Contacts of the helix formed by residues 412 - 444 (chain B) in PDB entry 4L6V
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 HIS 412 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A TRP* 6.0 2.2 - - + -
408B ARG* 2.9 26.4 + - + +
409B MET* 3.3 25.7 + - + +
410B LEU 3.2 0.2 - - - -
411B GLU* 1.3 85.5 - - + +
413B LYS* 1.3 58.3 + - - +
414B GLU* 3.1 7.2 - - - -
415B ALA* 2.9 34.6 + - + +
416B LEU* 3.2 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A SER* 5.5 1.1 - - - +
409B MET 3.2 10.2 + - - +
410B LEU* 3.4 21.3 + - + +
411B GLU 3.6 0.2 - - - -
412B HIS* 1.3 76.3 - - - +
414B GLU* 1.3 79.4 + - - +
416B LEU* 3.4 4.5 + - - +
417B ILE* 3.0 36.1 + - + +
536B LEU* 3.8 39.0 + - + +
537B ASP* 2.5 33.7 + - - +
540B GLY 2.7 24.5 + - - -
541B SER* 4.2 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A GLU 4.9 0.4 - - - +
699A SER* 3.6 31.8 - - - +
702A TRP* 3.4 42.7 - - + +
410B LEU 4.5 0.5 - - - +
411B GLU 3.5 21.7 - - - +
412B HIS* 3.9 2.0 - - - -
413B LYS* 1.3 99.3 + - + +
415B ALA* 1.3 60.6 + - - +
417B ILE 4.1 0.7 - - - -
418B SER* 2.8 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A TRP* 3.4 29.2 - - + -
412B HIS* 2.9 28.3 + - + +
414B GLU* 1.3 79.6 - - - +
416B LEU* 1.3 63.1 + - - +
418B SER* 3.1 1.0 + - - -
419B HIS* 2.3 37.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B MET* 3.8 35.4 - - + +
412B HIS* 3.2 32.0 + - + +
413B LYS* 3.4 6.7 + - - +
415B ALA* 1.3 80.7 - - - +
417B ILE* 1.3 58.8 + - + +
419B HIS* 3.8 2.9 - - - +
420B LEU* 2.9 32.5 + - + +
532B ILE* 5.3 7.2 - - + -
536B LEU* 3.9 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A LEU* 3.9 17.9 - - + +
699A SER* 3.3 32.5 - - - +
700A ILE* 5.9 0.9 - - + -
413B LYS* 3.0 21.8 + - + +
416B LEU* 1.3 75.0 - - + +
418B SER* 1.3 57.7 + - - +
420B LEU* 3.7 7.6 - - + +
421B SER* 2.8 29.7 + - - -
529B LEU* 3.8 18.9 - - + +
532B ILE* 5.2 2.2 - - + -
533B LYS* 3.8 37.7 - - + +
536B LEU* 4.2 15.0 - - + -
537B ASP* 4.0 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A SER* 3.4 20.8 - - - -
700A ILE* 4.5 6.6 - - - +
702A TRP* 3.8 3.5 - - - -
703A ALA* 4.0 17.3 - - - +
414B GLU 2.8 24.0 + - - -
415B ALA* 3.1 1.2 + - - -
417B ILE* 1.3 79.7 - - - +
419B HIS* 1.3 79.8 + - - +
421B SER* 3.4 8.7 + - - -
422B TRP* 3.2 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A TRP* 4.5 9.0 - + - -
703A ALA* 5.8 2.2 - - + -
415B ALA* 2.3 40.3 + - + +
416B LEU* 3.3 3.3 + - - +
417B ILE 3.2 0.4 - - - -
418B SER* 1.3 89.6 + - - +
420B LEU* 1.3 58.3 + - - +
421B SER 2.9 4.9 - - - -
422B TRP* 2.8 29.6 + + + +
423B VAL* 3.0 20.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B LEU* 2.9 20.6 + - + +
417B ILE* 3.8 5.6 - - + +
419B HIS* 1.3 75.6 - - - +
421B SER* 1.3 59.1 + - - +
423B VAL* 4.1 4.8 + - - +
424B SER* 3.2 20.3 + - - -
525B HIS* 3.2 48.0 - - + +
528B ALA* 4.2 4.0 - - + -
529B LEU* 3.9 25.2 - - + +
532B ILE* 3.7 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A LEU* 5.7 3.1 - - - +
700A ILE* 4.3 23.4 - - - +
417B ILE* 2.8 19.3 + - - -
418B SER* 3.4 9.9 + - - -
420B LEU* 1.3 78.2 - - - +
422B TRP* 1.3 59.4 + - - +
424B SER* 3.3 2.8 + - - -
