Contacts of the helix formed by residues 792 - 824 (chain B) 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 VAL 792 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A LEU* 6.5 0.7 - - + -
525A ILE* 5.5 12.3 - - + -
611A ILE* 4.8 17.0 - - + -
612A ILE* 5.2 16.2 - - + -
615A SER* 5.1 12.3 - - - +
516B SER* 5.7 3.8 - - - -
624B LEU* 5.0 12.3 - - + -
788B SER* 5.4 10.1 - - - -
789B LEU 5.2 6.7 - - - +
790B SER* 5.1 1.6 - - - -
791B ASN* 1.3 78.0 - - + +
793B ALA* 1.3 67.0 + - - +
794B GLY 3.2 1.3 - - - -
795B VAL* 2.9 33.0 + - + +
796B PHE* 3.7 13.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 793 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790B SER* 3.1 25.5 + - - +
791B ASN 3.0 2.2 + - - -
792B VAL* 1.3 81.1 - - - +
794B GLY* 1.3 64.4 + - - +
796B PHE* 2.9 30.3 + - + +
797B TYR* 3.3 11.1 + - + +
154F ILE* 4.5 8.3 - - + +
158F SER* 4.3 23.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 794 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B GLY* 4.9 1.9 - - - -
514B VAL* 3.6 32.1 - - - +
790B SER 4.7 0.2 + - - -
791B ASN 3.7 4.8 + - - -
792B VAL 3.2 1.4 - - - -
793B ALA* 1.3 77.4 - - - +
795B VAL* 1.3 64.8 + - - +
796B PHE 2.9 1.6 + - - -
797B TYR* 3.0 33.8 + - - -
798B ILE* 3.4 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 795 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A PHE 5.1 1.8 - - - +
608A PHE* 4.7 21.3 - - + -
611A ILE* 4.8 11.7 - - + -
514B VAL* 4.8 6.0 - - - +
516B SER* 5.5 1.3 - - - -
517B PHE* 3.7 52.7 - - + +
791B ASN 5.6 0.2 - - - +
792B VAL* 2.9 28.7 + - + +
794B GLY* 1.3 73.1 - - - +
796B PHE* 1.3 67.1 + - + +
799B LEU* 3.1 41.8 + - + +
800B VAL* 4.6 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 796 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A ILE* 5.4 4.7 - - + -
528A CYS* 3.9 33.4 - - + -
529A ILE* 4.8 10.1 - - + -
532A ALA* 5.1 6.3 - - + -
608A PHE* 3.2 41.3 - + - -
612A ILE* 5.9 2.0 - - + -
792B VAL* 3.7 9.8 + - + -
793B ALA* 2.9 17.8 + - + +
794B GLY 2.9 0.4 + - - -
795B VAL* 1.3 80.3 - - + +
797B TYR* 1.3 55.1 + - - +
798B ILE 2.6 15.4 + - - -
800B VAL* 2.7 51.2 + - + +
154F ILE* 3.9 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 797 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B VAL* 4.6 11.4 - - + +
793B ALA* 3.3 16.5 + - + +
794B GLY* 3.0 30.4 + - - -
796B PHE* 1.3 72.4 - - - +
798B ILE* 1.3 66.7 + - + +
800B VAL* 5.2 0.9 - - - -
801B GLY* 4.8 5.9 + - - +
97F PHE* 5.4 13.9 - + - -
98F LEU* 3.4 38.9 - - + +
107F PHE* 5.7 9.0 - + + -
151F ILE* 4.7 21.8 - - + +
154F ILE* 4.5 16.8 - - + -
155F VAL* 5.7 6.7 - - + +
158F SER* 5.8 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 798 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B VAL* 3.6 35.0 - - + -
794B GLY 3.4 5.5 + - - +
796B PHE 2.6 5.3 + - - -
797B TYR* 1.3 89.8 - - + +
799B LEU* 1.3 79.4 + - + +
800B VAL 3.4 0.2 - - - -
801B GLY* 2.9 13.0 + - - -
802B GLY* 3.0 11.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 799 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A VAL* 4.0 19.5 - - + +
607A PHE* 4.7 15.7 - - + +
608A PHE* 6.2 0.2 - - - -
514B VAL* 5.2 9.6 - - + -
517B PHE* 3.9 41.1 - - + -
795B VAL* 3.1 32.5 - - + +
796B PHE 2.9 1.2 + - - -
798B ILE* 1.3 93.6 - - + +
800B VAL* 1.3 62.0 + - + +
802B GLY* 2.9 13.3 + - - +
803B LEU* 3.2 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 800 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A ALA* 4.9 15.3 - - + -
604A VAL* 5.5 0.2 - - - -
608A PHE* 5.8 3.8 - - + -
795B VAL 4.6 0.7 - - - +
796B PHE* 2.7 53.8 + - + +
797B TYR* 5.2 0.2 - - - -
799B LEU* 1.3 72.4 - - + +
801B GLY* 1.3 56.1 + - - +
803B LEU* 2.8 50.7 - - + +
804B GLY 3.8 0.9 + - - -
147F LEU* 5.7 8.8 - - + +
150F ILE* 6.2 2.7 - - + -
