Contacts of the helix formed by residues 413 - 439 (chain H) in PDB entry 6MZL
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 413 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406H VAL* 5.8 0.2 - - - +
410H PRO* 6.0 3.7 - - - +
411H VAL 3.0 6.1 + - - +
412H LEU* 1.3 77.8 + - - +
414H ASN* 1.3 52.5 + - - +
415H ILE* 3.3 4.7 - - - +
416H ASP* 3.1 27.5 + - - +
417H ARG* 2.7 32.2 + - - +
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Residues in contact with ASN 414 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320H ARG* 4.5 15.2 - - - +
411H VAL* 2.9 20.3 - - - +
412H LEU* 3.5 29.5 - - - +
413H SER* 1.3 71.6 - - - +
415H ILE* 1.3 62.5 + - - +
417H ARG* 3.4 22.1 + - - -
418H ILE* 2.9 45.2 + - + +
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Residues in contact with ILE 415 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316H GLN* 4.1 27.8 - - + +
320H ARG* 3.4 62.1 - - + +
324H ASP* 4.7 15.6 - - - +
370H TRP* 5.5 1.2 - - + +
413H SER* 4.9 1.1 - - - -
414H ASN* 1.3 76.2 - - - +
416H ASP* 1.3 69.1 + - - +
418H ILE* 4.5 0.7 - - - +
419H GLY* 2.8 28.4 + - - -
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Residues in contact with ASP 416 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316H GLN* 4.2 7.6 + - - +
370H TRP* 3.1 39.6 - - + +
406H VAL* 4.1 9.1 - - + +
413H SER* 3.1 28.2 + - - +
415H ILE* 1.3 88.3 - - - +
417H ARG* 1.3 58.4 + - - +
420H ALA* 2.9 31.4 + - - +
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Residues in contact with ARG 417 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406H VAL* 3.8 30.2 + - + +
407H LEU* 4.5 17.9 - - + +
408H ASP 4.9 4.6 - - - +
409H GLY 5.3 0.2 - - - +
410H PRO 2.4 31.9 + - - -
411H VAL* 3.4 27.4 + - - +
413H SER 2.7 18.0 + - - +
414H ASN* 3.4 18.8 + - - -
415H ILE 3.3 0.4 - - - -
416H ASP* 1.3 75.1 - - - +
418H ILE* 1.3 65.0 + - + +
420H ALA* 3.3 2.9 + - - +
421H ASP* 2.9 27.0 + - + +
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Residues in contact with ILE 418 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324H ASP* 4.3 16.4 - - + +
414H ASN* 2.9 28.0 + - + +
417H ARG* 1.3 81.2 - - + +
419H GLY* 1.3 55.0 + - - +
421H ASP* 3.8 14.4 - - + +
422H HIS* 2.4 46.6 + - + +
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Residues in contact with GLY 419 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324H ASP* 4.8 3.3 + - - -
370H TRP* 4.7 13.2 - - - -
374H TYR* 4.4 1.4 - - - -
415H ILE 2.8 20.5 + - - -
416H ASP 3.7 1.3 - - - -
417H ARG 3.2 0.2 - - - -
418H ILE* 1.3 76.6 - - - +
420H ALA* 1.3 57.6 + - - +
422H HIS* 3.3 18.2 + - - -
423H VAL* 2.9 32.7 + - - +
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Residues in contact with ALA 420 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370H TRP* 3.9 23.3 - - + -
403H ILE* 3.7 23.2 - - + +
406H VAL* 4.0 10.3 - - + -
416H ASP 2.9 18.4 + - - +
417H ARG 3.8 2.9 - - - +
419H GLY* 1.3 74.9 - - - +
421H ASP* 1.3 56.6 + - - +
423H VAL* 3.2 12.5 - - - +
424H GLN* 2.9 33.7 + - - +
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Residues in contact with ASP 421 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417H ARG* 2.9 14.8 + - + +
418H ILE* 3.4 21.1 - - + +
419H GLY 3.1 0.2 - - - -
420H ALA* 1.3 77.1 - - - +
422H HIS* 1.3 59.6 + - - +
424H GLN* 3.1 24.9 + - - +
425H SER* 3.0 25.7 + - - -
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Residues in contact with HIS 422 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324H ASP* 3.3 49.3 + - + +
325H ASN* 4.6 10.5 - - - +
