Contacts of the helix formed by residues 522 - 546 (chain C) in PDB entry 5VOT
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 522 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C LEU 4.7 6.4 + - - -
519C ASP 5.3 1.1 - - - -
521C LEU* 1.3 80.9 - - - +
523C TYR* 1.3 60.5 + - - +
524C GLU* 3.1 31.2 - - - +
525C ILE* 3.5 18.3 - - + +
526C TRP* 2.8 27.6 + - - -
788D SER 4.5 0.4 - - - +
789D LEU* 4.9 5.2 - - + -
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Residues in contact with TYR 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C LEU* 6.1 5.4 - - + -
522C ALA* 1.3 70.4 - - - +
524C GLU* 1.3 91.4 + - + +
525C ILE 3.1 1.6 - - - -
526C TRP* 2.8 28.2 + - - +
527C MET* 2.9 41.2 + - + +
174H TYR* 5.2 6.9 + + - -
175H SER* 5.4 2.9 - - - -
176H TYR* 3.3 28.7 + + - -
181H TYR* 4.1 11.8 + - - -
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Residues in contact with GLU 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522C ALA* 3.1 22.7 - - + +
523C TYR* 1.3 96.3 + - + +
525C ILE* 1.3 66.6 + - + +
527C MET* 3.1 24.5 + - + +
528C CYS* 2.9 28.4 + - - -
789D LEU* 5.3 6.0 - - - +
157H ILE* 4.5 19.1 - - + -
174H TYR* 5.3 7.7 + - - -
176H TYR* 3.7 29.7 + - + +
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Residues in contact with ILE 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521C LEU* 3.7 22.9 - - + -
522C ALA* 3.5 24.7 + - + +
523C TYR 3.1 0.4 - - - -
524C GLU* 1.3 80.6 - - + +
526C TRP* 1.3 62.8 + - + +
528C CYS* 3.0 11.3 + - + +
529C ILE* 2.9 43.0 + - + +
612C ILE* 4.8 6.3 - - + -
788D SER* 3.1 28.0 - - - +
789D LEU* 3.2 25.6 - - - +
792D VAL* 5.5 11.7 - - + -
796D PHE* 5.9 4.0 - - + -
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Residues in contact with TRP 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B PHE* 5.1 16.4 - + - -
610B LEU* 6.2 3.6 - - + -
517C PHE* 5.4 2.7 - + - -
518C LEU* 3.3 52.5 + - + +
520C PRO* 6.1 0.2 - - - +
521C LEU* 4.8 15.3 - - + +
522C ALA 2.8 28.1 + - - -
523C TYR* 2.8 15.3 + - - +
525C ILE* 1.3 74.3 - - + +
527C MET* 1.3 57.6 + - + +
529C ILE* 3.0 30.4 + - + +
530C VAL* 2.9 34.9 + - + +
584C PHE* 4.5 22.2 - + - -
613C ILE* 5.9 4.0 - - + -
616C TYR* 4.5 27.6 - + + -
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Residues in contact with MET 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523C TYR* 2.9 48.3 + - + +
524C GLU* 3.1 18.1 + - + +
526C TRP* 1.3 75.8 - - + +
528C CYS* 1.3 57.2 + - - +
530C VAL* 3.2 10.6 + - + +
531C PHE* 2.9 51.1 + - + -
157H ILE* 6.4 0.4 - - + -
176H TYR* 5.3 1.1 - - + -
180H PHE* 5.1 8.3 - - + -
181H TYR* 4.3 27.6 - - + +
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Residues in contact with CYS 528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524C GLU 2.9 18.7 + - - -
525C ILE* 3.0 10.3 + - - +
527C MET* 1.3 76.1 - - - +
529C ILE* 1.3 57.8 + - - +
531C PHE* 3.0 22.0 + - + +
532C ALA* 2.9 30.5 + - - +
796D PHE* 3.8 24.0 - - + -
150H ILE* 5.4 0.5 - - - +
153H ILE* 5.3 1.6 - - - -
154H ILE* 4.7 20.2 - - + -
157H ILE* 4.2 24.2 - - - -
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Residues in contact with ILE 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521C LEU* 5.2 2.0 - - + -
525C ILE* 2.9 37.2 + - + +
526C TRP* 3.0 39.2 + - + +
528C CYS* 1.3 76.9 - - - +
530C VAL* 1.3 59.4 + - + +
532C ALA* 3.9 5.1 - - - +
533C TYR* 2.9 31.5 + - + +
584C PHE* 4.1 28.5 - - + -
605C TRP* 5.0 2.5 - - + -
608C PHE* 4.5 20.2 - - + -
612C ILE* 4.2 18.8 - - + -
796D PHE* 4.8 6.7 - - + -
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Residues in contact with VAL 530 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526C TRP* 2.9 22.3 + - + +
527C MET* 3.2 11.0 + - - +
529C ILE* 1.3 77.8 - - + +
531C PHE* 1.3 69.2 + - + +
