Contacts of the helix formed by residues 325 - 354 (chain C) in PDB entry 7A62
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 ASP 325 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C ARG* 2.7 55.1 + - - +
320C VAL 4.7 2.4 + - - +
323C LYS* 3.2 12.8 - - + +
324C GLY* 1.3 75.2 - - - +
326C ALA* 1.3 62.8 + - - +
327C GLY 3.0 10.7 + - - -
328C LEU* 3.0 24.9 + - + +
329C ARG* 3.1 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 326 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C GLY 4.1 1.6 + - - -
325C ASP* 1.3 70.2 + - - +
327C GLY* 1.3 61.0 + - - +
329C ARG* 3.3 28.2 + - - +
330C GLU* 2.8 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 327 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C ARG* 3.9 5.5 - - - +
197C LEU* 3.3 23.6 - - - +
325C ASP* 3.0 9.0 + - - -
326C ALA* 1.3 80.0 - - - +
328C LEU* 1.3 60.3 + - - +
330C GLU* 3.4 6.2 + - - +
331C ALA* 3.1 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 328 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C ARG* 4.2 17.0 - - + +
196C LEU* 4.0 28.0 - - + -
197C LEU* 3.8 32.8 - - + +
200C LEU* 4.3 5.9 - - + +
319C PHE* 4.9 4.0 - - + -
320C VAL* 4.0 23.2 - - + +
323C LYS* 4.6 16.4 - - + -
325C ASP* 3.0 38.9 + - + +
326C ALA 3.2 0.2 - - - -
327C GLY* 1.3 74.2 - - - +
329C ARG* 1.3 60.3 + - - +
331C ALA* 3.4 1.8 + - - +
332C TYR* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 329 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C VAL* 3.7 26.5 - - + +
321C LEU* 4.5 10.2 + - - +
324C GLY* 3.6 11.1 - - - +
325C ASP 3.1 40.2 + - - +
326C ALA* 3.5 29.8 - - - +
328C LEU* 1.3 76.0 - - - +
330C GLU* 1.3 57.6 + - - +
332C TYR* 3.7 1.1 - - - +
333C ASP* 2.9 34.5 + - - +
400C LEU* 3.8 20.9 - - + -
402C GLU* 3.0 55.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 330 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C LEU* 5.3 2.0 - - + -
326C ALA* 2.8 18.8 + - - +
327C GLY* 3.8 6.3 - - - +
329C ARG* 1.3 79.8 - - - +
331C ALA* 1.3 56.7 + - - +
333C ASP* 3.4 7.8 + - + +
334C ALA* 3.1 25.3 + - - +
337C LYS* 6.3 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 331 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C LEU* 3.8 17.0 - - + +
200C LEU* 3.8 14.5 - - + +
201C LEU* 3.5 35.6 - - + +
327C GLY 3.1 17.1 + - - +
328C LEU* 4.0 3.4 - - - +
330C GLU* 1.3 73.4 - - - +
332C TYR* 1.3 67.9 + - - +
334C ALA* 3.2 12.2 + - - +
335C CYS* 3.4 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 332 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C LEU* 4.0 14.2 - - + +
277C LEU* 2.5 50.1 + - + +
316C VAL* 4.5 13.5 - - + -
317C ARG* 2.8 51.0 + - + +
320C VAL* 4.3 11.0 - - + -
328C LEU 2.9 19.0 + - - +
329C ARG* 3.7 5.4 - - - +
331C ALA* 1.3 76.0 - - - +
333C ASP* 1.3 74.5 + - - +
335C CYS* 3.0 16.3 + - - +
336C VAL* 3.2 30.7 + - + +
398C SER* 3.7 4.3 + - - -
400C LEU* 3.6 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 333 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C ARG* 2.9 19.5 + - - +
330C GLU* 3.7 7.4 - - - +
332C TYR* 1.3 87.9 - - - +
334C ALA* 1.3 57.8 + - - +
336C VAL* 3.0 3.9 + - - +
337C LYS* 2.8 45.0 + - - +
399C LEU* 3.6 18.0 - - + +
400C LEU* 2.8 25.9 + - - +
401C LYS* 2.9 28.3 + - - -
402C GLU 4.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 334 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C LEU* 4.6 9.4 - - + -
204C ALA* 3.5 18.0 - - + +
208C GLU* 4.4 7.1 - - - +
330C GLU 3.1 13.7 + - - +
331C ALA* 3.5 12.8 - - - +
332C TYR 3.2 0.4 - - - -
333C ASP* 1.3 76.1 - - - +
335C CYS* 1.3 61.2 + - - +
337C LYS* 3.5 10.9 + - - +
338C ALA* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 335 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C LEU* 3.2 43.1 - - - -
203C ILE* 3.8 22.9 - - + -
204C ALA* 3.8 7.9 - - - +
