Contacts of the helix formed by residues 249 - 281 (chain I) in PDB entry 4DVQ
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 249 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I TRP* 3.2 27.9 + - - -
236I GLN* 5.5 0.2 + - - -
237I LEU* 4.9 6.5 - - - -
240I MET* 5.6 2.5 - - - -
245I SER 3.4 13.9 + - - +
248I ILE* 1.3 80.7 - - - +
250I PRO* 1.3 65.8 - - - +
251I LYS* 3.2 3.5 + - - +
252I VAL* 3.6 32.4 + - - +
253I TRP* 3.5 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 250 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246I ARG 4.1 17.5 - - - +
247I TRP* 3.6 16.3 - - - +
248I ILE 3.7 3.8 - - - +
249I SER* 1.3 85.8 - - - +
251I LYS* 1.3 76.8 + - + +
253I TRP* 3.9 6.9 + - + +
254I LYS* 3.6 17.2 + - - +
56J TRP* 5.5 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 251 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249I SER* 3.2 0.6 - - - -
250I PRO* 1.3 88.1 - - + +
252I VAL* 1.3 67.2 + - + +
254I LYS* 3.0 11.9 + - + +
255I GLU* 2.8 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 252 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233I SER* 4.0 10.8 - - - +
236I GLN* 3.1 45.5 - - + +
237I LEU* 3.5 28.3 - - + -
249I SER* 3.6 29.8 + - - +
250I PRO 3.5 0.4 - - - -
251I LYS* 1.3 79.2 - - + +
253I TRP* 1.3 55.2 + - - +
255I GLU* 3.4 11.8 + - - +
256I HIS* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 253 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I GLU* 4.4 3.1 - - + -
115I PRO* 3.9 20.0 - - + -
118I ALA* 3.4 34.8 - - + -
122I HIS* 5.9 1.8 - + - -
237I LEU* 3.3 31.8 - - + +
242I ARG* 4.7 18.6 - - + -
245I SER* 2.7 39.0 + - - -
246I ARG* 4.0 13.2 - - + +
249I SER 3.5 19.9 + - - -
250I PRO* 4.0 8.1 - - + +
251I LYS 3.1 1.0 - - - -
252I VAL* 1.3 74.6 - - - +
254I LYS* 1.3 60.2 + - - +
256I HIS* 3.8 1.5 - + - +
257I PHE* 2.9 64.8 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 254 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250I PRO 3.6 10.5 + - - +
251I LYS* 3.0 12.2 + - + +
253I TRP* 1.3 77.2 - - - +
255I GLU* 1.3 57.2 - - - +
257I PHE* 3.5 6.3 + - - +
258I GLU* 2.8 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 255 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229I VAL* 3.9 23.3 - - + +
232I LYS* 4.4 11.7 - - - -
233I SER* 3.8 16.4 - - - -
236I GLN* 3.9 13.0 + - - +
251I LYS* 2.8 17.0 + - - +
252I VAL* 3.5 9.7 - - - +
254I LYS* 1.3 76.3 - - - +
256I HIS* 1.3 55.4 + - - +
258I GLU* 3.2 9.1 + - - +
259I ALA* 2.8 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 256 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115I PRO* 3.5 38.5 - - + +
116I TRP* 3.9 2.2 - + - -
230I MET* 3.6 5.4 + - - -
233I SER* 2.8 32.1 + - - +
234I THR* 3.3 26.4 + - - -
237I LEU* 4.4 11.2 - - + -
252I VAL 2.9 17.6 + - - +
253I TRP 3.8 2.9 - - - +
255I GLU* 1.3 75.9 - - - +
257I PHE* 1.3 71.8 + + - +
259I ALA* 3.7 5.0 + - - +
260I TRP* 3.0 60.6 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 257 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115I PRO 4.4 2.2 - - - -
118I ALA 3.9 7.0 - - - -
119I TYR* 3.7 49.0 - + + -
122I HIS* 3.6 35.9 - + + -
123I ARG* 5.1 10.1 - - - +
