Contacts of the helix formed by residues 284 - 314 (chain D) in PDB entry 2CX9
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 PHE 284 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLU* 3.0 26.7 - - + +
377C LEU* 6.4 0.7 - - + -
276D ALA* 3.4 22.4 - - + -
277D PHE* 3.6 29.2 - + + -
279D ARG* 3.1 48.7 - - + -
281D ILE* 3.3 24.9 - - + +
282D ALA 3.0 0.6 - - - +
283D GLU* 1.3 85.9 - - + +
285D GLU* 1.3 60.0 + - - +
286D GLY 4.2 0.9 - - - +
287D VAL* 2.9 25.6 + - + +
288D SER* 2.9 12.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 285 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A PHE* 3.4 30.4 - - + +
285A GLU* 3.1 10.9 + - + +
286A GLY* 2.7 40.8 + - - +
373B GLU* 5.9 0.6 - - - +
377B LEU* 3.0 38.0 - - + +
283D GLU 3.7 4.0 + - - +
284D PHE* 1.3 71.6 - - - +
286D GLY* 1.3 57.8 + - - +
288D SER* 2.9 9.6 - - - +
289D PHE* 2.7 54.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 286 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLU* 2.8 17.4 + - - +
289A PHE* 3.8 29.8 - - - -
373C GLU* 5.0 3.4 - - - -
284D PHE* 5.0 0.2 - - - -
285D GLU* 1.3 78.6 - - - +
287D VAL* 1.3 59.0 + - - +
289D PHE* 4.3 2.5 - - - +
290D LYS* 3.1 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 287 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C GLU* 6.3 1.8 - - + -
271D ALA* 4.1 16.4 - - + -
281D ILE* 2.9 46.7 - - + +
282D ALA* 3.6 13.2 - - - -
284D PHE* 2.9 8.8 + - + +
286D GLY* 1.3 76.1 - - - +
288D SER* 1.3 66.2 + - - +
290D LYS* 3.1 14.0 + - + +
291D LEU* 3.0 28.2 + - + +
343D ILE* 4.4 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 288 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B LYS 5.0 0.2 - - - -
377B LEU* 3.9 14.6 - - - +
380B ALA* 3.5 27.0 - - - +
384B LEU* 5.7 0.7 - - - -
282D ALA 3.5 18.4 + - - -
283D GLU 5.1 0.3 - - - -
284D PHE 2.9 5.7 + - - -
285D GLU* 2.9 27.2 + - - -
287D VAL* 1.3 77.0 - - - +
289D PHE* 1.3 57.9 + - - +
291D LEU* 3.4 8.8 + - - +
292D ALA* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 289 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLY* 3.7 21.1 - - - -
290A LYS* 5.8 1.6 - - - -
373B GLU* 3.7 43.3 - - + -
376B LYS* 3.7 32.4 - - + +
377B LEU* 3.5 26.5 - - + -
285D GLU* 2.7 48.5 + - + +
286D GLY* 4.3 2.9 - - - +
288D SER* 1.3 75.8 - - - +
290D LYS* 1.3 63.2 + - + +
292D ALA* 3.4 2.7 + - - +
293D GLU* 3.0 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 290 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A PHE* 5.6 2.4 - - - -
366C ARG* 5.9 0.6 - - - +
373C GLU* 3.2 38.3 + - - +
286D GLY 3.1 23.1 + - - +
287D VAL* 3.1 7.1 + - - +
289D PHE* 1.3 78.0 - - + +
291D LEU* 1.3 64.0 + - - +
293D GLU* 3.4 7.8 + - - +
294D ALA* 3.1 26.3 + - - +
339D GLU* 2.7 46.4 + - + +
342D GLN* 4.4 8.6 - - - +
343D ILE* 3.7 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 291 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ALA* 5.0 4.0 - - + +
383B LEU* 3.8 13.1 - - + +
384B LEU* 4.3 27.1 - - + -
264D LEU* 3.8 24.3 - - + +
267D ALA* 4.2 3.6 - - + +
