Contacts of the helix formed by residues 416 - 448 (chain B) in PDB entry 5WJ9
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 416 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ASN* 3.1 25.2 + - + +
413B ILE 4.6 0.2 - - - -
415B ILE* 1.3 75.4 - - + +
417B THR* 1.3 63.3 + - - +
418B LEU 3.1 2.2 - - - -
419B ARG* 3.1 34.0 + - + +
420B VAL* 3.2 17.5 + - + +
524B ILE* 4.7 9.2 - - + -
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Residues in contact with THR 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A LEU* 3.6 29.8 - - + -
413B ILE 3.8 14.4 + - - +
414B LEU* 3.2 22.0 - - - +
415B ILE 4.3 0.9 - - - +
416B ALA* 1.3 78.3 - - - +
418B LEU* 1.3 55.1 + - + +
420B VAL* 3.3 6.1 + - - +
421B ALA* 2.8 34.2 + - - +
517B ILE* 4.0 3.0 + - + +
520B ALA* 3.2 9.9 - - - +
521B TYR* 3.1 29.7 + - + -
524B ILE* 4.0 12.3 - - - +
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Residues in contact with LEU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A LEU* 4.5 10.5 - - + -
508A MET* 4.0 42.0 - - + +
509A VAL* 6.2 0.7 - - + -
415B ILE 3.4 11.8 + - - +
416B ALA 3.1 0.6 - - - -
417B THR* 1.3 82.5 - - + +
419B ARG* 1.3 64.8 + - + +
421B ALA* 4.3 6.1 - - + -
422B LEU* 2.8 54.9 + - + +
517B ILE* 5.7 5.4 - - + -
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Residues in contact with ARG 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B GLY* 5.5 5.3 - - - +
354B TRP* 3.4 41.6 - - - +
415B ILE* 5.4 2.1 - - - +
416B ALA* 3.1 27.2 + - + +
418B LEU* 1.3 81.1 - - + +
420B VAL* 1.3 61.2 + - + +
422B LEU* 4.5 4.9 - - - +
423B PRO* 3.4 17.2 - - - +
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Residues in contact with VAL 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B ALA 3.2 13.7 + - - +
417B THR* 3.6 8.7 - - - +
419B ARG* 1.3 78.7 - - + +
421B ALA* 1.3 62.0 + - - +
423B PRO* 3.4 15.8 - - - +
424B SER* 4.8 3.1 + - - -
520B ALA* 4.4 7.6 - - + +
523B THR* 3.9 22.2 - - + +
524B ILE* 4.0 22.7 - - + -
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Residues in contact with ALA 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B THR 2.8 21.5 + - - +
418B LEU* 4.0 4.5 - - + +
420B VAL* 1.3 74.0 - - - +
422B LEU* 1.3 51.5 + - - +
424B SER* 2.8 31.2 + - - -
425B VAL* 2.8 30.2 + - + +
516B LEU* 4.4 5.2 - - + +
517B ILE* 4.0 16.6 - - + -
520B ALA* 3.7 18.4 - - + -
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Residues in contact with LEU 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B LEU* 2.8 39.5 + - + +
419B ARG* 4.5 4.3 - - - +
421B ALA* 1.3 71.8 - - - +
423B PRO* 1.4 69.9 - - + +
425B VAL* 4.1 9.8 - - - +
426B MET* 2.8 62.9 + - + +
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Residues in contact with PRO 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ARG 3.4 13.9 - - - +
420B VAL 3.4 16.8 - - - +
422B LEU* 1.4 104.6 - - + +
424B SER* 1.3 61.9 + - - +
426B MET* 3.9 5.4 - - + +
427B ARG* 3.1 46.2 + - - +
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Residues in contact with SER 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B VAL 5.0 2.8 + - - -
421B ALA* 2.8 14.1 + - - -
423B PRO* 1.3 75.1 - - - +
425B VAL* 1.3 53.7 + - - -
427B ARG* 3.3 7.5 + - - +
428B PHE* 2.8 35.9 + - - +
516B LEU* 3.4 27.3 - - - +
414C LEU* 4.1 6.6 - - - +
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Residues in contact with VAL 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A MET* 4.7 12.1 - - + -