253I TRP* 2.9 55.0 + + - +
254I LYS* 3.8 5.6 - - - +
256I HIS* 1.3 82.9 - + - +
258I GLU* 1.3 60.6 + - - +
260I TRP 3.4 0.2 + - - -
261I ASP* 2.8 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 258 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254I LYS* 2.8 26.2 + - + +
255I GLU* 3.2 8.8 + - - +
257I PHE* 1.3 73.8 - - - +
259I ALA* 1.3 66.1 + - - +
261I ASP* 3.1 14.8 + - + +
262I CYS* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 259 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226I ALA* 3.7 13.5 - - - +
229I VAL* 4.0 13.7 - - + -
230I MET* 3.9 28.7 - - - +
255I GLU 2.8 17.2 + - - +
256I HIS* 3.7 6.3 - - - +
258I GLU* 1.3 75.4 - - - +
260I TRP* 1.3 61.9 + - - +
262I CYS* 3.2 6.2 + - - +
263I ILE* 3.1 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 260 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I TRP* 3.6 32.8 - + - +
119I TYR* 3.5 35.4 - + + -
120I ARG* 3.6 19.1 - - - -
230I MET* 3.2 36.3 - - + +
256I HIS* 3.0 59.9 + + - +
257I PHE 3.8 0.2 - - - +
258I GLU 3.3 0.2 - - - -
259I ALA* 1.3 72.4 - - - +
261I ASP* 1.3 61.3 + - - +
263I ILE* 3.8 26.4 - - + +
264I PHE* 2.9 68.3 + + - -
309I MET* 4.6 3.4 - - + -
313I ALA* 4.7 10.8 - - + -
602I 1CA 5.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 261 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119I TYR* 2.8 32.8 + - - -
123I ARG* 3.3 28.0 + - - -
257I PHE* 2.8 29.9 + - - +
258I GLU* 3.1 14.5 + - + +
260I TRP* 1.3 75.9 - - - +
262I CYS* 1.3 61.1 + - - +
264I PHE* 4.2 1.5 - - - +
265I GLN* 3.3 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 262 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222I ASN* 3.6 28.3 - - - -
223I PHE* 4.6 2.7 - - - -
226I ALA* 3.6 21.1 - - + -
258I GLU 3.1 11.1 + - - +
259I ALA* 3.5 9.6 - - - +
260I TRP 3.1 0.2 - - - -
261I ASP* 1.3 76.0 - - - +
263I ILE* 1.3 64.0 + - - +
265I GLN* 3.6 16.0 + - - +
266I TYR* 3.3 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 263 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223I PHE* 4.0 27.2 - - + -
226I ALA* 3.8 13.0 - - + -
227I LEU* 4.0 21.5 - - + +
230I MET* 3.7 37.7 - - + -
259I ALA 3.1 12.7 + - - +
260I TRP* 3.8 21.8 - - + +
262I CYS* 1.3 75.9 - - - +
264I PHE* 1.3 63.6 + - - +
266I TYR* 3.1 4.7 + - - +
267I GLY 3.0 18.5 + - - -
309I MET* 3.4 22.8 - - + +
312I THR* 6.5 0.2 - - + -
313I ALA* 4.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 264 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119I TYR* 3.6 24.0 - + - +
120I ARG* 3.7 27.4 - - - -
125I HIS* 3.4 42.4 - + + +
260I TRP* 2.9 52.1 + + - +
261I ASP 4.2 2.0 - - - +
263I ILE* 1.3 76.8 - - - +
265I GLN* 1.3 53.3 + - - +
268I ASP* 2.7 41.9 + - + +
306I ALA* 6.4 1.8 - - - -
309I MET* 3.5 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 265 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222I ASN* 6.3 0.8 - - - +
261I ASP 3.3 18.0 + - - +
262I CYS* 3.6 17.8 + - - +
264I PHE* 1.3 75.4 - - - +
266I TYR* 1.3 75.3 + - - +
268I ASP* 4.0 7.0 - - - -
269I ASN* 3.3 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 266 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197I ILE* 3.7 12.9 - - + +