151F ILE* 4.3 21.5 - - + +
154F ILE* 5.1 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 801 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796B PHE 3.8 1.2 + - - -
797B TYR* 4.8 4.3 - - - +
798B ILE* 2.9 12.2 + - - +
800B VAL* 1.3 78.6 - - - +
802B GLY* 1.3 62.8 + - - +
803B LEU 2.9 1.4 + - - -
804B GLY* 2.9 14.0 + - - -
805B LEU* 3.3 8.1 + - - +
151F ILE* 4.3 18.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 802 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A VAL* 5.6 5.2 - - - -
798B ILE 3.0 9.1 + - - -
799B LEU* 2.9 11.0 + - - -
801B GLY* 1.3 74.3 - - - +
803B LEU* 1.3 62.3 + - - +
805B LEU* 2.9 16.8 + - - +
806B ALA* 2.8 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 803 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A ALA* 5.7 0.9 - - + -
536A VAL* 3.6 30.7 - - + -
539A VAL* 5.2 7.6 - - + +
601A VAL* 4.0 30.2 - - + +
604A VAL* 3.6 32.9 - - + +
605A TRP* 5.0 3.8 - - + +
799B LEU 3.2 4.2 + - - +
800B VAL* 2.8 50.5 + - + +
801B GLY 2.9 0.6 + - - -
802B GLY* 1.3 77.5 - - - +
804B GLY* 1.3 63.5 + - - +
806B ALA* 3.0 19.4 + - - +
807B MET* 3.4 4.3 + - - +
147F LEU* 5.8 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 804 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A VAL* 5.5 2.2 - - - -
800B VAL 3.8 0.8 + - - -
801B GLY 2.9 10.4 + - - -
803B LEU* 1.3 75.9 - - - +
805B LEU* 1.3 62.3 + - - +
807B MET* 2.9 19.2 + - - +
808B LEU* 2.9 15.1 + - - +
144F SER* 6.4 0.7 - - - -
147F LEU* 4.4 22.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 805 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801B GLY 3.3 5.6 + - - +
802B GLY* 2.9 20.3 + - - +
804B GLY* 1.3 74.1 - - - +
806B ALA* 1.3 66.3 + - - +
808B LEU* 3.0 26.5 + - + +
809B VAL* 3.7 27.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 806 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A SER* 4.5 4.6 - - - -
600A ILE* 3.7 37.3 - - + +
601A VAL* 3.8 14.6 - - + +
604A VAL* 5.9 2.5 - - + -
802B GLY 2.8 14.8 + - - +
803B LEU* 3.0 12.1 + - - +
805B LEU* 1.3 72.2 - - - +
807B MET* 1.3 60.6 + - - +
810B ALA* 3.1 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 807 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A VAL* 4.2 24.5 - - + -
542A LEU* 5.8 3.4 - - + -
543A VAL* 5.3 8.7 - - + -
597A SER* 5.4 3.4 - - - -
601A VAL* 5.0 2.1 - - + +
803B LEU 3.4 2.3 + - - +
804B GLY* 2.9 10.6 + - - +
806B ALA* 1.3 80.1 - - - +
808B LEU* 1.3 54.9 + - - +
810B ALA* 2.9 7.7 + - - +
811B LEU* 2.6 51.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 808 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804B GLY 2.9 14.6 + - - +
805B LEU* 3.0 20.8 + - + +
807B MET* 1.3 74.6 - - - +
809B VAL* 1.3 69.2 + - + +
811B LEU* 2.9 27.6 + - + +
812B ILE* 3.1 23.2 + - + +
140F ILE* 5.5 3.8 - - + -
141F PHE* 5.1 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 809 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805B LEU* 3.7 22.2 + - + +
808B LEU* 1.3 84.8 - - + +
810B ALA* 1.3 53.8 + - - +
812B ILE* 3.0 14.4 + - + +
813B GLU* 2.6 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 810 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A LEU* 5.1 9.2 - - + -
597A SER* 4.1 15.0 - - - -
806B ALA 3.1 18.2 + - - +
807B MET* 3.0 12.7 - - - +
809B VAL* 1.3 78.2 - - - +
811B LEU* 1.3 47.3 + - - +
813B GLU* 2.9 14.3 - - - +
814B PHE* 2.5 54.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 811 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A LEU* 4.4 25.1 - - + +
543A VAL* 6.2 2.7 - - + -
546A PHE* 4.4 19.6 - - + -
807B MET* 2.6 35.8 + - + +
808B LEU* 2.9 15.5 + - + +
810B ALA* 1.3 72.2 - - - +
812B ILE* 1.3 63.0 + - + +
814B PHE* 2.9 25.3 + - + +
815B CYS* 2.9 21.2 + - - +