421B ALA* 2.8 38.7 + - + +
422B LEU* 4.0 8.1 - - - +
424B SER* 1.3 69.3 - - - +
426B MET* 1.3 56.4 + - + +
428B PHE* 3.9 0.7 - - - +
429B CYS* 2.8 39.5 + - + +
513B PHE* 3.4 31.5 - - + -
516B LEU* 4.1 22.0 - - + -
517B ILE* 4.0 17.0 - - + -
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Residues in contact with MET 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B LEU* 2.8 55.4 + - + +
423B PRO* 3.9 7.0 - - - +
425B VAL* 1.3 74.8 - - + +
427B ARG* 1.3 63.3 + - + +
429B CYS* 3.4 6.5 + - - +
430B CYS* 3.3 27.4 + - - -
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Residues in contact with ARG 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B PRO* 3.1 45.1 + - - +
424B SER* 3.3 8.1 + - - +
426B MET* 1.3 81.7 - - + +
428B PHE* 1.3 60.5 + - - +
430B CYS* 3.8 5.4 + - - +
431B CYS* 3.7 7.1 - - - -
408C PHE* 4.8 17.4 - - - -
410C ASN* 3.3 39.8 - - - +
411C TYR* 3.2 51.7 + - + +
414C LEU* 4.3 7.0 - - + -
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Residues in contact with PHE 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B SER 2.8 20.6 + - - +
425B VAL 3.9 1.3 - - - +
427B ARG* 1.3 71.3 - - - +
429B CYS* 1.3 65.5 + - - +
430B CYS 3.3 0.7 + - - -
431B CYS* 3.3 10.3 + - + +
432B VAL* 3.3 44.1 + - + +
509B VAL* 3.4 33.2 - - + -
512B LEU* 3.4 28.9 - - + -
513B PHE* 3.8 36.3 - + + -
516B LEU* 3.6 19.1 - - + -
900B AQV 5.2 1.1 - - + -
414C LEU* 3.6 30.9 - - + +
415C ILE* 6.2 0.9 - - + -
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Residues in contact with CYS 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B VAL* 2.8 28.0 + - + +
426B MET* 3.4 8.3 + - - +
428B PHE* 1.3 74.3 - - - +
430B CYS* 1.3 53.2 + - - +
432B VAL* 3.9 1.0 - - - +
433B ALA* 2.8 38.7 + - - +
900B AQV 3.4 63.2 - - + -
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Residues in contact with CYS 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B MET 3.3 14.9 + - - -
427B ARG* 3.8 12.3 - - - +
428B PHE 3.2 0.8 - - - -
429B CYS* 1.3 78.4 - - - +
431B CYS* 1.3 54.1 + - - +
433B ALA* 3.6 5.4 - - - +
434B VAL* 2.8 40.5 + - + +
405C LEU* 4.5 15.5 - - + -
411C TYR* 4.8 8.1 - - + -
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Residues in contact with CYS 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B ARG 3.7 16.8 - - - -
428B PHE* 3.3 10.7 + - + +
430B CYS* 1.3 73.8 - - - +
432B VAL* 1.3 63.6 + - + +
434B VAL* 3.5 8.3 - - - +
435B ILE* 3.2 30.3 + - + +
402C ILE* 4.0 13.9 - - + +
405C LEU* 3.6 24.5 - - - -
411C TYR* 3.8 13.0 - - - -
414C LEU* 6.2 1.1 - - - -
415C ILE* 3.9 29.4 - - + -
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Residues in contact with VAL 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B PHE* 3.3 51.4 + - + +
429B CYS 3.9 3.8 - - - +
431B CYS* 1.3 75.1 - - + +
433B ALA* 1.3 54.9 + - - +
435B ILE* 3.3 8.0 + - + -
436B TYR* 2.8 31.4 + - - +
505B PHE* 3.4 15.1 - - + -
509B VAL* 3.4 26.9 - - + -
900B AQV 3.2 33.7 - - + +
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Residues in contact with ALA 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B CYS* 2.8 23.8 + - - +
430B CYS* 3.6 5.8 - - - +
432B VAL* 1.3 70.8 - - - +
434B VAL* 1.3 57.0 + - - +
436B TYR* 3.3 2.4 - - - +
437B LEU* 2.8 45.3 + - + +
900B AQV 3.4 37.6 - - + +
