Contacts of the helix formed by residues 228 - 279 (chain D) in PDB entry 1YSA
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 228 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D LYS 5.8 0.4 - - - +
227D PRO* 1.3 85.7 - - + +
229D ALA* 1.3 61.8 + - - +
230D LEU 3.0 1.7 + - - -
231D LYS* 3.0 20.6 + - + +
232D ARG* 3.3 20.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D LYS 4.9 1.0 + - - -
226D ASP* 3.4 31.2 - - + +
227D PRO* 3.4 2.0 + - - +
228D ALA* 1.3 73.9 - - - +
230D LEU* 1.3 58.2 + - - +
232D ARG* 4.2 27.0 + - - +
233D ALA* 3.5 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D ASP* 3.9 6.2 + - - +
227D PRO 3.2 11.8 + - - +
228D ALA 3.0 1.2 + - - -
229D ALA* 1.3 77.0 - - - +
231D LYS* 1.3 66.3 + - - +
233D ALA* 3.5 5.4 + - + -
234D ARG* 3.2 67.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A C 5.0 8.7 - - - -
5A T 4.5 23.8 - - - +
36B T 5.6 8.3 - - - -
227D PRO 3.9 2.2 + - - +
228D ALA* 3.0 16.4 + - + +
230D LEU* 1.3 77.7 - - - +
232D ARG* 1.4 58.7 + - + +
234D ARG* 4.0 7.1 - - - +
235D ASN* 3.0 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B T 2.8 55.0 + - + +
34B C 3.5 28.3 - - - +
228D ALA* 3.3 14.8 + - + +
229D ALA* 4.2 27.4 + - - +
231D LYS* 1.4 73.6 - - + +
233D ALA* 1.4 58.4 + - - +
234D ARG 2.7 12.0 + - - -
235D ASN* 2.9 17.7 + - - +
236D THR* 2.9 17.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 233 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B T 5.0 2.9 + - - -
229D ALA 3.5 20.1 + - - +
230D LEU* 3.5 6.7 + - + +
232D ARG* 1.4 73.3 - - - +
234D ARG* 1.3 57.5 + - + +
236D THR* 4.3 8.3 - - - +
237D GLU* 3.4 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 234 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A C 4.8 17.1 + - - -
5A T 3.9 30.4 + - - +
230D LEU* 3.2 54.1 + - + +
231D LYS* 4.0 6.3 - - - +
232D ARG 2.7 4.4 + - - -
233D ALA* 1.3 74.5 - - + +
235D ASN* 1.3 65.5 + - - +
236D THR 3.3 1.3 - - - -
237D GLU* 3.0 8.7 + - - +
238D ALA* 3.0 19.5 + - - +
241D ARG* 4.8 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 235 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A A 3.6 20.2 + - - +
7A T 3.2 25.3 + - - +
33B T 3.8 13.8 - - + +
34B C 3.0 29.9 + - + +
35B A 3.8 3.5 - - - +
231D LYS* 3.0 20.5 + - + +
232D ARG* 2.9 11.5 + - - +
234D ARG* 1.3 70.5 - - - +
236D THR* 1.3 52.6 + - - +
238D ALA* 2.9 11.7 + - - +
239D ALA* 2.8 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 236 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B G 3.6 35.3 + - + +
33B T 3.0 41.4 + - + +
232D ARG* 2.9 15.8 + - - +
233D ALA* 4.3 6.7 - - - +
235D ASN* 1.3 74.0 - - - +
237D GLU* 1.4 67.1 + - - +
239D ALA* 4.1 1.6 - - - +
240D ARG* 3.2 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D ALA 3.4 17.2 + - - +
234D ARG* 3.0 15.4 + - - +
236D THR* 1.4 73.4 - - - +
238D ALA* 1.3 71.1 + - - +
240D ARG* 2.7 41.3 + - - +