201I ASN* 3.9 5.8 + - - -
209I LEU* 3.4 29.7 - - + +
211I LEU* 5.3 0.6 - - + +
219I ALA* 4.3 25.4 - - + -
220I SER* 4.9 3.8 - - - -
223I PHE* 3.7 57.2 - + + -
262I CYS* 3.3 13.9 + - - +
263I ILE 3.1 8.8 + - - +
265I GLN* 1.3 85.7 - - - +
267I GLY* 1.3 67.5 + - - +
269I ASN* 3.3 14.8 + - - +
270I CYS* 3.3 29.2 + - - -
312I THR* 3.9 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 267 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205I PHE* 4.8 0.3 - - - -
263I ILE 3.0 9.7 + - - -
266I TYR* 1.3 78.4 - - - +
268I ASP* 1.3 60.2 + - - +
270I CYS* 3.0 15.2 + - - +
271I ILE* 2.9 37.0 + - - +
309I MET* 3.8 15.0 - - - -
312I THR* 4.4 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 268 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125I HIS* 6.0 2.1 - - - -
264I PHE* 2.7 28.3 + - + +
265I GLN* 4.2 5.2 - - - -
267I GLY* 1.3 73.4 - - - +
269I ASN* 1.3 54.5 + - - +
271I ILE* 3.7 15.3 - - + +
272I GLN* 2.6 60.4 + - - +
305I LYS* 4.6 20.3 + - - +
309I MET* 4.1 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 269 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265I GLN* 3.3 22.6 + - - +
266I TYR* 3.6 6.8 + - - +
267I GLY 3.1 1.0 - - - -
268I ASP* 1.3 74.4 - - - +
270I CYS* 1.3 71.0 + - - +
272I GLN* 3.5 8.8 + - - +
273I LYS* 3.2 49.3 + - - +
496L LEU* 4.7 14.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 270 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201I ASN* 3.8 23.1 - - - +
205I PHE* 3.6 33.1 - - + +
209I LEU* 6.2 2.2 - - - -
266I TYR* 3.3 33.2 - - - -
267I GLY* 3.0 11.8 + - - +
269I ASN* 1.3 83.0 - - - +
271I ILE* 1.3 62.0 + - - +
273I LYS* 3.3 11.6 + - - +
274I ILE* 3.2 22.5 + - - +
312I THR* 4.9 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 271 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205I PHE* 4.4 4.0 - - + -
267I GLY 2.9 21.7 + - - +
268I ASP* 3.7 18.2 - - + +
269I ASN 3.2 0.4 - - - -
270I CYS* 1.3 76.1 - - - +
272I GLN* 1.3 60.4 + - + +
274I ILE* 3.0 13.2 - - + +
275I TYR* 2.9 33.7 + - + +
290I VAL* 5.9 2.2 - - + -
294I LEU* 6.0 4.0 - - + -
301I LEU* 5.5 3.1 - - + -
304I ILE* 6.2 2.5 - - + -
305I LYS* 3.9 58.6 - - + +
308I SER* 3.7 26.9 - - - +
309I MET* 4.4 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 272 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268I ASP* 2.6 42.2 + - - +
269I ASN* 4.0 7.9 - - - +
270I CYS 3.4 0.2 - - - -
271I ILE* 1.3 79.5 - - + +
273I LYS* 1.3 56.9 + - - +
275I TYR* 4.0 6.4 - - - +
276I GLN* 3.1 29.8 + - - +
305I LYS* 6.1 4.5 - - - +
496L LEU* 3.8 26.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 273 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207I GLU* 3.2 43.3 + - + +
209I LEU* 5.1 10.9 - - - +
269I ASN* 3.2 43.4 + - - +
270I CYS* 3.6 10.5 - - - +
271I ILE 3.2 0.8 - - - -
272I GLN* 1.3 75.2 - - - +
274I ILE* 1.3 67.7 + - - +
276I GLN* 3.4 1.4 + - - +
277I GLU* 3.0 31.0 + - - +
184L LEU* 5.4 3.4 - - - +
185L THR* 3.5 46.0 + - + +
496L LEU* 4.6 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 274 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205I PHE* 3.5 31.2 - - + +
270I CYS 3.2 10.8 + - - +
