Contacts of the helix formed by residues 895 - 925 (chain D) in PDB entry 6MZL
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 HIS 895 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894D LEU* 1.3 79.4 + - - +
896D PRO* 1.4 79.2 - - + +
897D ASP* 3.1 29.5 + - - -
898D VAL* 3.2 19.1 + - + +
899D VAL* 3.1 22.6 + - - +
110Q THR* 4.9 5.2 - - + +
111Q LEU 3.5 17.0 + - - +
112Q GLU* 5.2 3.8 - - + -
113Q VAL* 5.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 896 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875D GLN* 4.3 20.0 + - - +
879D GLN* 5.4 4.3 - - - +
894D LEU* 4.2 11.9 - - + +
895D HIS* 1.4 101.1 - - + +
897D ASP* 1.3 62.9 + - + +
899D VAL* 3.3 5.8 + - + +
900D SER* 3.0 24.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 897 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895D HIS* 3.1 27.0 + - - -
896D PRO* 1.3 77.4 - - + +
898D VAL* 1.3 68.2 + - - +
900D SER* 3.4 11.3 + - - -
901D TYR* 2.8 26.3 + - - +
188P ARG* 5.3 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 898 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895D HIS* 3.5 30.7 - - + +
896D PRO 3.2 1.0 - - - -
897D ASP* 1.3 89.2 - - - +
899D VAL* 1.3 56.5 + - - +
901D TYR* 3.1 11.4 + - + +
902D VAL* 2.9 26.6 + - - +
111Q LEU* 3.8 12.8 - - + -
112Q GLU* 3.3 29.8 - - - +
113Q VAL* 3.8 28.3 - - + +
116Q VAL* 4.1 8.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 899 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875D GLN* 5.8 6.1 - - + +
878D LEU* 5.6 4.4 - - + +
879D GLN* 4.8 15.0 - - + +
882D ILE* 3.7 31.4 - - + -
894D LEU* 3.7 38.4 - - + -
895D HIS 3.1 14.4 + - - +
896D PRO* 3.3 7.4 + - + +
898D VAL* 1.3 74.1 - - - +
900D SER* 1.3 65.0 + - - +
902D VAL* 3.1 9.0 + - + +
903D SER* 3.0 21.1 + - - -
111Q LEU* 4.7 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 900 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870D GLU* 5.7 0.9 + - - -
871D THR* 5.0 10.9 + - - -
872D PHE* 5.7 4.5 - - - -
875D GLN* 5.3 12.4 - - - +
896D PRO 3.0 13.8 + - - -
897D ASP* 3.5 15.3 - - - -
899D VAL* 1.3 77.9 - - - +
901D TYR* 1.3 55.9 + - - +
903D SER* 3.4 10.6 + - - -
904D HIS* 2.9 27.3 + - - +
188P ARG* 4.5 16.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 901 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897D ASP 2.8 15.7 + - - +
898D VAL* 3.1 15.7 + - + +
900D SER* 1.3 75.5 - - - +
902D VAL* 1.3 57.2 + - - +
904D HIS* 3.5 31.9 - + - -
905D ALA* 3.0 26.4 + - + +
188P ARG* 5.7 8.0 - - - +
195P LYS* 3.7 1.7 + - - -
113Q VAL* 6.1 1.1 - - + -
116Q VAL* 3.8 16.5 - - + +
117Q GLN* 5.8 0.9 - - - -
120Q LEU* 3.5 20.9 - - + -
126Q MET* 3.2 40.2 - - + +
128Q ILE* 3.3 53.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 902 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878D LEU* 5.5 4.7 - - + -
882D ILE* 4.8 15.3 - - + -
898D VAL 2.9 19.4 + - - +
899D VAL* 3.1 17.2 + - + +