241D ARG* 2.9 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A T 4.7 3.4 - - + -
6A A 3.8 41.5 + - + +
7A T 4.2 5.2 - - + -
234D ARG 3.0 9.5 + - - +
235D ASN* 2.9 16.2 + - - +
237D GLU* 1.3 79.9 - - - +
239D ALA* 1.4 58.8 + - - +
241D ARG* 2.9 27.9 + - - +
242D SER* 2.9 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 239 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A T 4.0 16.6 - - + +
8A G 5.6 1.3 - - - +
33B T 3.7 23.8 - - + +
235D ASN* 2.8 13.8 + - - +
236D THR 4.2 3.1 - - - +
238D ALA* 1.4 68.1 - - - +
240D ARG* 1.3 62.4 + - - +
242D SER* 4.4 2.5 - - - +
243D ARG* 3.1 57.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 240 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B A 4.3 5.7 + - - -
32B G 2.5 50.5 + - - +
236D THR* 3.2 18.4 + - - +
237D GLU* 2.7 42.3 + - - +
239D ALA* 1.3 69.2 - - - +
241D ARG* 1.3 52.7 + - + +
243D ARG* 3.7 5.7 - - - +
244D ALA* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 241 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A T 4.4 9.1 + - - -
6A A 3.2 27.7 + - - +
234D ARG 4.8 1.8 + - - -
237D GLU* 2.9 38.5 + - - +
238D ALA* 2.9 27.6 + - - +
240D ARG* 1.3 77.8 - - + +
242D SER* 1.3 63.8 + - - +
244D ALA* 3.2 15.5 + - - +
245D ARG* 3.3 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A A 4.7 1.3 - - - -
7A T 3.2 59.0 + - - +
238D ALA 2.9 15.2 + - - -
239D ALA* 4.0 3.5 - - - -
241D ARG* 1.3 71.2 - - - +
243D ARG* 1.4 67.2 + - - +
245D ARG* 3.4 25.3 - - - +
246D LYS* 3.4 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A A 3.9 8.5 - - - +
10A C 5.0 0.2 - - - +
31B A 3.7 25.8 + - - +
32B G 2.6 54.5 + - - -
33B T 4.1 3.1 + - - +
239D ALA* 3.1 40.4 + - - +
240D ARG* 3.9 5.3 - - - +
242D SER* 1.4 80.0 - - - +
244D ALA* 1.3 65.0 + - - +
246D LYS* 3.6 18.7 + - + +
247D LEU* 3.3 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D ARG 2.9 18.6 + - - +
241D ARG* 3.2 10.5 + - - +
243D ARG* 1.3 69.6 - - - +
245D ARG* 1.3 64.0 + - - +
247D LEU* 2.9 21.7 + - + +
248D GLN* 2.9 15.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A A 3.8 26.4 + - - +
7A T 2.9 29.7 + - - -
238D ALA 5.5 0.2 + - - -
241D ARG* 3.3 30.1 + - - +
242D SER* 3.4 18.7 - - - +
243D ARG 3.4 0.2 - - - -
244D ALA* 1.3 76.7 - - - +
246D LYS* 1.3 65.8 + - - +
248D GLN* 3.1 6.1 + - - +
249D ARG* 2.9 59.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C LYS* 4.5 26.7 - - + +
250C MET* 6.0 6.4 - - - +
242D SER 3.4 11.4 + - - +
243D ARG* 4.1 18.4 - - + +
244D ALA 3.4 0.2 - - - -
245D ARG* 1.3 78.1 - - - +
247D LEU* 1.3 79.8 + - - +
249D ARG* 3.3 18.2 + - - +
250D MET* 3.0 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D ARG 3.3 14.0 + - - +
244D ALA* 2.9 14.9 + - + +
246D LYS* 1.3 86.8 - - - +
248D GLN* 1.3 65.1 + - + +
250D MET* 3.6 14.8 - - + +
251D LYS* 3.1 61.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D ALA 2.9 11.5 + - - +
245D ARG* 3.9 7.2 - - - +