327H TRP* 5.0 1.0 - - - +
328H ALA* 4.9 1.3 - - + -
374H TYR* 3.0 40.2 + + - +
418H ILE* 2.4 43.5 + - + +
419H GLY* 3.3 19.2 + - - -
421H ASP* 1.3 74.8 - - - +
423H VAL* 1.3 60.1 + - - +
425H SER* 3.4 14.6 - - - +
426H LEU* 2.9 30.8 + - - +
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Residues in contact with VAL 423 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370H TRP* 4.1 16.6 - - + -
373H ARG* 5.4 2.0 - - + +
374H TYR* 3.5 34.7 - - + +
377H ILE* 4.3 15.7 - - + -
403H ILE* 3.7 22.9 - - + -
419H GLY 2.9 19.6 + - - +
420H ALA* 3.2 14.1 - - - +
422H HIS* 1.3 73.6 - - - +
424H GLN* 1.3 60.6 + - - +
426H LEU* 3.0 6.8 + - - +
427H LEU* 2.9 39.9 + - + +
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Residues in contact with GLN 424 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403H ILE* 3.4 33.0 - - + +
407H LEU* 4.2 21.8 - - - +
420H ALA 2.9 19.7 + - - +
421H ASP* 3.1 24.8 + - - +
423H VAL* 1.3 75.4 - - - +
425H SER* 1.3 57.1 + - - +
427H LEU* 3.7 10.5 - - + +
428H LEU* 2.9 33.1 + - - +
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Residues in contact with SER 425 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421H ASP* 3.0 16.3 + - - -
422H HIS* 3.4 20.0 - - - +
424H GLN* 1.3 78.0 - - - +
426H LEU* 1.3 57.6 + - - +
428H LEU* 4.9 2.9 - - - -
429H LYS* 2.9 41.8 + - - +
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Residues in contact with LEU 426 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328H ALA* 6.0 0.2 - - + -
331H ASP* 4.0 10.3 - - + +
374H TYR* 3.5 59.5 - - + +
377H ILE* 3.7 22.4 - - + -
378H ALA* 4.3 9.9 - - + +
422H HIS 2.9 18.8 + - - +
423H VAL* 3.0 8.5 + - + +
425H SER* 1.3 75.3 - - - +
427H LEU* 1.3 58.4 + - - +
429H LYS 5.1 0.7 - - - -
430H HIS* 2.9 38.9 + - + +
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Residues in contact with LEU 427 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363H TRP* 5.8 1.8 - - + +
377H ILE* 4.2 27.1 - - + -
392H ILE* 4.4 21.5 - - + -
396H LEU* 4.8 21.5 - - + +
399H GLU* 5.8 6.7 - - + +
400H GLY* 5.9 3.8 - - - +
403H ILE* 4.5 9.9 - - + -
423H VAL* 2.9 38.0 + - + +
424H GLN* 3.7 9.6 - - + +
425H SER 3.3 0.2 - - - -
426H LEU* 1.3 75.2 - - - +
428H LEU* 1.3 55.7 + - - +
431H CYS* 2.6 42.0 + - + +
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Residues in contact with LEU 428 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424H GLN 2.9 17.9 + - - +
425H SER* 4.2 2.7 - - - +
427H LEU* 1.3 74.8 - - - +
429H LYS* 1.3 76.8 + - + +
430H HIS 3.1 1.6 + - - -
431H CYS* 5.0 0.2 - - - -
432H ALA* 3.0 37.4 + - + +
455H LEU* 3.7 18.4 - - + +
458H LEU* 3.6 28.0 - - + +
459H LEU* 3.5 36.1 - - + +
462H GLN* 4.8 6.1 - - + -
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Residues in contact with LYS 429 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425H SER* 2.9 25.6 + - - +
426H LEU* 3.6 2.9 - - - -
428H LEU* 1.3 89.6 - - + +
430H HIS* 1.3 61.2 + - - +
432H ALA* 5.4 2.9 - - - -
433H PRO* 5.9 0.4 - - - -
462H GLN* 5.5 9.0 - - + -
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Residues in contact with HIS 430 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381H ALA* 2.7 57.1 + - + +
382H GLU* 5.1 9.2 - - - -
384H GLY* 5.2 2.0 - - - -
388H ILE* 4.3 17.1 - - + +
426H LEU* 2.9 21.3 + - + +
429H LYS* 1.3 80.9 + - - +
431H CYS* 1.3 57.4 + - + +
432H ALA 3.6 2.0 - - - -
433H PRO* 3.3 19.7 - - - +
434H VAL* 5.3 1.4 - - - +
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Residues in contact with CYS 431 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388H ILE* 3.7 29.6 - - + -