901D TYR* 1.3 78.2 - - - +
903D SER* 1.3 63.7 + - - +
904D HIS 3.2 0.2 + - - -
905D ALA* 3.5 3.7 + - - +
906D THR* 3.1 27.1 + - - +
92Q ILE* 5.7 3.6 - - + -
95Q VAL* 3.7 29.5 - - + +
96Q VAL* 5.5 4.9 - - + -
99Q ALA* 5.7 4.0 - - + -
111Q LEU* 4.7 5.4 - - + -
116Q VAL* 3.7 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 903 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872D PHE* 4.0 8.1 + - - +
873D LEU* 3.2 54.0 + - - +
878D LEU* 5.0 5.5 - - - +
899D VAL 3.0 12.1 + - - -
900D SER* 3.4 14.1 - - - -
902D VAL* 1.3 76.4 - - - +
904D HIS* 1.3 57.4 + - - +
906D THR* 3.3 4.9 + - - +
907D GLN* 3.0 27.7 + - - +
192P ARG* 4.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 904 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872D PHE* 3.5 21.2 - + - -
900D SER* 2.9 17.8 + - - +
901D TYR* 3.3 38.6 - + - +
902D VAL 3.1 0.4 - - - -
903D SER* 1.3 75.8 - - - +
905D ALA* 1.3 64.3 + - - +
907D GLN 3.2 6.2 + - - -
908D GLN 3.2 2.9 + - - -
185P LYS 4.9 0.4 - - - -
188P ARG* 3.2 49.8 + - + +
189P GLU 3.9 4.0 - - - -
192P ARG* 2.7 79.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 905 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901D TYR* 3.0 16.2 + - + +
902D VAL* 4.1 4.9 - - - +
904D HIS* 1.3 77.5 - - - +
906D THR* 1.3 58.0 + - - +
908D GLN* 3.6 2.6 + - - +
909D ARG* 2.9 26.7 + - - +
192P ARG* 5.5 0.4 - - - -
91Q PHE* 5.0 3.9 - - + -
95Q VAL* 6.4 2.9 - - + -
116Q VAL* 5.9 1.6 - - + -
120Q LEU* 3.7 31.6 - - + -
124Q TRP* 4.5 10.2 + - - +
126Q MET* 4.4 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 906 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873D LEU* 3.9 15.0 - - + +
902D VAL* 3.1 18.8 + - - +
903D SER* 3.4 11.2 - - - +
904D HIS 3.2 0.2 - - - -
905D ALA* 1.3 79.0 - - - +
907D GLN* 1.3 58.5 + - - +
909D ARG* 3.0 10.0 + - - +
910D LEU* 2.9 28.6 + - + +
58Q LEU* 6.1 0.2 - - + -
88Q ALA* 4.7 11.7 - - + +
91Q PHE* 4.6 11.3 - - + -
92Q ILE* 3.6 44.8 - - + +
95Q VAL* 4.9 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 907 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872D PHE* 4.0 26.0 - - + -
873D LEU* 5.8 2.7 - - + -
903D SER 3.0 12.0 + - - +
904D HIS 3.2 0.6 + - - -
906D THR* 1.3 79.3 - - + +
908D GLN* 1.3 77.9 + - - +
910D LEU* 3.3 24.7 - - + +
911D GLN 3.0 13.9 + - - -
176P TRP* 5.7 1.2 - - - -
189P GLU* 3.5 6.4 + - - +
192P ARG* 2.9 40.2 + - - +
58Q LEU* 5.8 4.3 - - + -
62Q LYS* 4.3 18.7 + - + +
63Q LEU* 5.7 1.0 - - - +
66Q LEU* 3.6 32.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 908 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904D HIS 3.2 9.8 + - - +
905D ALA* 3.8 2.7 - - - +
907D GLN* 1.3 105.7 + - - +
909D ARG* 1.3 59.8 + - - +
910D LEU 3.2 0.2 - - - -
911D GLN* 3.0 35.4 + - + +
912D ASN* 2.9 20.6 + - - +
189P GLU* 2.8 40.5 + - - +
192P ARG* 3.0 51.1 - - + +
193P ARG* 3.7 2.4 - - + +
196P SER* 3.7 14.8 + - - +
66Q LEU* 4.5 0.2 - - - +