207C LEU* 4.5 6.1 - - + +
273C PHE* 6.3 0.2 - - + -
276C LEU* 6.2 0.2 - - - -
277C LEU* 3.7 23.9 - - + +
331C ALA 3.4 7.6 + - - -
332C TYR 3.0 9.4 + - - +
334C ALA* 1.3 75.2 - - - +
336C VAL* 1.3 65.6 + - - +
338C ALA* 3.2 4.1 + - - +
339C LEU* 3.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 336 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C LEU* 4.0 17.0 - - + -
279C ILE* 4.6 9.4 - - + -
332C TYR* 3.2 39.4 + - + +
333C ASP* 3.0 8.1 + - - +
335C CYS* 1.3 74.5 - - - +
337C LYS* 1.3 59.0 + - - +
339C LEU* 3.2 6.1 + - - +
340C VAL* 2.8 30.5 + - + +
395C THR 3.5 25.1 - - - +
398C SER* 4.4 5.2 - - - +
399C LEU* 3.8 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 337 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A GLU* 3.6 29.2 + - - +
330C GLU* 6.3 0.8 - - - +
333C ASP* 2.8 30.5 + - - +
334C ALA* 4.0 7.8 - - - +
336C VAL* 1.3 75.5 - - - +
338C ALA* 1.3 53.3 + - - +
340C VAL* 3.0 8.0 + - - +
341C SER* 2.6 42.1 + - - +
399C LEU* 3.7 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 338 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C ALA* 3.9 11.9 - - - +
207C LEU* 3.6 27.0 - - + +
208C GLU* 4.2 15.9 - - + +
211C LEU* 5.4 1.1 - - - +
334C ALA 3.0 18.1 + - - +
335C CYS 3.2 3.8 + - - +
337C LYS* 1.3 75.8 - - - +
339C LEU* 1.3 57.8 + - - +
341C SER* 3.3 8.1 + - - -
342C LEU* 2.9 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 339 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C LEU* 4.6 7.5 - - + +
270C PHE* 4.2 30.3 - - + -
273C PHE* 3.9 30.1 - - + +
274C ASP* 3.5 27.1 - - - +
277C LEU* 4.5 4.3 - - + -
279C ILE* 4.1 14.1 - - + -
335C CYS 3.0 11.9 + - - +
336C VAL* 3.5 9.0 - - - +
338C ALA* 1.3 74.3 - - - +
340C VAL* 1.3 63.6 + - - +
342C LEU* 3.3 12.6 + - + +
343C ARG* 3.0 38.5 + - - +
395C THR* 4.0 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 340 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C VAL* 2.8 21.4 + - + +
337C LYS* 3.5 10.8 - - - +
339C LEU* 1.3 75.9 - - - +
341C SER* 1.3 60.2 + - - +
343C ARG* 3.1 5.6 + - - +
344C SER* 2.8 37.6 + - - +
392C ARG* 4.3 11.1 - - + +
395C THR* 3.5 24.7 - - + +
396C GLU* 3.8 43.5 - - + +
399C LEU* 5.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 341 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C LEU* 3.7 24.8 - - - +
337C LYS* 2.6 25.2 + - - +
338C ALA* 3.6 8.0 - - - -
340C VAL* 1.3 74.2 - - - +
342C LEU* 1.3 63.6 + - - +
344C SER* 3.2 7.6 + - - -
345C TYR* 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 342 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C VAL* 6.5 0.2 - - + -
207C LEU* 4.0 36.1 - - + +
210C ALA* 4.1 8.5 - - + +
211C LEU* 3.6 40.2 - - + +
214C PHE* 4.3 16.5 - - + -
269C VAL* 6.0 2.0 - - + -
270C PHE* 4.1 27.1 - - + -
338C ALA 2.9 18.5 + - - +
339C LEU* 3.5 16.4 - - + +
340C VAL 3.2 0.2 - - - -
341C SER* 1.3 76.9 - - - +
343C ARG* 1.3 59.1 + - - +
345C TYR* 3.3 1.9 + - - +
346C HIS* 2.8 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 343 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C PHE* 3.4 32.2 + - + +
274C ASP* 2.6 42.8 + - - -
281C GLN* 3.7 0.6 - - - +
292C LEU* 6.0 0.2 - - - +
339C LEU* 3.0 28.8 + - - +
340C VAL* 3.1 4.0 + - - +
342C LEU* 1.3 77.4 - - - +
344C SER* 1.3 58.9 + - - +
346C HIS* 3.7 9.2 + - + +
347C LEU* 2.9 29.6 + - - +
388C LEU 5.3 1.6 - - - +
391C VAL* 3.3 18.1 - - - +
392C ARG* 4.3 22.1 - - + +
395C THR* 3.2 25.2 + - - +
504C HEM 2.6 50.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 344 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A LYS* 6.3 1.3 - - - -
340C VAL* 2.8 24.3 + - - +
341C SER* 3.5 8.1 - - - -
343C ARG* 1.3 73.6 - - - +
345C TYR* 1.3 64.8 + - - +
347C LEU* 3.1 6.5 + - - +
348C GLN* 3.1 31.0 + - - +
