Contacts of the helix formed by residues 359 - 390 (chain F) in PDB entry 6M04
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 359 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E HIS* 4.9 1.0 - - - -
333F ILE* 4.3 11.6 - - + +
334F SER 3.8 19.3 - - - +
335F PHE* 3.6 34.3 - - + -
356F HIS* 3.9 6.6 + - + +
357F ASN 3.6 3.0 + - - -
358F MET* 1.3 79.8 - - - +
360F TYR* 1.3 68.1 + - + +
361F MET 3.5 0.2 - - - -
362F LEU* 3.8 0.3 - - - +
363F LYS* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 360 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E HIS* 3.9 40.6 - + + +
156E LEU* 4.2 12.8 - - + +
163E LYS* 5.3 2.9 - - - +
164E TYR* 3.5 18.2 - - - +
335F PHE* 3.6 45.5 - + + +
357F ASN 5.4 0.2 + - - -
359F ALA* 1.3 80.1 - - + +
361F MET* 1.3 60.8 + - - +
363F LYS* 3.3 19.2 + - - +
364F LYS* 2.9 45.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 361 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E GLN* 6.2 0.2 - - - +
155E HIS* 6.1 0.4 + - - -
163E LYS 5.3 0.2 - - - +
164E TYR* 3.6 43.1 + - + +
167E TYR* 3.7 32.8 - - + +
41F PHE* 5.6 2.7 - - - -
45F MET* 3.6 38.4 - - + -
49F LYS* 5.0 13.7 - - - +
357F ASN 5.8 1.1 + - - +
358F MET* 4.5 11.6 - - + -
359F ALA 3.5 0.8 - - - +
360F TYR* 1.3 77.9 - - - +
362F LEU* 1.3 57.9 + - - +
364F LYS* 3.9 4.6 - - - +
365F LEU* 3.0 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 362 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F ALA* 6.3 4.7 - - + -
45F MET* 6.1 0.9 - - - -
46F GLN* 4.1 27.8 - - + -
161F TYR 5.3 2.7 - - - +
162F SER* 4.3 18.6 - - - +
163F LYS* 5.6 1.8 - - - -
165F PHE* 5.3 17.9 - - + -
166F PRO* 5.6 9.4 - - + -
333F ILE* 3.7 26.9 - - + -
358F MET* 3.3 33.4 + - + +
359F ALA 3.4 1.8 + - - +
360F TYR 3.3 0.2 - - - -
361F MET* 1.3 80.6 - - - +
363F LYS* 1.3 58.5 + - - +
365F LEU* 3.4 6.8 + - - +
366F LEU* 2.9 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 363 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330F VAL* 4.7 13.7 - - + +
333F ILE* 4.5 26.0 - - + +
359F ALA 2.9 18.8 + - - +
360F TYR* 3.9 20.4 - - - +
361F MET 3.3 0.2 - - - -
362F LEU* 1.3 79.1 - - - +
364F LYS* 1.3 73.7 + - + +
366F LEU* 3.3 8.1 + - + +
367F ILE* 3.0 45.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 364 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160E TRP* 5.7 8.9 - - - +
164E TYR* 3.5 37.9 - - + -
360F TYR* 2.9 30.1 + - - +
361F MET* 4.0 5.4 - - - +
363F LYS* 1.3 88.9 - - + +
365F LEU* 1.3 65.4 + - - +
367F ILE* 3.2 20.3 - - + +
368F SER* 3.0 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 365 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F VAL* 4.1 24.7 - - + +
41F PHE* 4.0 24.0 - - + -
42F ALA* 3.7 35.7 - - + -
45F MET* 4.2 11.4 - - + -
361F MET* 3.0 23.6 + - + +
362F LEU* 3.8 6.7 - - - +
363F LYS 3.3 0.2 - - - -
364F LYS* 1.3 76.4 - - - +
366F LEU* 1.3 57.5 + - - +
368F SER* 3.4 10.5 + - - -
369F TYR* 3.0 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 366 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F PHE* 3.6 41.5 - - + -
326F THR* 4.9 4.0 - - - +
329F PHE* 3.9 16.8 - - + +
330F VAL* 4.4 14.6 - - + +
333F ILE* 3.8 26.5 - - + -
362F LEU* 2.9 21.3 + - + +
363F LYS* 3.4 8.1 - - + +
365F LEU* 1.3 77.2 - - - +
367F ILE* 1.3 59.7 + - + +
369F TYR* 3.3 16.8 - - + +
370F ILE* 2.9 43.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 367 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330F VAL* 4.8 18.6 - - + -
363F LYS* 3.0 30.6 + - + +
364F LYS* 3.2 27.8 - - + +
366F LEU* 1.3 78.3 - - + +
368F SER* 1.3 61.5 + - - +
370F ILE* 3.8 8.2 - - + +
371F SER* 3.0 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 368 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F VAL* 5.4 4.8 - - - +
364F LYS 3.0 16.9 + - - -
365F LEU* 3.7 14.5 - - - +
366F LEU 3.3 0.2 - - - -
367F ILE* 1.3 76.8 - - - +
