Contacts of the helix formed by residues 434 - 461 (chain j) in PDB entry 6QX2
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 THR 434 (chain j).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431j ARG* 3.4 12.8 + - - +
432j ARG 3.4 0.5 - - - +
433j LEU* 1.3 84.4 - - - +
435j GLY* 1.3 65.1 + - - +
436j LEU* 4.3 1.9 + - - +
437j GLU* 3.5 24.9 + - - +
438j ARG* 3.7 7.4 + - - +
398l ILE* 3.9 20.0 - - + +
399l ARG 5.2 0.4 - - - -
401l SER 3.7 7.9 - - - -
402l ASP 3.9 10.5 + - - -
403l THR* 3.9 15.8 - - - +
404l ASP* 3.2 32.2 + - - +
407l ALA* 4.4 4.7 - - + -
426l LEU* 5.2 0.7 - - + -
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Residues in contact with GLY 435 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434j THR* 1.3 71.3 - - - +
436j LEU* 1.3 64.7 + - - +
437j GLU 3.3 0.7 + - - -
438j ARG* 3.5 14.5 + - - +
439j ASP* 3.8 15.5 + - - +
399l ARG 4.9 3.9 + - - -
401l SER 3.4 8.8 + - - -
402l ASP* 3.2 12.3 + - - -
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Residues in contact with LEU 436 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434j THR* 3.5 2.9 - - - +
435j GLY* 1.3 74.6 - - - +
437j GLU* 1.3 57.9 + - + +
439j ASP* 3.4 14.7 + - + +
440j LYS* 3.0 31.0 + - + +
402l ASP* 3.2 16.9 + - + +
403l THR* 3.8 25.8 - - + -
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Residues in contact with GLU 437 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431j ARG* 3.7 24.4 - - + +
432j ARG* 3.5 49.0 + - + +
434j THR* 3.5 14.4 + - - +
435j GLY 3.2 1.0 - - - -
436j LEU* 1.3 77.0 - - + +
438j ARG* 1.3 63.6 + - - +
440j LYS* 3.1 38.5 + - - +
441j ILE* 3.2 27.4 + - - +
404l ASP* 4.9 6.3 - - - +
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Residues in contact with ARG 438 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385j ARG* 3.6 30.9 + - - +
388j LEU* 3.6 38.4 - - + +
389j ASP* 3.1 37.5 + - - +
432j ARG 4.7 0.2 + - - -
434j THR 3.7 6.9 + - - +
435j GLY* 3.5 10.6 + - - +
436j LEU 3.4 0.6 - - - -
437j GLU* 1.3 77.2 - - - +
439j ASP* 1.3 65.1 + - - +
441j ILE* 3.5 3.2 + - - +
442j GLU* 3.3 45.8 + - - +
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Residues in contact with ASP 439 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435j GLY 3.8 11.2 + - - +
436j LEU* 3.4 18.2 + - + +
437j GLU 3.3 0.2 - - - -
438j ARG* 1.3 80.3 - - - +
440j LYS* 1.3 53.9 + - - +
442j GLU* 3.2 7.5 + - - +
443j ALA* 2.9 35.7 + - - +
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Residues in contact with LYS 440 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436j LEU* 3.0 18.4 + - + +
437j GLU* 3.1 39.6 + - - +
439j ASP* 1.3 75.5 - - - +
441j ILE* 1.3 56.4 + - + +
443j ALA* 3.6 7.9 - - - +
444j GLU* 3.1 28.8 + - - +
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Residues in contact with ILE 441 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381j LEU* 4.0 23.7 - - + +
384j LEU* 4.2 15.0 - - + -
385j ARG* 3.9 26.5 - - + +
388j LEU* 3.5 27.4 - - + -
432j ARG* 4.0 39.9 - - + +
437j GLU* 3.2 17.6 + - - +
438j ARG* 3.7 7.6 - - - +
439j ASP 3.2 0.4 - - - -
440j LYS* 1.3 74.2 - - + +
442j GLU* 1.3 60.1 + - - +
444j GLU* 3.5 8.2 + - - +
445j TYR* 3.0 25.1 + - - +
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Residues in contact with GLU 442 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385j ARG* 3.2 33.2 + - - +
438j ARG* 3.3 32.1 + - - +
439j ASP* 3.2 9.4 + - - +
441j ILE* 1.3 76.0 - - - +
443j ALA* 1.3 62.9 + - - +