268D LEU* 4.1 25.6 - - + +
271D ALA* 4.4 7.2 - - + -
282D ALA* 4.7 3.1 - - + -
287D VAL* 3.0 32.1 + - + +
288D SER* 3.6 13.2 - - - +
290D LYS* 1.3 77.8 - - - +
292D ALA* 1.3 62.0 + - - +
295D ALA* 3.1 25.5 + - - +
343D ILE* 4.1 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 292 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LEU* 5.3 1.1 - - - -
376B LYS* 3.3 41.7 - - + +
379B ILE* 3.7 22.8 - - + +
380B ALA 4.2 1.3 - - - +
383B LEU* 4.4 1.5 - - - +
288D SER 3.0 13.9 + - - +
289D PHE 3.8 3.6 - - - +
291D LEU* 1.3 77.2 - - - +
293D GLU* 1.3 60.9 + - - +
295D ALA* 3.4 1.6 + - - +
296D THR* 2.9 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 293 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LEU* 5.2 5.4 - - + -
376B LYS* 2.7 42.1 + - + +
289D PHE* 3.0 28.0 + - - +
290D LYS* 3.9 5.8 - - - +
292D ALA* 1.3 77.0 - - - +
294D ALA* 1.3 62.8 + - - +
296D THR* 3.5 4.8 + - - -
297D GLU* 3.1 39.9 + - - +
335D LYS* 4.0 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D LEU* 4.3 15.3 - - + -
290D LYS 3.1 15.2 + - - +
291D LEU 4.1 2.5 - - - +
293D GLU* 1.3 77.4 - - - +
295D ALA* 1.3 60.6 + - - +
297D GLU* 3.9 6.1 - - - +
298D LEU* 2.9 35.3 + - - +
332D ALA 6.0 0.4 - - - -
336D ALA* 3.8 32.1 - - + -
339D GLU* 5.8 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B GLN* 3.9 10.8 - - - +
379B ILE* 4.8 0.7 - - + -
383B LEU* 3.5 27.8 - - + -
261D GLN* 5.8 0.2 + - - -
264D LEU* 3.5 19.9 - - + +
291D LEU 3.1 20.1 + - - +
292D ALA 3.7 3.6 - - - +
293D GLU 3.3 0.4 - - - -
294D ALA* 1.3 75.7 - - - +
296D THR* 1.3 62.3 + - - +
298D LEU* 3.4 2.4 + - - +
299D GLU* 3.0 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU* 4.4 4.3 - - + +
324B GLN* 3.5 54.9 + - + +
327B LEU* 4.1 11.7 - - + +
328B PHE* 3.8 21.5 - - + -
379B ILE* 3.7 10.4 - - - +
292D ALA 2.9 18.4 + - - -
293D GLU 3.8 3.8 - - - -
295D ALA* 1.3 76.4 - - - +
297D GLU* 1.3 63.0 + - - +
299D GLU* 3.2 5.2 + - - +
300D ALA* 3.0 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B PHE* 4.0 14.8 - - + -
293D GLU* 3.1 31.9 + - - +
294D ALA* 4.0 5.5 - - - +
296D THR* 1.3 76.0 - - - +
298D LEU* 1.3 58.8 + - + +
300D ALA* 3.1 3.1 + - - -
301D ALA* 2.8 27.0 + - - +
328D PHE* 3.2 29.1 - - + -
332D ALA* 3.7 30.9 - - + +
335D LYS* 4.6 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 298 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D VAL* 4.1 25.1 - - + +
260D GLY* 3.5 43.1 - - - +
261D GLN* 3.5 20.9 - - - +
264D LEU* 3.9 17.9 - - + -
294D ALA 2.9 21.2 + - - +
295D ALA* 3.9 3.8 - - - +
297D GLU* 1.3 76.1 - - + +
299D GLU* 1.3 58.2 + - - +
301D ALA* 3.6 5.4 - - + +
302D ARG* 3.0 32.7 + - - +
332D ALA* 4.8 4.5 - - + +
333D ALA* 4.3 19.7 - - + +
336D ALA* 4.4 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 299 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU* 4.5 9.0 - - + -
307B LYS* 3.2 26.4 + - - +
320B LEU* 5.4 5.2 - - - +
321B GLU* 5.6 1.4 - - - +
324B GLN* 3.9 25.9 + - - +
261D GLN* 5.9 2.0 - - - +
295D ALA* 3.0 25.7 + - + +
296D THR 3.2 7.4 + - - +