369F TYR* 1.3 61.8 + - - +
371F SER* 2.6 23.4 + - - -
372F ILE* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 369 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F MET* 3.5 37.9 - - + -
38F VAL* 4.3 23.4 - - + +
39F ALA* 5.5 1.3 - - + -
165F PHE* 4.6 8.0 - + - -
168F LEU* 5.9 1.0 - - - +
169F ALA* 4.2 24.2 - - + +
172F HIS* 3.9 23.4 - - - +
322F ILE* 4.0 9.4 - - + +
326F THR* 4.4 14.7 - - + +
365F LEU 3.0 15.1 + - - +
366F LEU* 3.3 19.5 - - + +
368F SER* 1.3 75.1 - - - +
370F ILE* 1.3 77.9 + - + +
372F ILE* 3.3 8.2 + - - +
373F ILE* 3.0 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 370 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322F ILE* 6.2 0.7 - - + -
323F LEU* 5.6 14.3 - - + +
326F THR* 3.2 33.7 - - - +
327F ALA* 6.3 2.2 - - + -
330F VAL* 5.0 14.4 - - + -
366F LEU* 2.9 29.8 + - + +
367F ILE* 3.8 8.7 - - + +
368F SER 3.3 0.4 - - - -
369F TYR* 1.3 91.3 - - + +
371F SER* 1.3 61.2 + - - +
373F ILE* 3.4 7.0 + - + +
374F CYS* 2.9 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 371 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367F ILE 3.0 13.2 + - - -
368F SER* 2.6 26.9 + - - -
370F ILE* 1.3 77.4 - - - +
372F ILE* 1.3 63.0 + - - +
374F CYS* 3.3 6.6 + - - +
375F VAL* 3.0 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 372 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F LEU* 3.7 33.6 - - + +
34F VAL* 3.9 26.5 - - + -
35F MET* 4.9 6.3 - - + -
38F VAL* 4.5 14.4 - - + -
368F SER* 3.0 26.1 + - - +
369F TYR* 3.7 5.8 - - - +
371F SER* 1.3 84.2 + - - +
373F ILE* 1.3 63.6 + - + +
375F VAL* 3.3 8.0 + - - +
376F TYR* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 373 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F LEU* 4.6 7.9 - - + -
35F MET* 3.8 32.1 - - + -
172F HIS* 5.0 5.8 - - - +
176F LEU* 5.7 2.5 - - + -
319F PHE* 3.3 22.2 - - + -
322F ILE* 3.7 24.9 - - + -
323F LEU* 5.5 5.2 - - + -
369F TYR* 3.0 37.3 + - + +
370F ILE* 4.1 7.4 - - + +
372F ILE* 1.3 83.8 - - + +
374F CYS* 1.3 57.5 + - - +
376F TYR* 3.3 14.4 - - + +
377F GLY 2.9 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 374 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319F PHE* 4.3 10.1 - - - -
323F LEU* 4.8 13.2 - - + +
370F ILE* 2.9 20.8 + - + +
371F SER* 3.6 8.1 - - - +
372F ILE 3.2 0.2 - - - -
373F ILE* 1.3 75.5 - - - +
375F VAL* 1.3 62.1 + - + +
377F GLY* 3.5 0.5 + - - -
378F PHE* 3.0 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 375 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F LEU* 5.0 10.1 - - + -
371F SER* 3.0 15.6 + - - +
372F ILE* 3.7 8.7 - - - +
374F CYS* 1.3 75.8 - - + +
376F TYR* 1.3 63.2 + - - +
378F PHE* 3.4 6.6 + - + +
379F ILE* 3.0 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 376 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F MET* 3.6 45.9 - - + +
31F LEU* 3.6 34.3 - - + +
172F HIS* 5.9 2.2 - + - -
176F LEU* 3.3 45.0 - - + +
315F LYS* 4.4 25.6 - - + +
319F PHE* 4.8 8.1 - + + -
372F ILE 3.0 14.1 + - - +
373F ILE* 3.3 26.0 - - + +
375F VAL* 1.3 76.2 - - - +
377F GLY* 1.3 61.0 + - - +
379F ILE* 3.4 3.6 + - - +
380F CYS* 3.0 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 377 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315F LYS* 4.2 4.3 + - - -
319F PHE* 3.5 37.5 - - - -
373F ILE 2.9 11.3 + - - -
376F TYR* 1.3 78.3 - - - +
378F PHE* 1.3 59.4 + - - +
380F CYS* 4.7 3.6 - - - -
381F LEU* 2.9 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 378 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319F PHE* 4.5 1.6 - - - -
374F CYS* 3.0 22.3 + - - +
375F VAL* 3.7 7.0 - - + +
377F GLY* 1.3 75.5 - - - +
379F ILE* 1.3 73.5 + - + +
381F LEU* 3.9 7.4 - - + +
382F TYR* 3.0 49.8 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 379 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F TRP* 4.4 26.9 - - + -