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Residues in contact with VAL 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B CYS* 2.8 23.5 + - + +
431B CYS* 3.5 8.1 - - - +
433B ALA* 1.3 78.6 - - - +
435B ILE* 1.3 61.3 + - - +
437B LEU* 3.7 4.0 + - + +
438B GLY 3.4 13.2 + - - -
398C TRP* 3.1 53.8 - - + +
399C VAL* 4.0 1.6 - - - -
401C VAL* 3.8 30.3 - - + -
402C ILE* 3.9 20.4 - - + -
405C LEU* 4.6 3.6 - - + -
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Residues in contact with ILE 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B CYS* 3.2 20.0 + - + +
432B VAL* 3.6 7.4 - - + +
434B VAL* 1.3 72.4 - - - +
436B TYR* 1.3 65.6 + - - +
438B GLY* 3.1 11.6 + - - -
439B TYR* 3.2 37.0 + - + -
504B LEU* 3.7 18.8 - - + -
505B PHE* 3.6 22.7 - - + -
509B VAL* 5.2 6.1 - - + -
395C LEU* 4.5 0.7 - - - +
399C VAL* 3.7 20.9 - - + -
402C ILE* 3.5 25.8 - - + -
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Residues in contact with TYR 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B VAL 2.8 16.2 + - - +
433B ALA* 3.3 9.2 - - - +
435B ILE* 1.3 76.0 - - - +
437B LEU* 1.3 56.5 + - + +
439B TYR* 3.2 8.5 + - - +
440B CYS* 2.8 47.1 + - + +
461B SER* 2.6 49.4 + - - -
464B LEU* 3.3 33.4 - - + +
465B PHE* 3.4 4.9 + - - +
468B ILE* 5.5 2.2 - - + -
501B PHE* 4.0 8.3 - + - -
505B PHE* 3.9 19.7 - + + -
900B AQV 3.2 54.9 - + - +
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Residues in contact with LEU 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B ALA* 2.8 29.5 + - + +
434B VAL* 4.0 4.9 - - + +
436B TYR* 1.3 78.2 - - + +
438B GLY* 1.3 57.5 + - - +
440B CYS* 3.6 12.3 - - + -
441B PHE* 2.8 60.3 + - + +
457B LEU* 5.7 5.6 - - + -
900B AQV 5.1 5.4 - - + +
398C TRP* 4.3 32.8 - - + -
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Residues in contact with GLY 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B VAL 3.4 5.5 + - - -
435B ILE* 3.1 9.3 + - - -
437B LEU* 1.3 78.6 - - - +
439B TYR* 1.3 56.6 + - - +
441B PHE* 4.0 1.3 - - - +
442B CYS* 3.0 31.2 + - - +
394C THR 4.5 1.3 - - - -
395C LEU* 3.7 23.7 + - - -
398C TRP* 3.9 22.6 - - - +
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Residues in contact with TYR 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B ILE* 3.2 44.5 + - + -
436B TYR 3.2 6.9 + - - +
438B GLY* 1.3 73.2 - - - +
440B CYS* 1.3 55.5 + - - +
442B CYS* 4.2 0.2 - - - -
443B GLY 2.8 20.1 + - - -
464B LEU* 3.9 4.3 - - + -
497B TYR* 2.5 55.9 + + - +
500B SER* 3.1 36.4 + - - -
501B PHE* 3.6 38.0 + + + -
504B LEU* 4.3 11.6 - - + +
395C LEU* 3.7 28.8 - - + +
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Residues in contact with CYS 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B TYR* 2.8 25.0 + - + +
437B LEU* 3.7 16.4 - - + +
439B TYR* 1.3 76.9 - - - +
441B PHE* 1.3 57.3 + - - +
444B TRP* 3.1 29.5 + - - +
457B LEU* 3.9 20.1 - - + +
460B VAL* 3.5 26.6 - - - +
461B SER* 3.7 28.0 - - - -
464B LEU* 3.6 11.2 - - + +
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Residues in contact with PHE 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B LEU* 2.8 49.0 + - + +
438B GLY* 4.3 1.8 - - - +
440B CYS* 1.3 70.9 - - - +
442B CYS* 1.3 65.0 + - - +
444B TRP* 3.8 14.7 - + - +
445B ILE* 3.6 16.5 + - - +
457B LEU* 3.4 28.7 - - + -
77C THR* 3.9 21.3 - - + -
80C LEU* 3.5 24.0 - - + +
81C ILE* 3.7 23.1 - - + -
394C THR* 5.1 2.2 - - - +
398C TRP* 3.9 29.8 - + + -