271I ILE* 3.0 22.2 - - + +
273I LYS* 1.3 77.5 - - - +
275I TYR* 1.3 57.9 + - - +
277I GLU* 3.1 2.7 + - - +
278I LEU* 2.8 43.4 + - + +
287I THR 4.6 0.2 - - - +
290I VAL* 4.4 5.4 - - + -
291I ALA* 3.9 26.5 - - + +
294I LEU* 4.0 13.2 - - + -
181L ARG* 3.3 45.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 275 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271I ILE* 2.9 24.3 + - + +
272I GLN* 4.0 6.3 - - - +
274I ILE* 1.3 78.3 - - - +
276I GLN* 1.3 56.0 + - - +
278I LEU* 3.8 2.6 - - + +
279I ALA* 2.9 30.9 + - + +
294I LEU* 4.1 24.9 - - + -
301I LEU* 3.7 45.2 - - + +
305I LYS* 6.4 0.4 - - - -
476L LEU* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 276 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272I GLN 3.1 18.5 + - - +
273I LYS* 4.0 4.3 - - - +
274I ILE 3.2 0.2 - - - -
275I TYR* 1.3 73.8 - - - +
277I GLU* 1.3 66.7 + - - +
279I ALA* 3.6 3.5 + - - +
280I PHE* 3.5 22.5 - - + +
185L THR* 3.9 5.8 - - + +
474L GLU 3.2 11.6 + - - +
475L THR* 3.8 2.8 - - - +
476L LEU* 2.9 51.0 + - + +
477L THR* 4.5 2.4 + - - +
496L LEU* 3.0 35.0 + - + +
497L LEU 3.7 0.6 - - - -
498L THR* 2.7 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 277 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207I GLU* 3.4 18.8 - - - +
273I LYS 3.0 16.6 + - - +
274I ILE 3.5 2.9 - - - +
276I GLN* 1.3 77.7 - - - +
278I LEU* 1.3 62.7 + - - +
280I PHE 3.0 12.5 + - - -
281I ASN 3.2 11.5 + - - +
179L ASN* 6.1 0.5 - - - +
181L ARG* 2.6 51.3 + - - +
183L SER* 3.4 28.8 + - - +
185L THR* 2.6 35.6 + - - +
498L THR* 4.0 8.5 - - + -
500L ARG* 3.2 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 278 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274I ILE* 2.8 26.3 + - + +
275I TYR* 3.9 5.4 - - + +
277I GLU* 1.3 71.5 - - - +
279I ALA* 1.3 66.3 + - - +
280I PHE 3.1 0.7 + - - -
281I ASN 3.2 16.2 + - - +
282I ARG* 3.9 15.3 + - - +
283I PRO* 3.6 32.3 - - + -
291I ALA* 3.6 38.4 - - + +
294I LEU* 3.9 25.8 - - + -
295I LEU* 4.3 13.5 - - + -
181L ARG* 4.0 17.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 279 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275I TYR* 2.9 24.4 + - + +
276I GLN 3.7 7.9 - - - +
277I GLU 3.3 0.4 - - - -
278I LEU* 1.3 77.1 - - - +
280I PHE* 1.3 59.7 + - + +
282I ARG* 5.7 1.0 - - - +
476L LEU* 3.9 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 280 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276I GLN* 3.5 15.9 - - + +
277I GLU* 3.0 8.4 + - - +
279I ALA* 1.3 81.1 - - + +
281I ASN* 1.3 65.2 + - - +
282I ARG* 5.7 0.7 - - - -
331L ALA 5.5 3.6 - - - -
334L PRO* 5.8 8.7 - - + -
474L GLU* 3.3 57.2 - - + +
475L THR* 3.3 36.6 - - - -
476L LEU* 4.1 14.1 - - + -
478L GLN* 5.8 2.5 - - - -
498L THR* 6.3 0.4 - - - -
500L ARG* 4.2 1.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 281 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277I GLU 3.2 3.2 + - - +
278I LEU* 3.2 22.9 + - - +
280I PHE* 1.3 81.9 + - - +
282I ARG* 1.3 69.0 + - - +
283I PRO* 3.6 25.3 - - - +
181L ARG* 5.6 0.7 - - - -
500L ARG* 3.6 37.1 + - - +
----------------------------------------------------------
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