445j TYR* 3.3 4.8 + - + +
446j ASN* 2.8 48.8 + - - +
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Residues in contact with ALA 443 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439j ASP 2.9 17.2 + - - +
440j LYS* 3.6 10.1 - - - +
442j GLU* 1.3 77.7 - - - +
444j GLU* 1.3 61.1 + - - +
446j ASN* 3.3 6.1 + - - +
447j GLU* 3.2 22.9 + - - +
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Residues in contact with GLU 444 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377j ARG* 2.9 47.1 + - - +
381j LEU* 3.7 13.5 - - + +
432j ARG* 5.1 1.6 + - - -
440j LYS 3.1 15.3 + - - +
441j ILE* 3.8 7.1 - - - +
443j ALA* 1.3 78.1 - - - +
445j TYR* 1.3 58.7 - - - +
447j GLU* 3.6 6.3 + - - +
448j LEU* 3.1 31.5 + - + +
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Residues in contact with TYR 445 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378j ALA* 3.6 30.5 - - + -
381j LEU* 3.7 27.6 - - + -
382j GLU* 2.8 32.8 + - + +
385j ARG* 3.8 37.4 + - - -
441j ILE 3.0 17.3 + - - +
442j GLU* 3.6 8.7 - - + +
443j ALA 3.2 0.2 - - - -
444j GLU* 1.3 77.8 - - - +
446j ASN* 1.3 67.7 + - - +
448j LEU* 3.4 5.0 - - + +
449j LEU* 3.2 55.6 + - + +
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Residues in contact with ASN 446 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442j GLU* 2.8 43.3 + - - +
443j ALA* 3.9 5.8 - - - +
445j TYR* 1.3 78.2 - - - +
447j GLU* 1.3 63.7 + - - +
449j LEU* 3.2 26.9 + - - +
450j ASN* 3.3 17.3 + - - +
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Residues in contact with GLU 447 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443j ALA 3.2 15.7 + - - +
444j GLU* 3.9 6.7 - - - +
446j ASN* 1.3 75.0 - - - +
448j LEU* 1.3 57.0 + - - +
450j ASN* 2.5 33.9 + - - +
451j TYR* 2.9 15.9 + - - +
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Residues in contact with LEU 448 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374j ALA* 3.5 38.6 - - + +
377j ARG* 3.4 31.6 - - + -
378j ALA* 3.7 21.3 - - + +
381j LEU* 3.8 18.2 - - + -
444j GLU* 3.1 20.8 + - + +
445j TYR 3.4 7.6 - - - +
446j ASN 3.2 0.2 - - - -
447j GLU* 1.3 76.5 - - - +
449j LEU* 1.3 52.3 + - - +
451j TYR* 3.3 12.9 + - + +
452j ILE* 2.8 40.8 + - + +
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Residues in contact with LEU 449 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378j ALA* 5.1 3.1 - - + -
382j GLU* 5.4 1.3 - - - +
445j TYR* 3.2 57.7 + - + +
446j ASN* 3.2 17.7 + - - +
448j LEU* 1.3 74.0 - - - +
450j ASN* 1.3 64.0 + - - +
452j ILE* 3.4 17.4 + - + +
453j SER* 3.2 22.7 + - - -
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Residues in contact with ASN 450 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446j ASN 3.3 13.0 + - - +
447j GLU* 2.5 34.5 + - - +
449j LEU* 1.3 75.0 - - - +
451j TYR* 1.3 61.8 + - - +
453j SER* 3.2 9.6 + - - -
454j GLU* 3.0 44.1 + - + +
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Residues in contact with TYR 451 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370j ASN* 3.2 39.5 + - + +
374j ALA* 4.2 13.7 - - + -
447j GLU 2.9 13.4 + - - +
448j LEU* 3.3 15.5 + - + +
450j ASN* 1.3 75.5 - - - +
452j ILE* 1.3 65.0 + - - +
454j GLU* 3.2 21.1 + - + +
455j LEU* 2.9 62.0 + - + +
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Residues in contact with ILE 452 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371j LEU* 3.7 15.5 - - + -
374j ALA* 3.8 28.9 - - + +
375j LYS* 4.2 16.4 - - + +
