Contacts of the helix formed by residues 485 - 509 (chain B) in PDB entry 5TTE
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 ASN 485 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B LYS* 2.3 61.5 + - - +
484B LYS* 1.3 76.7 - - - +
486B ASN* 1.3 67.7 + - - +
487B GLN 3.1 8.1 - - - +
488B SER* 3.1 20.2 + - - +
489B ILE* 3.7 11.6 + - - +
551B LEU 3.2 23.8 - - - +
552B TRP* 3.5 21.2 - - + +
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Residues in contact with ASN 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B ASN* 1.3 77.3 + - - +
487B GLN* 1.3 65.4 + - + +
489B ILE* 3.5 16.9 - - - +
490B ILE* 3.3 25.5 - - + +
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Residues in contact with GLN 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B ASN* 3.1 1.4 - - + +
486B ASN* 1.3 80.1 - - + +
488B SER* 1.3 59.1 + - - +
489B ILE 3.5 0.2 - - - -
490B ILE* 3.8 17.8 - - - +
491B PHE* 3.0 28.2 + - - +
542B HIS* 2.7 34.5 + - + -
546B GLY* 5.8 3.0 - - - -
551B LEU* 3.8 42.7 - - + +
552B TRP* 3.3 28.2 - - + -
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Residues in contact with SER 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B LEU* 4.8 14.7 - - - +
483B LYS 4.0 5.3 - - - -
484B LYS* 4.0 15.4 - - - +
485B ASN* 3.1 31.2 + - - +
487B GLN* 1.3 75.6 - - - +
489B ILE* 1.3 62.0 + - - +
491B PHE* 3.1 8.2 + - - +
492B GLU* 2.7 42.8 + - - +
552B TRP* 4.3 5.1 - - - -
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Residues in contact with ILE 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ARG* 5.0 0.2 + - - -
393B ASN* 5.3 9.4 - - - +
484B LYS* 5.1 11.7 - - + -
485B ASN 4.1 9.9 - - - +
486B ASN* 3.5 21.8 - - - +
488B SER* 1.3 78.8 - - - +
490B ILE* 1.3 68.2 + - + +
492B GLU* 3.4 21.1 + - - +
493B ASN* 3.1 32.0 + - - +
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Residues in contact with ILE 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B ASN* 3.3 20.9 - - + +
487B GLN* 3.7 23.3 + - - +
488B SER 3.2 0.4 - - - -
489B ILE* 1.3 82.1 - - + +
491B PHE* 1.3 61.2 + - - +
493B ASN* 3.2 22.5 + - - +
494B ASN* 3.3 18.7 + - - +
542B HIS* 3.4 26.2 - - + +
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Residues in contact with PHE 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B PRO* 5.7 1.3 - - + -
475B THR* 3.4 41.5 - - + -
478B PHE* 3.9 14.8 - + - -
479B ALA* 3.7 23.8 - - + -
482B LEU* 4.3 11.0 - - + -
487B GLN 3.0 19.7 + - - +
488B SER* 3.4 5.8 - - - +
490B ILE* 1.3 78.2 - - - +
492B GLU* 1.3 65.3 + - + +
494B ASN* 3.1 6.8 + - + +
495B GLN* 2.9 32.6 + - + +
539B LEU* 4.1 18.4 - - + -
542B HIS* 3.8 9.6 - - + -
543B VAL* 3.7 29.2 - - + -
552B TRP* 3.9 12.6 - + + -
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Residues in contact with GLU 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ASN* 3.2 10.1 + - - +
391B ARG* 3.3 51.2 + - + +
392B TYR* 4.4 2.9 + - - +
393B ASN* 3.9 16.5 + - - +
417B TYR* 4.8 7.3 + - - -
479B ALA* 6.4 1.1 - - + -
484B LYS* 5.8 1.6 - - - +
488B SER* 2.7 35.1 + - - +
489B ILE* 3.7 22.6 - - - +
490B ILE 3.3 0.4 - - - -
491B PHE* 1.3 81.6 - - + +
493B ASN* 1.3 56.6 + - - +
495B GLN* 3.3 12.0 + - - +
496B ALA 2.9 23.6 + - - -
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Residues in contact with ASN 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ARG* 2.6 33.8 + - - +
489B ILE* 3.1 18.1 + - - +
490B ILE* 3.5 14.7 - - - +
491B PHE 3.1 0.8 - - - -
492B GLU* 1.3 74.3 - - - +
494B ASN* 1.3 62.4 + - - +
496B ALA* 3.3 1.7 + - - +
497B ASP* 2.8 42.2 + - - +