425B LEU* 2.9 46.4 + - - +
529B LEU* 4.4 17.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B SER 3.2 10.1 + - - +
419B HIS* 2.8 17.6 + + + +
421B SER* 1.3 78.0 + - - +
423B VAL* 1.3 83.8 + - + +
425B LEU* 3.1 14.6 + - + +
426B PHE* 2.6 66.7 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B HIS* 3.0 14.3 + - + +
420B LEU* 4.4 3.6 - - - +
422B TRP* 1.3 100.4 - - + +
424B SER* 1.3 57.3 + - - +
426B PHE* 3.5 7.6 - - + +
427B LEU* 2.8 44.8 + - + +
525B HIS* 3.4 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B LEU 3.2 13.8 + - - -
421B SER* 3.3 10.9 + - - -
422B TRP 3.2 0.2 - - - -
423B VAL* 1.3 76.5 - - - +
425B LEU* 1.3 62.6 + - - +
427B LEU* 4.6 2.0 - - - -
428B GLY* 2.9 26.9 + - - -
522B LEU* 3.3 14.1 - - - +
525B HIS* 3.7 5.5 - - - +
526B THR* 3.2 41.4 + - - -
529B LEU* 4.5 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B SER* 2.9 39.1 + - - +
422B TRP* 3.4 15.9 - - + +
424B SER* 1.3 78.3 - - - +
426B PHE* 1.3 61.5 + - - +
428B GLY* 5.3 0.2 - - - -
429B PHE* 3.0 57.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B TRP* 2.6 53.2 + + + +
423B VAL* 3.5 12.8 - - + +
425B LEU* 1.3 75.5 - - - +
427B LEU* 1.3 74.3 + - + +
430B HIS* 2.4 65.7 + + + +
518B HIS* 6.5 1.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B VAL* 2.8 37.7 + - + +
426B PHE* 1.3 88.7 - - + +
428B GLY* 1.3 58.2 + - - +
430B HIS* 5.3 0.7 - - - -
431B THR* 2.9 37.7 + - - +
518B HIS* 4.1 35.7 - - + +
521B ALA* 3.8 17.3 - - + +
522B LEU* 3.7 40.2 - - + +
525B HIS* 4.2 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B SER 2.9 15.9 + - - -
425B LEU* 5.3 0.2 - - - -
427B LEU* 1.3 78.2 - - - +
429B PHE* 1.3 61.7 + - - +
431B THR* 4.8 0.2 - - - -
432B LEU* 3.1 30.8 + - - +
522B LEU* 3.6 24.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B LEU* 3.0 51.6 + - + +
428B GLY* 1.3 76.3 - - - +
430B HIS* 1.3 68.3 + + + +
432B LEU* 4.4 1.8 - - - +
433B GLY* 3.0 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B PHE* 2.4 66.0 + + + +
427B LEU* 3.6 1.3 + - - +
428B GLY 3.3 0.2 - - - -
429B PHE* 1.3 84.8 - + + +
431B THR* 1.3 57.5 + - - +
433B GLY* 2.8 2.6 + - - -
434B LEU* 2.7 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LEU* 2.9 32.0 + - - +
428B GLY* 4.5 1.8 - - - -
430B HIS* 1.3 73.7 - - - +
432B LEU* 1.3 64.8 + - - +
434B LEU* 3.4 7.9 + - - +
435B TYR* 3.2 37.8 + - + -
515B LEU* 4.1 11.0 - - + +
518B HIS* 3.5 25.8 + - + +
519B ALA* 4.0 33.0 - - + +
522B LEU* 5.3 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A PHE* 3.6 41.7 - - + -
428B GLY 3.1 18.9 + - - +
429B PHE* 4.4 2.0 - - - +
431B THR* 1.3 79.7 - - - +
433B GLY* 1.3 57.2 + - - +
435B TYR* 3.3 9.5 + - + +
436B VAL* 2.9 51.5 + - + +
522B LEU* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B PHE 3.0 17.8 + - - -
430B HIS* 2.8 9.7 + - - -
432B LEU* 1.3 77.9 - - - +
434B LEU* 1.3 57.3 + - - -
436B VAL* 3.9 4.6 - - - +
437B HIS* 3.0 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B HIS* 2.7 29.2 + - + +
431B THR* 4.0 5.4 - - - +
432B LEU 3.4 0.2 - - - -
433B GLY* 1.3 72.5 - - - +
435B TYR* 1.3 58.4 + - - +
437B HIS* 3.2 5.4 + - + +
438B ASN* 2.9 37.7 + - - +