533C TYR* 3.1 11.3 + - + +
534C ILE* 2.9 38.8 + - + +
188H ILE* 6.1 3.4 - - + -
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Residues in contact with PHE 531 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527C MET* 2.9 40.1 + - + -
528C CYS* 3.0 24.7 + - - +
530C VAL* 1.3 83.5 - - + +
532C ALA* 1.3 64.3 + - - +
534C ILE* 3.2 10.7 - - + +
535C GLY* 2.9 20.8 + - - -
150H ILE* 3.6 42.8 - - + +
153H ILE* 4.7 17.3 - - + -
157H ILE* 6.0 0.7 - - + -
180H PHE* 5.8 3.6 - + - -
184H ALA* 3.5 33.0 - - + -
187H PHE* 6.5 0.4 - - + -
188H ILE* 4.2 24.7 - - + -
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Residues in contact with ALA 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528C CYS 2.9 16.6 + - - +
529C ILE* 4.2 5.2 - - - +
531C PHE* 1.3 73.2 - - - +
533C TYR* 1.3 57.2 + - - +
535C GLY* 4.5 1.6 - - - +
536C VAL* 2.9 40.4 + - + +
605C TRP* 4.5 14.8 - - + -
608C PHE* 5.5 2.2 - - + -
796D PHE* 5.1 10.5 - - + -
800D VAL* 4.9 22.7 - - + -
803D LEU* 5.7 0.2 - - + -
150H ILE* 4.8 5.4 - - + +
154H ILE* 6.4 1.8 - - + -
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Residues in contact with TYR 533 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529C ILE* 2.9 23.0 + - + +
530C VAL* 3.1 12.8 - - + +
531C PHE 3.0 0.2 - - - -
532C ALA* 1.3 77.4 - - - +
534C ILE* 1.3 77.4 + - + +
536C VAL* 3.9 1.6 - - - +
537C SER* 3.0 25.5 + - - -
577C LEU* 3.4 34.5 + - + +
580C SER* 3.1 27.2 + - - -
581C LEU* 3.2 46.0 + - + +
584C PHE* 5.0 7.2 - + + -
605C TRP* 4.3 17.5 - + + -
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Residues in contact with ILE 534 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530C VAL* 2.9 25.0 + - + +
531C PHE* 3.2 18.2 - - + +
533C TYR* 1.3 87.1 - - + +
535C GLY* 1.3 77.3 + - - +
537C SER* 3.6 5.9 - - - -
538C VAL* 2.9 33.5 + - + +
577C LEU* 5.3 5.2 - - + -
150H ILE* 4.2 9.9 - - + -
188H ILE* 5.1 18.6 - - + -
191H GLU* 3.9 29.4 - - + -
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Residues in contact with GLY 535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531C PHE 2.9 15.9 + - - -
532C ALA* 3.9 2.0 - - - -
534C ILE* 1.3 83.4 - - - +
536C VAL* 1.3 63.4 + - - +
538C VAL* 3.1 6.3 + - - +
539C VAL* 2.9 30.5 + - - +
147H LEU* 4.5 18.2 - - - -
150H ILE* 5.3 2.0 - - - -
191H GLU* 4.8 6.7 - - - -
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Residues in contact with VAL 536 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532C ALA* 2.9 27.1 + - + +
533C TYR* 3.9 2.2 - - - +
535C GLY* 1.3 71.3 - - - +
537C SER* 1.3 63.5 + - - +
539C VAL* 3.3 6.0 + - - +
540C LEU* 2.9 41.1 + - + +
580C SER* 5.1 3.8 - - - +
601C VAL* 4.2 14.1 - - + +
605C TRP* 4.0 38.8 - - + -
803D LEU* 3.5 35.2 - - + -
147H LEU* 5.4 0.4 - - - +
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Residues in contact with SER 537 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533C TYR 3.0 17.9 + - - -
534C ILE* 3.6 5.6 - - - -
536C VAL* 1.3 78.6 - - - +
538C VAL* 1.3 65.5 + - - +
540C LEU* 3.2 9.4 + - - +
541C PHE* 3.0 21.1 + - - +
573C ILE* 4.6 5.6 - - - +
576C SER* 4.6 5.0 - - - -
577C LEU* 3.3 35.5 - - - +
580C SER* 3.2 24.7 + - - -
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Residues in contact with VAL 538 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534C ILE* 2.9 26.1 + - + +
535C GLY 3.6 3.6 - - - +
537C SER* 1.3 75.4 - - - +
539C VAL* 1.3 65.8 + - - +
541C PHE* 2.8 22.2 + - + +
542C LEU* 2.9 13.2 + - + +
573C ILE* 4.5 6.3 - - + -
143H VAL* 3.9 30.7 - - + -
191H GLU* 4.3 18.4 - - + +
192H MET* 6.2 1.8 - - - -
194H GLY 5.6 0.2 - - - -
195H VAL* 3.9 33.2 - - + +
198H VAL* 6.2 2.7 - - + -
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Residues in contact with VAL 539 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535C GLY 2.9 22.8 + - - +