298D LEU* 1.3 76.0 - - + +
300D ALA* 1.3 61.5 + - - +
302D ARG* 3.4 23.5 + - - +
303D LEU* 3.1 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 300 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ALA* 3.9 19.7 - - + +
304B LEU* 4.1 23.0 - - + +
328B PHE* 4.6 2.9 - - + -
296D THR 3.0 13.5 + - - +
297D GLU* 3.3 9.2 - - - +
299D GLU* 1.3 75.6 - - - +
301D ALA* 1.3 63.7 + - - +
303D LEU* 3.3 5.9 + - - +
304D LEU* 3.0 26.5 + - - +
328D PHE* 3.6 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 301 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D VAL* 3.7 13.4 - - + +
297D GLU 2.8 20.0 + - - +
298D LEU* 3.6 9.9 - - + +
300D ALA* 1.3 72.8 - - - +
302D ARG* 1.3 64.2 + - - +
304D LEU* 3.2 7.3 + - - +
305D TYR* 3.2 22.9 + - - +
325D ALA* 5.0 0.9 - - - +
328D PHE* 3.6 13.8 - - + -
329D ALA* 3.6 33.1 - - - +
332D ALA* 4.9 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 302 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D PHE 5.7 2.0 - - - -
73D ARG* 4.4 15.7 - - - +
76D GLU* 2.8 35.0 + - - +
257D VAL* 3.5 13.8 - - + +
261D GLN* 2.9 35.8 - - - +
298D LEU 3.0 17.9 + - - +
299D GLU* 3.6 28.3 + - - +
300D ALA 3.2 0.2 - - - -
301D ALA* 1.3 77.6 - - - +
303D LEU* 1.3 63.4 + - + +
305D TYR* 3.4 27.5 + - + -
306D LEU* 3.0 38.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 303 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TRP* 5.6 1.3 - - + -
303B LEU* 3.9 39.2 - - + +
304B LEU* 3.6 31.4 - - + -
307B LYS* 4.2 19.1 - - + +
4D TRP* 4.0 12.5 - - + -
5D PHE* 3.6 31.6 - - + +
299D GLU* 3.1 14.3 + - + +
300D ALA* 3.7 7.0 - - - +
302D ARG* 1.3 76.4 - - + +
304D LEU* 1.3 57.5 + - - +
306D LEU* 3.2 10.7 + - + +
307D LYS* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B THR* 4.3 8.3 - - + +
299B GLU* 4.3 11.4 - - + -
300B ALA* 4.0 26.5 - - + +
303B LEU* 3.7 21.3 - - + -
300D ALA 3.0 16.7 + - - +
301D ALA 3.2 7.2 + - - +
303D LEU* 1.3 76.8 - - - +
305D TYR* 1.3 57.4 + - - +
307D LYS* 3.3 9.4 + - + +
308D ALA* 3.0 23.6 + - - +
321D GLU* 4.5 2.6 - - - +
324D GLN* 4.1 18.4 - - + +
325D ALA* 3.7 17.3 - - + +
328D PHE* 3.6 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 305 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ALA* 3.4 29.4 - - + -
73D ARG* 3.7 21.6 - - - +
76D GLU* 2.6 29.9 + - - +
250D ILE* 3.9 9.0 - - + +
253D ALA* 3.9 23.3 - - + -
254D ALA* 3.7 29.4 - - + -
257D VAL* 4.1 9.2 - - + -
301D ALA 3.2 10.1 + - - +
302D ARG* 3.7 33.7 - - + +
303D LEU 3.4 0.2 - - - -
304D LEU* 1.3 74.6 - - - +
306D LEU* 1.3 82.5 + - + +
308D ALA* 3.9 3.2 - - - +
309D ALA* 2.9 30.0 + - + +
325D ALA* 3.6 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D TRP* 3.8 13.5 - - + -
5D PHE* 3.9 20.4 - - - +
69D ARG* 4.3 22.6 - - + +
73D ARG* 3.5 43.5 - - + +
302D ARG* 3.0 33.8 + - + +
303D LEU* 3.2 12.5 + - + +
305D TYR* 1.3 98.7 - - + +
307D LYS* 1.3 64.0 + - - +
309D ALA* 3.3 4.4 + - - +
310D GLU* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 307 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PHE* 3.8 49.7 - - + -