247D LEU* 1.3 83.3 - - + +
249D ARG* 1.3 63.9 + - - +
251D LYS* 4.4 5.8 - - + +
252D GLN* 2.9 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A T 4.3 11.9 + - - -
250C MET* 5.1 20.5 - - + +
245D ARG* 2.9 62.1 + - - +
246D LYS* 3.8 20.9 - - - +
248D GLN* 1.3 71.8 - - - +
250D MET* 1.3 63.7 + - - +
252D GLN* 3.3 19.5 - - - +
253D LEU* 3.0 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C ARG* 6.2 6.3 - - - -
250C MET* 5.6 15.3 - - + -
253C LEU* 4.5 7.8 - - + +
246D LYS* 3.0 30.2 + - + +
247D LEU* 3.6 18.4 - - + +
249D ARG* 1.3 77.5 - - - +
251D LYS* 1.3 71.1 + - + +
253D LEU* 3.3 4.1 + - - +
254D GLU* 3.3 43.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D LEU* 3.1 49.1 + - + +
248D GLN* 4.5 6.1 - - + +
250D MET* 1.3 83.3 - - + +
252D GLN* 1.3 64.2 + - - +
253D LEU 3.2 0.3 + - - -
254D GLU* 3.4 15.2 + - - +
255D ASP* 3.2 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248D GLN* 2.9 29.6 + - - +
249D ARG* 3.3 27.4 + - - +
251D LYS* 1.3 77.8 - - - +
253D LEU* 1.3 72.1 + - + +
255D ASP* 3.5 10.9 + - - +
256D LYS* 3.4 20.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C MET* 4.8 11.9 - - + -
253C LEU* 3.1 42.4 - - + +
254C GLU* 4.0 20.6 - - + -
257C VAL* 3.9 18.1 - - + +
249D ARG* 3.0 20.4 + - + +
250D MET* 3.3 1.8 + - - +
252D GLN* 1.3 87.2 - - - +
254D GLU* 1.3 58.7 + - - +
256D LYS* 2.9 15.0 + - + +
257D VAL* 2.8 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C LEU* 3.6 23.8 - - + +
250D MET* 3.3 37.9 + - + +
251D LYS* 3.8 16.5 - - - +
253D LEU* 1.3 75.3 - - - +
255D ASP* 1.3 66.1 + - - +
257D VAL* 3.7 10.8 - - - +
258D GLU* 3.2 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D LYS* 3.2 25.8 + - - +
252D GLN* 3.8 9.3 - - - +
253D LEU 3.2 0.8 - - - -
254D GLU* 1.3 73.5 - - - +
256D LYS* 1.3 66.5 + - - +
258D GLU* 2.9 13.5 + - - +
259D GLU* 2.9 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C VAL* 4.6 18.6 - - + +
261C LEU* 4.3 25.1 - - - +
252D GLN* 3.4 11.6 + - + +
253D LEU* 2.9 18.0 + - + +
255D ASP* 1.3 79.3 - - - +
257D VAL* 1.3 59.5 + - - +
259D GLU* 4.1 30.5 - - - +
260D LEU* 2.9 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C LEU* 4.1 21.5 - - + -
256C LYS* 4.3 19.1 - - + +
257C VAL* 3.4 34.5 - - + +
260C LEU* 3.6 16.6 - - + +
253D LEU 2.8 15.8 + - - +
254D GLU* 3.7 8.5 - - - +
255D ASP 3.3 0.2 - - - -
256D LYS* 1.3 70.6 - - - +
258D GLU* 1.3 65.6 + - - +
261D LEU* 3.0 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254D GLU* 3.2 13.8 + - - +
255D ASP* 2.9 16.5 + - - +
257D VAL* 1.3 76.3 - - - +
259D GLU* 1.3 64.6 + - - +
261D LEU* 3.1 14.6 + - + +
262D SER* 3.1 19.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D ASP 2.9 16.0 + - - +
256D LYS* 3.8 32.8 - - - +
258D GLU* 1.3 69.6 - - - +
260D LEU* 1.3 73.2 + - - +
262D SER* 2.9 17.4 + - - -
263D LYS* 3.0 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C VAL* 4.0 4.7 - - + +
260C LEU* 3.5 37.7 - - + +