378j ALA* 4.0 27.1 - - + -
448j LEU 2.8 28.2 + - - +
449j LEU* 3.8 15.9 - - + +
450j ASN 3.3 0.2 - - - -
451j TYR* 1.3 71.9 - - - +
453j SER* 1.3 57.7 + - - +
455j LEU* 3.4 5.6 + - - +
456j GLU* 3.1 49.7 + - - +
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Residues in contact with SER 453 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449j LEU 3.2 12.9 + - - -
450j ASN* 3.2 12.0 + - - -
452j ILE* 1.3 74.4 - - - +
454j GLU* 1.3 58.7 + - - +
456j GLU* 3.3 13.1 + - - +
457j THR* 2.8 35.2 + - - -
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Residues in contact with GLU 454 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450j ASN* 3.0 37.0 + - + +
451j TYR* 3.2 24.6 + - + +
453j SER* 1.3 75.0 + - - +
455j LEU* 1.3 62.9 + - + +
457j THR* 3.5 10.5 + - - -
458j ILE* 3.4 28.7 + - + +
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Residues in contact with LEU 455 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367j THR* 3.6 29.7 - - + +
370j ASN* 3.7 9.6 - - + +
371j LEU* 3.5 40.8 - - + +
374j ALA* 4.7 1.1 - - + -
451j TYR* 2.9 67.3 + - + +
452j ILE* 3.6 6.1 - - - +
454j GLU* 1.3 75.4 - - + +
456j GLU* 1.3 63.9 + - - +
458j ILE* 3.2 16.2 + - + +
459j LEU* 3.2 20.9 + - - +
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Residues in contact with GLU 456 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371j LEU* 4.0 15.7 - - + -
375j LYS* 3.6 23.3 + - - +
452j ILE* 3.1 34.9 + - - +
453j SER* 3.3 14.2 + - - +
455j LEU* 1.3 73.6 - - - +
457j THR* 1.3 56.8 + - - +
459j LEU* 3.3 8.2 + - + +
460j ALA* 2.9 36.1 + - - +
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Residues in contact with THR 457 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453j SER* 2.8 19.3 + - - -
454j GLU* 3.5 11.6 + - - -
456j GLU* 1.3 76.5 - - - +
458j ILE* 1.3 59.9 + - - +
460j ALA* 3.5 6.2 + - - +
461j ASP* 3.3 24.4 + - + +
464j VAL* 4.2 18.8 - - + +
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Residues in contact with ILE 458 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367j THR* 4.0 19.7 - - + +
454j GLU* 3.5 18.2 - - + +
455j LEU* 3.2 21.2 + - + +
457j THR* 1.3 76.5 - - - +
459j LEU* 1.3 63.7 + - + +
461j ASP 3.3 18.2 - - - +
462j GLU* 4.9 0.3 - - - -
464j VAL* 3.7 20.9 - - + -
465j LEU* 3.6 42.8 - - + +
468j LEU* 3.9 23.3 - - + -
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Residues in contact with LEU 459 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364j ARG* 4.1 21.6 - - + +
367j THR* 3.7 20.2 - - + -
368j GLN* 3.6 36.8 - - + +
371j LEU* 3.6 31.0 - - + -
455j LEU 3.2 15.2 + - - +
456j GLU* 3.3 8.7 + - + +
458j ILE* 1.3 77.5 - - + +
460j ALA* 1.3 62.1 + - - +
461j ASP 5.0 1.2 - - - -
462j GLU* 5.1 1.4 + - - +
465j LEU* 6.0 1.8 - - + -
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Residues in contact with ALA 460 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456j GLU 2.9 18.3 + - - +
457j THR* 3.7 9.0 - - - +
459j LEU* 1.3 77.7 - - - +
461j ASP* 1.3 59.2 + - + +
462j GLU* 4.1 3.3 + - - +
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Residues in contact with ASP 461 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457j THR* 3.3 7.7 + - + +
458j ILE 3.3 10.0 - - - +
460j ALA* 1.3 78.6 - - + +
462j GLU* 1.3 57.3 + - - +
463j GLU* 3.2 19.9 + - - +
464j VAL* 2.9 55.7 + - + +
465j LEU 3.3 1.0 + - - -
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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