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Residues in contact with CYS 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B GLY 3.0 22.2 + - - +
439B TYR 3.8 2.7 - - - +
441B PHE* 1.3 79.0 - - - +
443B GLY* 1.3 59.2 + - - +
444B TRP 3.3 0.2 + - - -
445B ILE* 3.7 0.2 - - - +
446B VAL* 3.0 34.5 + - - +
493B PHE* 3.4 36.1 - - - -
497B TYR* 4.2 8.7 - - + -
80C LEU* 4.4 0.9 - - - +
391C GLY* 3.4 36.1 - - - +
392C THR 4.1 0.2 - - - -
394C THR* 4.5 4.0 + - - +
395C LEU* 4.2 9.4 - - + -
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Residues in contact with GLY 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B TYR 2.8 14.9 + - - -
442B CYS* 1.3 71.6 - - - +
444B TRP* 1.3 63.2 + - - +
446B VAL* 4.9 0.4 - - - -
447B LEU* 3.1 35.5 + - - +
448B GLY 3.3 3.8 + - - -
454B PHE* 3.5 12.4 - - - +
497B TYR* 3.4 27.5 - - - -
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Residues in contact with TRP 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B CYS 3.1 21.1 + - - +
441B PHE* 3.8 19.7 - + - +
442B CYS 3.2 0.2 - - - -
443B GLY* 1.3 76.5 - - - +
445B ILE* 1.3 65.6 + - + +
448B GLY* 3.1 25.0 + - - -
449B PRO* 3.8 1.7 - - - +
454B PHE 3.7 13.2 - - - -
455B ARG 4.0 5.7 + - - -
456B SER* 3.9 12.5 - - - +
457B LEU* 3.8 42.6 - - + +
460B VAL* 3.8 12.7 - - + +
81C ILE* 3.7 46.2 - - + -
88C GLN* 5.6 8.3 + - - +
----------------------------------------------------------
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Residues in contact with ILE 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B PHE 3.6 9.4 + - - +
442B CYS 3.5 7.8 + - - +
444B TRP* 1.3 91.0 - - + +
446B VAL* 1.3 79.3 + - + +
449B PRO* 3.1 17.9 - - - +
80C LEU* 3.3 57.7 - - + +
81C ILE* 4.2 14.6 - - + -
83C PHE* 4.6 4.7 - - + -
84C GLY* 4.2 14.3 - - - -
87C ASN* 3.2 20.1 + - - +
387C SER* 3.9 16.8 - - - +
----------------------------------------------------------
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Residues in contact with VAL 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B CYS* 3.0 23.9 + - - +
445B ILE* 1.3 88.7 - - + +
447B LEU* 1.3 65.1 + - + +
449B PRO* 3.7 1.2 - - - +
450B TYR* 3.4 26.5 - - - -
490B VAL* 4.2 7.5 - - + +
493B PHE* 3.6 33.2 - - + -
87C ASN* 5.2 0.3 + - - -
387C SER* 3.1 42.9 + - - +
388C ILE* 4.4 7.9 - - + -
391C GLY* 4.1 8.5 - - - -
----------------------------------------------------------
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Residues in contact with LEU 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B GLY* 3.1 20.8 + - - +
446B VAL* 1.3 87.5 - - + +
448B GLY* 1.3 59.6 + - - +
449B PRO* 3.3 3.1 - - - -
450B TYR* 3.1 4.1 + - - +
451B HIS* 2.9 43.4 + - + +
454B PHE* 4.0 23.6 - - + -
480B MET* 4.2 11.2 - - + -
490B VAL* 4.4 9.0 - - + +
493B PHE* 4.6 2.7 - - + -
494B SER* 3.4 30.5 - - - -
497B TYR* 3.6 38.8 - - + -
498B LEU* 5.3 0.4 - - + -
----------------------------------------------------------
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Residues in contact with GLY 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B GLY 3.3 3.6 + - - -
444B TRP 3.1 10.0 + - - -
447B LEU* 1.3 76.9 - - - +
449B PRO* 1.4 66.9 - - - +
451B HIS 3.2 15.1 - - - +
454B PHE* 3.2 31.4 - - - -
455B ARG* 4.0 12.4 - - - +
88C GLN* 5.1 5.9 - - - +
----------------------------------------------------------
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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