299B GLU* 2.9 36.4 + - - +
303B LEU* 4.1 21.0 - - + +
4D TRP* 3.8 4.2 - - + -
303D LEU 2.9 14.3 + - - +
304D LEU* 3.4 13.7 - - + +
305D TYR 3.2 0.2 - - - -
306D LEU* 1.3 74.2 - - - +
308D ALA* 1.3 66.5 + - - +
310D GLU* 3.1 4.9 + - - +
311D LEU* 3.0 27.0 + - + +
321D GLU* 3.9 28.7 + - + +
324D GLN* 4.9 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 308 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D ILE* 3.7 15.7 - - + +
304D LEU 3.0 15.6 + - - +
305D TYR* 3.9 6.5 - - - +
306D LEU 3.4 0.2 - - - -
307D LYS* 1.3 76.4 - - - +
309D ALA* 1.3 63.5 + - - +
311D LEU* 3.2 5.4 + - - +
312D LYS* 3.1 23.4 + - - +
318D PHE* 4.2 3.8 - - + +
321D GLU* 3.7 37.0 - - + +
322D ALA* 3.8 11.2 - - + +
325D ALA* 4.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 309 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D THR* 3.8 11.4 - - + +
69D ARG* 3.7 32.5 - - + +
72D ALA* 5.0 1.8 - - + -
250D ILE* 3.8 16.3 - - + +
305D TYR 2.9 19.7 + - - +
306D LEU* 3.4 6.5 - - - +
307D LYS 3.2 0.2 - - - -
308D ALA* 1.3 78.5 - - - +
310D GLU* 1.3 56.6 + - - +
312D LYS* 3.5 2.9 + - - +
313D ASP* 3.0 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 310 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 4.6 14.0 - - + +
5B PHE* 4.0 14.1 - - + -
4D TRP* 2.7 35.9 + - + +
69D ARG* 2.9 34.2 + - - -
306D LEU 3.0 17.9 + - - +
307D LYS 3.1 7.1 + - - +
309D ALA* 1.3 74.8 - - - +
311D LEU* 1.3 61.4 + - - +
313D ASP* 3.6 10.2 - - - +
314D ALA* 2.8 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 311 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 3.5 26.0 - - + -
5B PHE* 3.8 11.7 - - + -
6B GLU* 4.7 1.1 - - - +
307D LYS* 3.0 24.7 + - + +
308D ALA* 3.2 6.3 + - - +
310D GLU* 1.3 76.5 - - - +
312D LYS* 1.3 62.7 + - - +
314D ALA* 3.1 4.6 + - - +
315D GLY 3.1 4.2 + - - -
316D ARG* 2.9 50.1 + - + +
317D PRO 3.8 10.8 - - - +
318D PHE* 3.8 9.6 - - + -
321D GLU* 3.3 45.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 312 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D LEU* 4.5 17.0 - - - +
68D THR* 3.1 33.2 + - + +
247D GLY* 4.5 12.3 - - - -
250D ILE* 4.2 5.8 - - + -
308D ALA 3.1 12.4 + - - +
309D ALA 3.7 7.4 - - - +
311D LEU* 1.3 78.1 - - - +
313D ASP* 1.3 59.3 + - - +
315D GLY* 2.8 19.9 + - - -
316D ARG 4.5 0.4 - - - -
318D PHE* 3.5 47.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 313 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D SER* 3.8 14.3 - - - -
68D THR* 2.9 39.9 + - - -
69D ARG* 3.5 12.0 + - - +
309D ALA 3.0 23.8 + - - +
310D GLU* 3.6 13.5 - - - +
312D LYS* 1.3 78.6 + - - +
314D ALA* 1.3 59.9 + - - +
315D GLY 3.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 314 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 4.4 15.5 - - + -
310D GLU 2.8 17.8 + - - +
311D LEU* 3.6 6.5 - - - +
312D LYS 3.1 0.6 - - - -
313D ASP* 1.3 75.6 - - - +
315D GLY* 1.3 62.9 + - - +
316D ARG* 3.4 24.1 + - + +
----------------------------------------------------------
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