7.5 + - - +
267D THR* 2.9 39.9 + - - +
294D TYR* 4.8 4.9 - - + +
297D VAL* 3.9 20.2 - - + +
298D PHE* 3.5 44.9 - - + -
301D LEU* 4.7 9.9 - - + -
246E LEU* 4.7 6.1 - - + -
247E ILE* 6.2 0.2 - - + -
250E LEU* 4.2 19.1 - - + -
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Residues in contact with LEU 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C LEU* 3.7 11.9 - - + -
260D VAL* 3.0 29.8 + - + +
261D THR* 3.2 13.0 + - - +
263D VAL* 1.3 76.1 - - - +
265D THR* 1.3 62.3 + - - +
267D THR* 3.2 6.3 + - - -
268D THR* 3.0 28.1 + - - +
247E ILE* 3.5 35.9 - - + -
250E LEU* 3.7 17.0 - - + -
268E LEU* 4.4 3.6 - - + -
271E THR* 3.5 28.3 - - + -
272E THR* 4.3 15.7 - - + +
275E THR* 4.1 10.9 - - - +
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Residues in contact with THR 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C VAL* 5.2 7.6 - - + +
259C LEU* 3.2 23.6 + - - +
262C THR* 4.3 26.0 - - + +
289C PHE* 6.2 1.3 - - + -
237D THR* 3.5 27.4 - - + +
261D THR* 2.9 17.9 + - - +
262D THR* 3.3 9.7 + - - -
264D LEU* 1.3 74.4 - - - +
266D MET* 1.3 58.7 + - - +
268D THR* 2.6 22.7 + - - -
269D LEU* 2.9 18.3 + - + +
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Residues in contact with MET 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D CYS* 5.3 0.7 - - + -
237D THR* 3.7 26.2 - - + -
238D VAL* 5.3 0.4 - - - -
262D THR 2.9 18.2 + - - +
263D VAL* 3.2 9.6 + - - +
265D THR* 1.3 76.0 - - - +
267D THR* 1.3 58.4 + - - +
269D LEU* 3.8 12.9 - - + +
270D SER* 2.9 33.5 + - - +
290D ILE* 4.4 8.1 - - + +
293D CYS* 3.4 50.7 - - + +
294D TYR* 3.6 25.6 - - + +
297D VAL* 4.1 20.0 - - + -
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Residues in contact with THR 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D VAL* 2.9 15.2 + - - +
264D LEU 3.6 7.4 - - - -
266D MET* 1.3 76.8 - - - +
268D THR* 1.3 63.9 + - - +
270D SER* 3.9 3.0 - - - -
271D ILE* 3.0 50.4 + - + +
294D TYR* 3.9 17.4 - - + +
243E PRO* 4.1 16.8 - - + +
246E LEU* 4.0 14.3 - - + +
247E ILE* 4.1 23.8 - - + +
275E THR* 5.2 3.1 - - + -
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Residues in contact with THR 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C LEU* 5.3 2.5 - - + +
262C THR* 4.2 13.2 - - - +
263C THR* 4.7 14.0 - - + +
266C THR* 4.8 8.5 - - - +
264D LEU 3.0 13.3 + - - +
265D THR* 2.6 28.0 + - - -
267D THR* 1.3 75.7 - - - +
269D LEU* 1.3 56.6 + - - +
271D ILE* 3.4 7.5 + - + +
272D SER* 3.0 29.9 + - - -
275E THR* 3.7 31.2 - - + +
278E THR* 3.9 18.6 - - - +
282E ILE* 4.9 3.3 - - - +
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Residues in contact with LEU 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C THR* 5.1 11.2 - - + -
266C THR* 5.2 9.9 - - + -
229D GLN* 4.4 9.9 - - - +
230D THR* 4.0 16.4 - - + +
233D PRO* 3.5 28.5 - - + +
234D CYS* 3.5 36.6 - - + +
237D THR* 4.8 5.4 - - - +
265D THR* 2.9 20.9 + - + +
266D MET* 3.9 11.9 - - + +
268D THR* 1.3 76.4 + - - +
270D SER* 1.3 57.0 + - - +
272D SER* 3.3 6.6 + - - -
273D ALA* 2.9 31.5 + - + +
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Residues in contact with SER 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D THR* 6.3 0.2 - - - -
266D MET* 2.9 19.8 + - - +
267D THR* 3.9 4.7 - - - -
269D LEU* 1.3 76.5 - - - +
271D ILE* 1.3 60.5 + - - +
273D ALA* 4.0 4.2 - - - +
274D ARG* 2.9 54.1 + - - +
290D ILE* 3.5 31.7 - - - +
294D TYR* 5.5 6.5 - - - -
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Residues in contact with ILE 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267D THR* 3.0 42.0 + - + +
268D THR* 3.8 6.3 - - + +
270D SER* 1.3 78.0 - - - +
272D SER* 1.3 63.0 + - - +
273D ALA 3.4 0.3 + - - -
274D ARG* 4.4 14.2 - - - +
275D ASN* 3.6 19.6 + - - +
243E PRO* 3.7 20.0 - - + -
275E THR* 6.3 1.1 - - + -
279E LEU* 3.6 36.1 - - + -
282E ILE* 3.7 33.3 - - + +
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Residues in contact with SER 272 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C THR* 3.9 35.4 + - - +
269C ARG* 5.5 2.6 - - - +
229D GLN* 4.7 13.3 + - - -
268D THR 3.0 17.8 + - - -
269D LEU* 3.3 6.9 + - - -
271D ILE* 1.3 77.0 - - - +
273D ALA* 1.3 60.9 + - - +
275D ASN* 4.0 11.1 + - - +
276D SER* 4.7 2.9 + - - -
282E ILE* 4.2 13.9 - - - +
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Residues in contact with ALA 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D GLN* 5.9 3.4 - - - +
230D THR* 3.3 39.0 - - + +
269D LEU* 2.9 18.4 + - + +
270D SER* 4.0 3.1 - - - +
272D SER* 1.3 75.6 - - - +
274D ARG* 1.3 61.6 + - - +
275D ASN 3.1 6.1 + - - -
276D SER* 3.3 20.5 + - - -
277D LEU 4.2 1.6 + - - -
286D MET* 4.4 12.2 - - + +
290D ILE* 4.6 10.1 - - + -
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Residues in contact with ARG 274 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D SER* 2.9 47.4 + - - +
271D ILE* 4.6 12.9 - - - +
273D ALA* 1.3 75.9 - - - +
275D ASN* 1.3 63.0 + - - +
276D SER 3.4 0.2 - - - -
277D LEU* 3.5 28.2 + - + +
286D MET* 4.9 5.4 - - + -
287D ASP* 4.6 17.3 - - - +
290D ILE* 5.5 6.0 - - + +
239E GLN* 3.6 32.2 + - - +
240E THR* 5.3 3.6 + - - +
243E PRO* 4.6 12.3 - - - +
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Residues in contact with ASN 275 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C GLU* 5.3 1.7 - - - +
56D HIS* 5.9 1.9 - - - -
271D ILE 3.6 15.5 + - - +
272D SER* 4.1 7.6 - - - +
273D ALA 3.1 1.4 - - - -
274D ARG* 1.3 80.0 - - - +
276D SER* 1.3 62.0 + - - +
277D LEU 3.3 6.6 + - - +
282E ILE* 3.6 27.6 - - + +
285E LYS* 5.9 1.2 - - - +
286E SER* 4.7 17.5 + - - -
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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