261C LEU* 3.4 44.0 - - + -
263C LYS* 5.7 0.2 - - - -
264C ASN* 4.2 17.0 - - + +
256D LYS* 2.9 29.2 + - + +
259D GLU* 1.3 79.3 - - - +
261D LEU* 1.3 63.8 + - - +
262D SER 3.1 0.2 + - - -
263D LYS* 3.1 23.7 + - - +
264D ASN* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C LEU* 3.6 26.9 - - + -
263C LYS* 4.9 7.5 + - - +
257D VAL* 3.0 32.3 + - + +
258D GLU* 3.1 17.0 + - - +
260D LEU* 1.3 78.4 - - - +
262D SER* 1.3 60.2 + - - +
264D ASN* 3.4 4.5 + - - +
265D TYR* 3.1 38.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D GLU 3.1 7.1 + - - -
259D GLU* 2.9 11.4 + - - -
261D LEU* 1.3 81.1 - - - +
263D LYS* 1.3 69.3 + - - +
264D ASN 3.5 0.2 + - - -
265D TYR* 3.6 10.2 + - - +
266D HIS* 3.6 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C ASN* 3.3 24.0 + - - +
259D GLU* 3.0 49.9 + - + +
260D LEU* 3.9 15.9 - - - +
262D SER* 1.3 74.0 - - - +
264D ASN* 1.3 60.0 + - - +
266D HIS* 2.8 33.1 + - - +
267D LEU* 3.4 12.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C LEU 3.2 8.2 + - - +
263C LYS* 3.1 39.1 + - - +
264C ASN* 2.6 63.8 + - - +
267C LEU* 3.8 6.0 - - + +
260D LEU* 2.9 18.4 + - - +
261D LEU 4.0 2.5 - - - +
263D LYS* 1.3 73.5 - - - +
265D TYR* 1.3 62.5 + - - +
267D LEU* 3.3 8.4 + - - +
268D GLU* 2.9 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C LYS* 6.5 0.4 - - - -
261D LEU* 3.1 25.9 + - + +
262D SER* 3.6 6.3 + - - +
263D LYS 3.1 0.6 + - - -
264D ASN* 1.3 72.7 - - - +
266D HIS* 1.3 65.0 + - - +
267D LEU 3.1 0.2 + - - -
268D GLU* 3.2 22.6 + - - +
269D ASN* 3.0 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D SER 3.6 7.2 + - - +
263D LYS* 2.8 17.8 + - - +
265D TYR* 1.3 76.0 - - - +
267D LEU* 1.3 77.5 + - + +
269D ASN* 3.5 13.6 + - - +
270D GLU* 3.0 46.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C ASN* 4.0 23.8 - - - +
267C LEU* 3.9 16.4 - - + -
268C GLU* 3.2 49.4 - - - +
271C VAL* 4.3 12.6 - - + -
263D LYS* 3.4 9.2 + - + +
264D ASN* 3.6 9.6 - - - +
266D HIS* 1.3 96.8 - - + +
268D GLU* 1.3 66.8 + - - +
270D GLU* 3.0 9.7 + - + +
271D VAL* 2.8 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 268 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C LYS* 4.9 12.6 - - - -
267C LEU* 3.7 19.6 - - + +
264D ASN 2.9 19.8 + - - +
265D TYR* 3.2 40.3 + - - +
267D LEU* 1.3 71.7 - - - +
269D ASN* 1.3 62.2 + - - +
271D VAL* 3.0 8.5 + - - +
272D ALA* 2.9 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 269 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D TYR* 3.0 34.5 + - - +
266D HIS* 3.5 15.2 + - - +
268D GLU* 1.3 70.5 - - - +
270D GLU* 1.4 58.6 + - - +
272D ALA* 3.0 9.8 + - - +
273D ARG* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 270 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C VAL* 3.9 17.8 - - + +
275C LYS* 4.5 12.9 + - - -
281C ARG 5.2 5.2 - - - +
266D HIS* 3.0 35.8 + - + +
267D LEU* 3.0 14.8 + - + +
269D ASN* 1.4 72.2 - - - +