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Residues in contact with ASN 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B ILE* 3.3 15.8 + - - +
491B PHE* 3.1 8.3 + - + +
493B ASN* 1.3 78.5 - - - +
495B GLN* 1.3 61.1 + - - +
497B ASP* 4.0 11.1 - - - +
498B LEU* 3.2 18.7 + - - +
535B ARG* 4.5 2.8 - - - +
538B VAL* 3.9 30.7 + - + +
539B LEU* 3.4 30.0 - - + +
542B HIS* 3.8 34.4 + - - +
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Residues in contact with GLN 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ASN* 2.8 33.6 + - - +
472B LEU* 4.8 5.1 - - + +
475B THR* 3.4 36.1 + - + +
476B TYR* 3.2 40.0 - - + +
479B ALA* 4.8 2.9 - - - +
491B PHE* 2.9 21.1 + - + +
492B GLU* 3.4 15.6 - - - +
493B ASN 3.1 0.2 - - - -
494B ASN* 1.3 75.2 - - - +
496B ALA* 1.3 55.0 + - - +
498B LEU* 3.1 2.6 + - - +
499B GLU* 2.7 43.7 + - + +
539B LEU* 3.7 9.6 - - + +
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Residues in contact with ALA 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B GLY* 6.0 2.2 - - - -
390B ASN* 3.3 28.0 - - - +
391B ARG* 3.8 15.9 - - - +
492B GLU 2.9 12.4 + - - +
493B ASN 3.9 1.8 - - - +
495B GLN* 1.3 76.9 - - - +
497B ASP* 1.3 63.5 + - - +
499B GLU* 4.5 4.7 - - - +
500B ASN* 3.3 25.3 + - - +
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Residues in contact with ASP 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B ASN* 2.8 28.8 + - - +
494B ASN* 4.0 10.9 - - - +
496B ALA* 1.3 81.4 - - - +
498B LEU* 1.3 58.2 + - - +
500B ASN* 4.5 2.1 - - - +
501B ALA* 3.5 14.7 + - - +
531B TYR* 4.2 6.9 + - - +
535B ARG* 3.4 36.6 + - - +
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Residues in contact with LEU 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B CYS* 3.9 14.8 - - + +
471B THR* 4.6 7.6 - - - +
472B LEU* 3.7 22.7 - - + -
475B THR* 5.2 1.6 - - - +
494B ASN 3.2 16.0 + - - +
495B GLN 3.1 4.0 + - - +
497B ASP* 1.3 75.9 - - - +
499B GLU* 1.3 60.8 + - - +
500B ASN 3.2 1.6 - - - -
501B ALA* 3.1 1.3 + - + +
502B THR* 2.9 33.3 + - - +
532B CYS* 3.2 29.4 - - - +
535B ARG* 3.7 9.8 - - + +
536B ARG* 3.5 34.8 - - + +
539B LEU* 4.0 15.0 - - + -
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Residues in contact with GLU 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ASN* 5.5 1.6 + - - -
374B VAL* 5.1 6.8 - - - +
389B CYS* 4.9 12.5 - - - -
390B ASN* 3.6 15.9 - - - +
420B ARG* 5.0 4.5 + - - -
424B HIS* 3.6 20.4 + - + -
472B LEU* 3.8 25.7 - - + +
476B TYR* 2.5 30.7 + - - -
495B GLN* 2.7 23.6 + - - +
496B ALA* 4.5 3.8 - - - +
498B LEU* 1.3 72.0 - - - +
500B ASN* 1.3 60.7 + - - +
502B THR* 3.6 1.6 + - - -
503B GLU* 3.2 30.1 + - - +
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Residues in contact with ASN 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B TRP* 3.9 23.7 + - - -
382B HIS* 4.3 22.3 + - + +
383B GLY* 4.6 10.3 - - - +
496B ALA 3.3 17.1 + - - +
497B ASP* 4.5 2.5 - - - +
498B LEU 3.2 0.4 - - - -
499B GLU* 1.3 77.4 - - - +
501B ALA* 1.3 65.5 + - - +
503B GLU* 3.2 5.3 + - - +
504B VAL* 3.1 30.8 + - - +
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Residues in contact with ALA 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B ASP 3.5 18.5 + - - +
498B LEU* 3.1 8.3 + - - +
500B ASN* 1.3 79.5 - - - +
502B THR* 1.3 60.9 + - - +
504B VAL* 3.6 7.0 + - - +
505B LEU* 3.2 18.0 + - - +
528B LYS 5.5 0.2 - - - +
531B TYR* 3.6 31.8 - - + -
532B CYS* 3.4 26.0 - - - +
535B ARG* 4.4 2.0 - - + -
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Residues in contact with THR 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B LEU* 3.8 20.4 - - + +