24F TRP* 5.4 0.2 - - + -
27F PHE* 5.2 10.3 - - + -
28F MET* 3.8 18.8 - - + -
375F VAL* 3.0 32.9 + - + +
376F TYR* 3.9 4.0 - - - +
378F PHE* 1.3 90.8 - - + +
380F CYS* 1.3 60.0 + - - +
382F TYR* 3.4 9.3 + - + +
383F THR* 3.0 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 380 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F MET* 3.6 33.0 - - + -
312F THR* 5.8 0.4 - - - -
315F LYS* 3.5 40.1 - - + -
376F TYR* 3.0 19.4 + - + +
379F ILE* 1.3 77.5 - - - +
381F LEU* 1.3 57.0 + - - +
384F LEU* 2.9 56.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 381 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312F THR* 6.2 0.4 - - - -
315F LYS* 3.4 19.6 - - - +
316F THR* 5.3 9.4 - - + -
319F PHE* 5.3 10.8 - - + -
320F ILE* 6.1 2.9 - - + -
377F GLY 2.9 19.9 + - - +
378F PHE* 3.9 7.9 - - + +
380F CYS* 1.3 75.9 - - - +
382F TYR* 1.3 60.5 + - - +
384F LEU* 5.1 0.2 - - - -
385F PHE* 2.9 47.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 382 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F TRP* 6.0 0.9 - + - -
378F PHE* 3.0 38.8 + + + +
379F ILE* 3.6 10.3 - - + +
381F LEU* 1.3 79.5 - - + +
383F THR* 1.3 73.9 + - - +
385F PHE* 5.2 0.2 - - - -
386F TRP* 3.0 84.7 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 383 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F TRP* 3.2 28.8 - - + -
24F TRP* 3.6 38.8 - - + -
379F ILE* 3.0 13.6 + - - +
382F TYR* 1.3 92.5 - - - +
384F LEU* 1.3 62.3 + - + +
386F TRP* 3.7 2.4 - - - -
387F LEU* 2.9 30.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 384 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F TRP* 3.5 41.3 - - + +
308F TYR* 3.4 38.6 + - + +
311F GLN* 6.1 1.8 - - + -
312F THR* 3.3 39.6 + - + +
380F CYS* 2.9 42.7 + - - +
383F THR* 1.3 82.2 - - - +
385F PHE* 1.3 56.9 + - - +
388F PHE* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 385 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312F THR* 5.0 5.3 - - + +
381F LEU* 2.9 31.4 + - + +
382F TYR 4.2 0.4 - - - +
384F LEU* 1.3 78.3 - - - +
386F TRP* 1.3 76.1 + + + +
388F PHE* 3.2 27.3 + + + +
389F ARG* 2.9 70.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 386 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382F TYR* 3.0 69.0 + + + +
383F THR* 3.7 3.4 - - - +
385F PHE* 1.3 101.2 - + + +
387F LEU* 1.3 60.1 + - - +
389F ARG* 4.1 13.0 - - - +
390F ILE* 3.4 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 387 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F TRP* 3.6 33.2 - - + -
305F TYR* 6.1 0.2 - - - -
308F TYR* 3.3 25.0 + - + +
383F THR* 2.9 18.5 + - + +
384F LEU* 4.9 0.2 - - - -
386F TRP* 1.3 79.9 - - - +
388F PHE* 1.3 63.7 + - - +
389F ARG 3.4 0.2 - - - -
390F ILE* 6.0 0.4 - - + -
391F PRO* 3.3 29.9 - - + +
418F PHE* 4.0 20.4 - - + -
421F HIS* 6.1 4.3 - - + -
422F MET* 6.0 6.1 - - + -
425F GLN* 5.1 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 388 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305F TYR* 3.2 37.3 + + - -
308F TYR* 3.9 11.2 + + + -
309F VAL* 4.3 25.8 - - + -
312F THR* 6.0 4.0 - - + +
384F LEU 2.9 18.1 + - - +
385F PHE* 3.2 33.0 + + + +
387F LEU* 1.3 78.9 - - - +
389F ARG* 1.3 70.9 + - + +
391F PRO* 4.4 2.8 - - - +
392F LEU* 4.5 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 389 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385F PHE* 2.9 54.1 + - + +
386F TRP* 4.1 9.0 - - - +
387F LEU 3.4 0.2 - - - -
388F PHE* 1.3 89.0 - - + +
390F ILE* 1.3 83.9 + - + +
392F LEU* 4.2 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 390 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386F TRP* 3.4 22.1 + - + +
387F LEU* 6.0 0.9 - - + -
389F ARG* 1.3 96.7 - - + +
391F PRO* 1.3 74.6 - - + +
392F LEU* 3.3 14.2 - - - +
----------------------------------------------------------
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