536C VAL* 3.8 6.1 - - - +
538C VAL* 1.3 75.6 - - - +
540C LEU* 1.3 63.9 + - + +
542C LEU* 2.9 17.0 + - + +
543C VAL* 2.9 23.4 + - + +
601C VAL* 5.2 11.7 - - + -
803D LEU* 5.2 10.3 - - + +
804D GLY* 5.5 2.2 - - - +
807D MET* 4.2 24.7 - - + -
143H VAL* 4.4 15.0 - - + -
147H LEU* 4.0 28.3 - - + -
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Residues in contact with LEU 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536C VAL* 2.9 33.5 + - + +
537C SER* 3.4 10.3 - - - +
539C VAL* 1.3 74.5 - - - +
541C PHE* 1.3 64.0 + - - +
543C VAL* 2.9 18.9 + - + +
544C SER* 2.9 11.6 + - - -
570C GLU* 5.6 2.4 - - + +
576C SER* 5.1 12.6 - - - +
579C PHE* 4.6 24.9 - - + -
580C SER* 5.6 3.6 - - - -
593C PRO* 5.8 4.9 - - + -
598C GLY* 4.0 23.1 - - - +
601C VAL* 3.6 34.5 - - + -
602C GLY* 4.3 5.2 - - - +
605C TRP* 6.1 1.8 - - + -
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Residues in contact with PHE 541 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537C SER 3.0 7.2 + - - +
538C VAL* 2.8 17.2 + - + +
540C LEU* 1.3 72.3 - - - +
542C LEU* 1.3 58.2 + - - +
544C SER* 2.8 18.7 + - - +
545C ARG* 2.9 34.5 + - + +
570C GLU 3.8 8.1 - - - -
571C PHE 3.4 18.6 - - - -
572C GLY* 3.3 9.0 - - - -
573C ILE* 3.1 63.7 - - + -
576C SER* 4.3 7.7 + - - +
195H VAL* 5.1 9.9 - - + -
198H VAL* 4.3 22.7 - - + -
199H HIS* 5.0 21.3 - + + -
202H ILE* 5.9 0.7 - - + -
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Residues in contact with LEU 542 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C VAL* 2.9 11.6 + - + +
539C VAL* 2.9 17.2 + - + +
541C PHE* 1.3 78.8 - - - +
543C VAL* 1.3 63.4 + - + +
544C SER 3.3 0.5 + - - -
545C ARG* 4.6 2.2 - - + +
546C PHE* 3.3 41.4 + - + +
807D MET* 5.8 2.9 - - + -
811D LEU* 4.4 22.2 - - + +
136H LEU* 5.5 3.4 - - + -
140H ILE* 4.1 32.3 - - + -
143H VAL* 5.9 7.4 - - + -
198H VAL* 3.8 33.0 - - + -
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Residues in contact with VAL 543 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539C VAL* 2.9 23.5 + - + +
540C LEU* 2.9 21.6 + - + +
542C LEU* 1.3 75.7 - - + +
544C SER* 1.3 62.0 + - - +
546C PHE* 4.6 4.9 - - - +
547C SER* 5.0 1.2 + - - -
595C SER* 3.2 21.1 + - - +
597C SER* 3.0 35.7 - - - +
598C GLY* 3.6 11.9 - - - +
601C VAL* 5.0 5.2 - - + -
807D MET* 5.3 8.7 - - + -
811D LEU* 6.2 3.6 - - + -
814D PHE* 4.7 17.0 - - + -
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Residues in contact with SER 544 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540C LEU 2.9 8.0 + - - -
541C PHE* 2.8 13.7 + - - -
543C VAL* 1.3 81.5 - - - +
545C ARG* 1.3 64.4 + - - -
546C PHE 3.3 7.3 - - - +
568C THR* 3.8 14.1 + - - +
570C GLU* 2.8 49.3 + - - +
571C PHE* 3.3 12.7 + - - -
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Residues in contact with ARG 545 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541C PHE* 2.9 40.3 + - + +
542C LEU* 4.9 3.4 - - + +
544C SER* 1.3 71.7 - - - +
546C PHE* 1.3 67.9 + - - +
547C SER 4.7 1.4 - - - -
548C PRO* 4.8 4.5 - - - +
571C PHE* 5.2 15.8 - - + +
198H VAL* 5.5 4.5 - - + +
202H ILE* 3.4 36.3 - - + +
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Residues in contact with PHE 546 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542C LEU* 3.3 31.9 + - + +
543C VAL 4.6 2.0 - - - +
544C SER 3.3 9.4 - - - +
545C ARG* 1.3 84.3 - - - +
547C SER* 1.3 98.4 + - - +
548C PRO* 3.7 2.9 - - + -
811D LEU* 4.4 17.5 - - + -
814D PHE* 3.4 39.9 - + + -
815D CYS* 4.7 10.8 - - + -
136H LEU* 3.5 46.2 - - + -
140H ILE* 5.6 8.3 - - + -
202H ILE* 4.7 5.4 - - + -
205H HIS* 5.3 3.4 - + - -
----------------------------------------------------------
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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