392H ILE* 4.7 13.7 - - + -
393H LEU* 5.6 3.6 - - - -
396H LEU* 4.9 16.4 - - - -
427H LEU* 2.6 26.0 + - + +
430H HIS* 1.3 76.5 - - + +
432H ALA* 1.3 66.3 + - - +
433H PRO* 3.5 2.2 - - - -
434H VAL* 3.3 16.0 - - - +
435H LEU* 3.9 19.1 + - - +
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Residues in contact with ALA 432 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428H LEU* 3.0 17.6 + - + +
429H LYS* 5.4 2.5 - - - -
431H CYS* 1.3 77.1 - - - +
433H PRO* 1.4 62.6 - - + +
435H LEU* 3.1 10.4 + - - +
436H ALA* 2.9 25.7 + - - +
459H LEU* 4.6 14.8 - - - +
462H GLN* 4.1 31.0 - - + +
463H VAL* 4.7 3.4 - - - +
466H ALA* 5.6 2.7 - - + -
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Residues in contact with PRO 433 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429H LYS 5.9 0.4 - - - -
430H HIS* 3.3 21.5 - - - +
431H CYS* 3.5 0.7 - - - -
432H ALA* 1.4 92.0 - - + +
434H VAL* 1.3 65.6 + - + +
436H ALA* 3.3 10.1 - - + +
437H LYS* 2.9 36.1 + - + +
466H ALA* 5.1 11.9 - - + -
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Residues in contact with VAL 434 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385H HIS* 3.4 54.5 - - + +
388H ILE* 3.9 26.0 - - + -
389H LYS* 4.8 15.4 - - + +
430H HIS 5.3 0.9 - - - +
431H CYS* 3.3 24.2 - - - +
433H PRO* 1.3 82.8 - - + +
435H LEU* 1.3 61.7 + - + +
437H LYS* 3.4 3.1 + - - +
438H LEU* 2.9 33.6 + - + +
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Residues in contact with LEU 435 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393H LEU* 4.5 21.1 - - + -
396H LEU* 5.3 11.7 - - + -
431H CYS* 4.1 21.8 - - - +
432H ALA* 3.1 9.0 + - - +
434H VAL* 1.3 80.4 - - + +
436H ALA* 1.3 60.5 + - - +
438H LEU* 4.1 15.5 - - + +
439H ARG* 2.6 68.6 + - + +
451H GLU* 5.4 5.8 - - + -
459H LEU* 5.7 9.6 - - + -
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Residues in contact with ALA 436 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432H ALA 2.9 13.1 + - - +
433H PRO* 3.2 15.9 + - + +
435H LEU* 1.3 78.0 - - - +
437H LYS* 1.3 61.7 + - + +
439H ARG 3.7 9.5 - - - +
440H PRO* 5.4 0.2 - - - +
441H PRO* 5.2 7.2 - - - +
463H VAL* 4.2 30.9 - - + +
466H ALA* 4.9 6.3 - - + -
467H ARG* 5.8 1.1 - - + +
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Residues in contact with LYS 437 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385H HIS* 3.4 40.4 + - + +
389H LYS* 5.7 2.2 - - - +
433H PRO* 2.9 18.7 + - - +
434H VAL 3.6 7.2 - - - +
436H ALA* 1.3 80.4 - - + +
438H LEU* 1.3 68.4 + - + +
439H ARG 4.7 0.9 - - - +
440H PRO* 5.7 0.2 - - - +
354I ARG* 5.7 3.0 - - - +
357I LYS* 5.7 2.4 + - - -
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Residues in contact with LEU 438 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389H LYS* 3.6 53.6 - - + +
393H LEU* 5.6 7.6 - - + -
434H VAL* 2.9 22.5 + - + +
435H LEU* 4.1 14.1 - - + +
437H LYS* 1.3 82.0 - - + +
439H ARG* 1.3 66.4 + - - +
440H PRO* 3.3 8.1 - - - +
357I LYS* 4.7 17.2 + - - +
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Residues in contact with ARG 439 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393H LEU* 5.4 7.3 - - - +
435H LEU* 2.6 54.4 + - + +
436H ALA* 3.7 11.0 - - - +
438H LEU* 1.3 74.8 - - - +
440H PRO* 1.3 82.8 - - + +
441H PRO* 3.7 2.4 - - - +
442H PRO 5.5 1.6 - - - +
447H ALA* 3.1 50.0 + - - +
450H ALA* 3.5 29.7 + - - +
451H GLU* 3.8 12.5 - - - +
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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