271D VAL* 1.3 62.9 + - - +
273D ARG* 2.8 38.0 + - - +
274D LEU* 2.9 50.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 271 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C LEU* 4.6 6.5 - - + +
270C GLU* 3.6 31.9 - - + +
271C VAL* 3.3 30.5 - - + +
274C LEU* 4.4 2.5 - - + -
267D LEU 2.8 12.9 + - - +
268D GLU* 3.4 11.4 - - - +
270D GLU* 1.3 78.0 - - - +
272D ALA* 1.3 62.8 + - - +
274D LEU* 4.8 3.4 - - - -
275D LYS* 3.1 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D GLU 2.9 11.8 + - - +
269D ASN* 3.0 10.7 + - - +
271D VAL* 1.3 76.4 - - - +
273D ARG* 1.3 64.7 + - - +
275D LYS* 3.4 6.9 + - - +
276D LYS* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 273 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C LYS* 5.8 1.0 - - - +
281C ARG* 5.5 9.2 - - - +
269D ASN 2.9 14.5 + - - +
270D GLU* 2.8 43.8 + - - +
272D ALA* 1.3 76.5 - - - +
274D LEU* 1.3 88.5 + - - +
276D LYS* 2.7 36.7 + - + +
277D LEU* 2.9 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 274 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C VAL* 3.9 22.2 - - + +
274C LEU* 4.1 17.5 - - + +
275C LYS* 4.0 28.3 - - + +
278C VAL* 3.7 30.1 - - + -
270D GLU* 2.9 37.7 + - - +
271D VAL* 4.3 2.5 - - - +
273D ARG* 1.3 95.8 - - - +
275D LYS* 1.3 56.9 + - - +
277D LEU* 3.6 9.1 - - + +
278D VAL* 3.1 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 275 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C GLU* 3.1 23.5 + - - -
273C ARG* 4.5 7.3 - - - +
274C LEU* 3.5 32.2 - - + +
271D VAL* 3.1 33.3 + - + +
272D ALA* 3.6 6.5 - - - +
274D LEU* 1.3 72.1 - - - +
276D LYS* 1.4 55.7 + - - +
278D VAL 3.9 0.3 - - - -
279D GLY* 3.0 29.4 - - - +
280D GLU* 3.7 58.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 276 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D ALA 3.0 10.5 + - - +
273D ARG* 2.7 36.6 + - + +
275D LYS* 1.4 70.0 - - - +
277D LEU* 1.3 72.4 + - + +
278D VAL* 3.3 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 277 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C VAL* 4.4 15.0 - - + -
281C ARG* 5.1 15.7 - - - +
273D ARG* 2.9 48.3 + - + +
274D LEU* 3.6 18.2 - - + +
276D LYS* 1.3 85.4 - - + +
278D VAL* 1.3 66.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 278 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C LEU* 4.7 5.6 - - + +
277C LEU* 3.4 46.9 - - + +
278C VAL* 3.5 26.2 - - + -
274D LEU 3.1 13.6 + - - +
275D LYS 3.9 3.2 - - - +
276D LYS 4.4 2.6 - - - +
277D LEU* 1.3 78.7 - - + +
279D GLY* 1.4 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 279 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C ARG* 4.6 3.6 + - - -
274C LEU* 3.7 18.0 - - - +
277C LEU* 5.3 2.9 - - - +
275D LYS* 3.0 26.2 + - - +
278D VAL* 1.4 82.8 - - - +
280D GLU* 1.4 63.3 - - - +
----------------------------------------------------------
Back to top of page
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