392C ARG* 3.2 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 345 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C LEU* 3.6 24.0 - - + -
214C PHE* 3.9 35.0 - + + -
215C HIS* 3.3 44.5 - + - -
218C HIS* 2.7 33.8 + - - -
341C SER 2.9 7.6 + - - +
342C LEU 3.7 1.6 - - - +
344C SER* 1.3 77.1 - - - +
346C HIS* 1.3 65.3 + - - +
348C GLN* 3.0 34.6 + - + +
349C ILE* 3.0 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 346 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C PHE* 3.9 19.0 - + + -
270C PHE* 4.7 9.6 - + + -
342C LEU 2.8 17.7 + - - +
343C ARG* 3.7 10.3 + - - +
345C TYR* 1.3 76.8 - - - +
347C LEU* 1.3 63.3 + - - +
349C ILE* 3.3 6.1 + - + +
350C VAL* 3.2 33.3 + - + +
388C LEU* 3.9 13.6 - - + +
504C HEM 2.4 96.4 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 347 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C ARG 2.9 18.6 + - - +
344C SER 3.5 3.8 - - - +
345C TYR 3.0 0.4 - - - -
346C HIS* 1.3 78.0 - - - +
348C GLN* 1.3 65.1 + - + +
350C VAL* 3.2 15.5 + - + +
351C THR* 3.3 17.8 + - + +
385C MET* 4.4 21.3 - - + +
388C LEU* 3.5 37.5 - - + +
389C LYS* 4.0 20.0 - - + +
392C ARG* 3.9 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 348 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A LYS* 4.8 13.7 - - - +
344C SER* 3.1 19.7 + - - +
345C TYR* 3.0 28.3 + - + +
347C LEU* 1.3 77.0 - - + +
349C ILE* 1.3 64.1 + - + +
351C THR* 2.5 23.3 + - - -
352C LYS* 3.1 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 349 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C PHE* 4.4 6.5 - - + -
217C ILE* 3.9 13.7 - - + -
218C HIS* 3.3 37.9 - - + +
345C TYR* 3.0 35.4 + - + +
346C HIS* 3.5 11.2 - - - +
347C LEU 3.2 0.2 - - - -
348C GLN* 1.3 78.8 - - + +
350C VAL* 1.3 60.0 + - - +
352C LYS* 3.2 3.2 + - + +
353C TYR* 2.8 43.4 + - + +
504C HEM 3.6 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 350 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C HIS* 3.2 37.3 + - + +
347C LEU* 3.6 9.2 - - + +
348C GLN 3.2 0.4 - - - -
349C ILE* 1.3 79.0 - - + +
351C THR* 1.3 57.4 + - + +
354C ILE* 2.8 37.4 + - + +
355C LEU* 3.1 17.5 + - + -
384C LEU* 4.2 26.0 - - + -
385C MET* 6.2 0.9 - - - -
388C LEU* 3.7 16.6 - - + -
504C HEM 3.9 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 351 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C LEU* 3.3 12.1 + - + +
348C GLN* 2.5 30.5 + - - -
350C VAL* 1.3 78.9 - - - +
352C LYS* 1.3 57.5 + - - -
355C LEU* 3.6 28.5 - - + -
356C ILE* 2.9 38.4 + - + +
385C MET* 5.8 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 352 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B HIS* 5.6 7.7 + - - -
218C HIS* 2.9 39.2 + - + +
221C VAL 5.4 0.2 - - - -
223C PRO* 3.5 23.9 - - + +
348C GLN 3.1 12.9 + - - +
349C ILE* 3.8 6.3 - - - +
351C THR* 1.3 77.8 - - - +
353C TYR* 1.3 90.0 + - + +
356C ILE* 3.4 19.3 - - + +
357C PRO* 3.3 19.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 353 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C ILE* 3.2 19.6 + - + -
218C HIS* 3.6 16.0 - - - -
221C VAL* 2.4 53.2 + - + -
223C PRO* 3.5 29.8 - - + +
226C PHE* 3.8 12.4 - + + -
227C PHE* 3.6 21.5 + - - +
349C ILE* 2.8 41.3 + - + +
352C LYS* 1.3 103.2 + - + +
354C ILE* 1.3 66.6 + - - +
357C PRO* 3.9 3.1 - - - +
504C HEM 4.3 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 354 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C PHE* 3.6 24.9 - - + -
227C PHE* 3.6 13.4 - - + -
231C ARG* 3.8 23.6 - - - +
350C VAL* 2.8 20.4 + - + +
352C LYS 3.5 0.4 - - - -
353C TYR* 1.3 83.3 - - - +
355C LEU* 1.3 72.3 + - + +
357C PRO* 3.2 4.2 - - - +
358C ALA* 3.0 27.0 + - + +
377C LYS* 5.4 10.5 - - + +
381C GLY* 6.3 0.2 - - - -
384C LEU* 4.5 19.7 - - + -
504C HEM 3.8 28.5 - - + -
----------------------------------------------------------
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