451B ILE* 4.1 30.3 - - + +
453B ILE* 3.8 20.9 - - + -
514B PHE* 4.6 5.4 - - + -
515B LEU* 3.4 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B THR* 3.2 33.9 + - + -
432B LEU* 3.3 14.5 + - + +
434B LEU* 1.3 79.5 - - - +
436B VAL* 1.3 59.1 + - + +
438B ASN* 3.5 7.7 + - + +
439B ASP* 2.9 37.6 + - - +
512B GLY* 4.1 6.4 + - - -
515B LEU* 3.0 49.6 - - + +
516B VAL* 3.5 18.5 + - + +
519B ALA* 5.2 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A PHE* 6.2 0.9 - - + -
432B LEU* 2.9 42.8 + - + +
433B GLY* 4.0 4.7 - - - +
435B TYR* 1.3 73.7 - - + +
437B HIS* 1.3 66.6 + - - +
439B ASP* 3.7 8.5 - - + +
440B VAL* 3.1 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B GLY 3.0 15.8 + - - +
434B LEU* 3.2 9.2 + - + +
436B VAL* 1.3 78.7 - - - +
438B ASN* 1.3 69.8 + - - +
440B VAL* 3.3 4.7 + - - +
441B VAL* 2.8 48.2 + - + +
449B LYS* 3.4 20.0 + - + -
451B ILE* 3.3 38.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B LEU* 2.9 17.3 + - - +
435B TYR* 3.8 7.6 - - + +
437B HIS* 1.3 79.6 - - - +
439B ASP* 1.3 58.3 + - - +
441B VAL* 4.1 5.8 - - - -
442B VAL* 2.6 40.4 + - + +
450B GLN* 3.1 31.8 + - + +
451B ILE* 3.0 42.8 + - - +
452B LEU* 4.6 2.4 - - - +
515B LEU* 4.7 13.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A TYR* 2.9 35.9 + - - +
670A ILE* 4.4 4.5 - - + -
673A LEU* 4.1 16.4 - - - +
435B TYR* 2.9 26.2 + - - +
436B VAL* 3.7 9.6 - - + +
438B ASN* 1.3 74.0 - - - +
440B VAL* 1.3 59.7 + - + +
442B VAL* 4.8 1.1 - - - -
443B ALA* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A ILE* 4.3 20.9 - - + -
436B VAL* 3.1 27.1 + - + +
437B HIS* 3.7 3.8 - - - +
439B ASP* 1.3 74.8 - - + +
441B VAL* 1.3 67.9 + - + +
443B ALA* 3.2 6.8 + - - +
444B PHE* 3.2 51.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B HIS* 2.8 39.5 + - + +
438B ASN* 3.0 6.3 + - - +
440B VAL* 1.3 81.0 - - + +
442B VAL* 1.3 61.7 + - - +
444B PHE* 3.7 3.7 + - - -
446B THR* 2.6 49.2 + - - +
449B LYS* 3.5 36.8 - - + +
450B GLN* 3.5 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A TYR* 3.8 21.5 - - + +
662A GLY 4.5 3.3 + - - -
438B ASN* 2.6 24.0 + - + +
439B ASP* 4.1 2.9 - - - +
441B VAL* 1.3 68.3 - - - +
443B ALA* 1.3 57.0 + - - +
444B PHE 3.1 2.5 - - - -
445B GLY* 2.8 25.1 + - - -
447B PRO* 3.8 19.7 - - + +
450B GLN* 3.1 40.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 4.3 0.3 - - - +
661A TYR* 3.7 20.4 - - + -
662A GLY* 3.1 12.6 + - - -
666A SER* 3.1 31.2 + - - +
670A ILE* 3.6 26.7 - - + -
439B ASP 2.9 20.7 + - - +
440B VAL* 3.2 7.6 + - - +
442B VAL* 1.3 76.0 - - - +
444B PHE* 1.3 62.6 + - + +
445B GLY 3.1 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A VAL* 3.4 29.8 - - + -
122A GLY* 3.3 17.5 - - - +
123A GLN* 4.0 21.1 - - + -
125A ILE* 3.4 37.9 - - + +
126A LEU* 4.3 13.2 - - + -
666A SER* 3.9 9.4 - - - -
667A ALA* 5.6 0.4 - - - -
670A ILE* 5.1 12.3 - - + -
440B VAL* 3.2 37.0 + - + +
441B VAL* 5.2 1.3 - - - -
442B VAL 3.1 0.8 - - - -
443B ALA* 1.3 81.9 - - + +
445B GLY* 1.3 62.7 + - - +
446B THR* 3.2 21.4 + - + +
449B LYS* 5.8 1.8 - - - +
----------------------------------------------------------
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