140F ILE* 3.7 46.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 812 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808B LEU* 3.1 19.5 + - + +
809B VAL* 3.0 14.4 + - + +
811B LEU* 1.3 73.0 - - + +
813B GLU* 1.3 54.9 + - - +
815B CYS* 2.9 22.4 + - - -
816B TYR* 2.6 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 813 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A LEU* 5.5 16.1 - - + +
809B VAL* 2.6 20.9 + - + +
810B ALA* 2.9 19.4 - - - +
812B ILE* 1.3 70.7 - - - +
814B PHE* 1.3 74.5 + - - +
816B TYR* 2.7 37.0 - - + +
817B LYS* 3.4 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 814 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A VAL* 4.7 18.2 - - + -
546A PHE* 3.4 22.4 - + + -
547A SER* 3.5 32.1 - - - -
595A SER* 5.5 5.8 - - - -
596A LEU* 6.3 1.6 - - + -
597A SER* 3.9 20.4 - - - -
810B ALA* 2.5 48.2 + - + -
811B LEU* 2.9 28.7 + - + +
813B GLU* 1.3 81.2 + - - +
815B CYS* 1.3 57.0 + - - +
816B TYR 2.9 6.1 + - - -
817B LYS* 2.9 18.7 + - - +
818B SER* 3.4 9.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 815 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A PHE* 4.7 10.7 - - + -
811B LEU 2.9 11.7 + - - +
812B ILE* 2.9 41.0 + - - -
814B PHE* 1.3 72.3 - - - +
816B TYR* 1.3 61.3 + - - +
818B SER* 3.1 13.5 + - - +
819B ARG* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 816 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812B ILE* 2.6 17.4 + - + +
813B GLU* 2.7 28.7 - - + +
814B PHE 2.9 0.4 + - - -
815B CYS* 1.3 72.2 - - - +
817B LYS* 1.3 71.1 + - + +
819B ARG* 2.9 23.8 + - + +
820B ALA* 3.2 11.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 817 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813B GLU* 3.4 5.3 + - - +
814B PHE* 2.9 12.7 + - - +
816B TYR* 1.3 83.3 - - + +
818B SER* 1.3 52.8 + - - +
820B ALA* 2.9 10.1 + - - +
821B GLU* 2.7 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 818 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814B PHE 3.4 5.3 + - - -
815B CYS* 3.1 22.9 + - - +
817B LYS* 1.3 77.4 - - - +
819B ARG* 1.3 65.4 + - - +
821B GLU* 2.9 21.1 + - - +
822B ALA* 3.0 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 819 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815B CYS 3.0 10.1 + - - +
816B TYR* 2.9 18.4 + - + +
818B SER* 1.3 80.7 + - - +
820B ALA* 1.3 61.9 + - - +
822B ALA* 2.9 17.7 + - - +
823B LYS* 3.3 11.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 820 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816B TYR* 3.2 10.8 + - + +
817B LYS* 2.9 10.4 + - - +
819B ARG* 1.3 78.5 - - - +
821B GLU* 1.3 56.5 + - - +
823B LYS* 2.9 8.3 + - - +
824B ARG* 2.9 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 821 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817B LYS 2.7 17.1 + - - +
818B SER* 2.9 18.4 + - - +
820B ALA* 1.3 72.1 - - - +
822B ALA* 1.3 57.7 + - - +
824B ARG* 4.2 6.4 + - - +
825B MET* 4.5 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 822 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818B SER 3.0 7.9 + - - +
819B ARG* 2.9 11.6 + - - +
821B GLU* 1.3 78.2 - - - +
823B LYS* 1.3 57.8 + - + +
824B ARG 3.5 0.4 + - - -
825B MET* 4.5 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 823 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819B ARG 3.3 11.7 + - - +
820B ALA* 2.9 8.5 + - - +
822B ALA* 1.3 76.5 - - - +
824B ARG* 1.3 60.3 + - - +
825B MET 3.4 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 824 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820B ALA* 2.9 18.2 + - + +
821B GLU* 4.2 4.0 + - - +
822B ALA 3.5 0.6 - - - -
823B LYS* 1.3 78.1 - - - +
825B MET* 1.3 59.2 + - - +
----------------------------------------------------------
Back to top of page
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