468B CYS* 3.4 27.8 + - + +
469B ARG* 3.6 37.5 - - + +
472B LEU* 4.1 8.3 - - + +
498B LEU* 2.9 18.3 + - - +
499B GLU 3.9 4.5 - - - -
500B ASN 3.2 0.2 - - - -
501B ALA* 1.3 75.3 - - - +
503B GLU* 1.3 55.6 + - - +
505B LEU* 3.2 2.7 + - - +
506B SER* 2.7 33.6 + - - -
532B CYS* 3.5 8.6 - - - -
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Residues in contact with GLU 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B CYS* 3.5 14.1 - - - -
358B ASN* 2.5 44.9 + - + +
359B HIS* 4.3 2.0 + - - +
379B TRP* 3.4 36.3 - - + -
424B HIS* 5.5 0.7 + - - -
469B ARG* 2.4 36.4 + - - -
472B LEU* 5.2 1.0 - - - +
499B GLU* 3.2 25.6 + - - +
500B ASN* 3.2 9.4 + - - +
502B THR* 1.3 78.9 - - - +
504B VAL* 1.3 58.8 + - - +
506B SER* 4.5 2.9 - - - -
507B GLY* 2.9 22.3 + - - -
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Residues in contact with VAL 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B TRP* 5.7 5.6 - - + +
500B ASN* 3.1 29.4 + - - +
501B ALA* 3.9 7.2 - - - +
503B GLU* 1.3 76.1 - - + +
505B LEU* 1.3 65.8 + - - +
507B GLY* 3.1 1.7 + - - -
508B TYR* 3.0 23.9 + - - +
528B LYS* 3.7 28.9 - - + +
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Residues in contact with LEU 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B ALA 4.1 2.5 - - - +
464B VAL 4.8 1.3 - - - -
465B LEU* 3.9 34.1 - - + +
501B ALA 3.2 14.3 + - - +
502B THR 3.2 4.1 + - - +
504B VAL* 1.3 79.8 - - - +
506B SER* 1.3 60.5 + - - +
508B TYR* 3.6 1.2 + - - +
509B LEU* 3.3 40.0 + - + +
525B VAL* 4.6 12.3 - - + -
528B LYS* 3.6 33.8 - - + +
529B TYR* 3.7 34.1 - - + +
532B CYS* 3.9 17.0 - - + -
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Residues in contact with SER 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B CYS* 3.5 10.7 + - - -
431B GLU* 2.5 32.2 + - - +
434B LEU* 5.3 1.1 - - - +
465B LEU* 3.6 15.9 - - - +
469B ARG* 4.8 0.7 - - - -
502B THR* 2.7 22.8 + - - -
503B GLU* 4.2 4.3 - - - -
505B LEU* 1.3 72.4 - - - +
507B GLY* 1.3 63.9 + - - +
508B TYR 3.5 0.3 + - - -
509B LEU* 3.5 7.0 + - - +
510B GLU* 3.1 35.5 + - - +
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Residues in contact with GLY 507 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B CYS* 3.6 16.5 - - - -
503B GLU 2.9 19.2 + - - -
504B VAL* 3.1 2.4 + - - -
506B SER* 1.3 75.9 - - - +
508B TYR* 1.3 62.6 + - - +
510B GLU* 3.4 2.8 + - - +
511B ARG* 3.4 32.6 + - - +
512B ASP* 3.9 10.0 - - - +
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Residues in contact with TYR 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B VAL 3.0 14.3 + - - +
505B LEU* 4.0 5.2 - - + +
506B SER 3.3 0.2 - - - -
507B GLY* 1.3 72.4 - - - +
509B LEU* 1.3 63.8 + - + +
510B GLU 3.0 9.5 + - - -
512B ASP* 3.4 35.2 + - + -
513B ILE* 3.1 44.8 + - + +
516B ASP* 2.8 30.2 + - - +
521B ILE* 4.2 6.5 - - + +
524B LYS* 3.4 35.8 - - + +
525B VAL* 3.5 32.3 - - + -
528B LYS* 3.8 26.5 - - + -
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Residues in contact with LEU 509 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B LEU* 3.4 34.2 - - + +
437B GLN* 5.2 2.4 - - - +
438B VAL* 5.8 3.4 - - + -
458B LEU* 5.8 7.4 - - + +
461B ALA* 4.9 4.3 - - + -
462B VAL* 4.3 32.5 - - + +
465B LEU* 4.8 3.6 - - + -
505B LEU* 3.3 30.8 + - + +
506B SER 3.5 1.5 + - - +
507B GLY 3.4 0.6 - - - -
508B TYR* 1.3 93.5 - - + +
510B GLU* 1.3 64.6 + - - +
513B ILE* 4.4 20.3 - - + +
525B VAL* 4.3 19.3 - - + -
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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