124Q TRP* 3.6 12.5 - - + -
126Q MET* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 909 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905D ALA 2.9 16.2 + - - +
906D THR 3.0 10.5 + - - +
908D GLN* 1.3 75.4 - - - +
910D LEU* 1.3 62.6 + - - +
912D ASN* 3.1 37.0 + - - +
913D LEU* 3.1 48.8 + - + +
916D LYS* 6.0 1.2 - - - +
88Q ALA* 6.0 4.3 - - + -
91Q PHE* 3.6 54.4 - - + -
123Q GLN* 5.5 2.2 - - - -
124Q TRP* 3.6 21.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 910 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906D THR* 2.9 14.3 + - + +
907D GLN* 3.3 28.7 - - + +
909D ARG* 1.3 75.8 - - - +
911D GLN* 1.3 57.1 + - - +
913D LEU* 3.2 18.2 + - + +
914D VAL* 2.9 29.3 + - + +
58Q LEU* 3.7 29.8 - - + -
63Q LEU* 4.1 28.7 - - + -
66Q LEU* 5.2 1.8 - - + -
84Q LEU* 4.1 14.6 - - + +
85Q LEU* 4.2 5.4 - - + -
88Q ALA* 3.8 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 911 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907D GLN 3.0 6.9 + - - -
908D GLN* 3.0 38.8 + - + +
909D ARG 3.3 0.4 - - - -
910D LEU* 1.3 73.8 - - - +
912D ASN* 1.3 60.7 + - - +
914D VAL* 3.7 11.0 - - + -
915D GLU* 2.7 42.6 + - + +
193P ARG* 2.9 49.7 + - - +
196P SER* 5.4 2.7 - - - +
197P LYS* 5.4 2.6 - - - +
66Q LEU* 3.5 23.3 - - + +
70Q VAL* 3.6 15.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 912 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908D GLN 2.9 7.2 + - - +
909D ARG* 3.1 32.4 + - - +
911D GLN* 1.3 75.2 - - - +
913D LEU* 1.3 61.7 + - - +
915D GLU* 3.3 17.9 + - - +
916D LYS* 3.1 35.5 + - - +
196P SER* 4.7 7.4 + - - +
124Q TRP* 3.3 36.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 913 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909D ARG* 3.1 41.4 + - + +
910D LEU* 3.3 28.5 - - + +
912D ASN* 1.3 76.2 - - - +
914D VAL* 1.3 54.8 + - + +
916D LYS* 3.3 12.4 + - + +
917D ILE* 2.8 33.2 + - + +
84Q LEU* 3.9 39.7 - - + +
87Q ILE* 5.9 6.5 - - + -
88Q ALA* 5.2 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 914 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910D LEU* 2.9 20.8 + - + +
911D GLN* 3.0 12.5 + - + +
913D LEU* 1.3 72.4 - - + +
915D GLU* 1.3 60.8 + - - +
917D ILE* 3.1 25.3 + - + +
918D SER* 2.8 27.0 + - - -
63Q LEU* 5.5 4.9 - - + -
66Q LEU* 3.7 28.5 - - + +
67Q VAL* 4.3 19.1 - - + +
70Q VAL* 4.0 28.2 - - + +
71Q ASP* 6.4 0.4 - - + -
84Q LEU* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 915 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911D GLN* 2.7 35.5 + - + +
912D ASN* 3.6 13.7 - - - +
914D VAL* 1.3 72.1 - - - +
916D LYS* 1.3 60.2 + - + +
918D SER* 2.5 24.9 + - - +
919D GLU* 3.0 22.3 + - - +
193P ARG* 4.3 1.4 - - - +
196P SER* 3.2 35.6 - - - +
197P LYS* 3.3 33.9 + - - +
70Q VAL* 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 916 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LEU* 4.2 17.0 - - - +
909D ARG* 6.0 1.1 - - - +
912D ASN* 3.1 26.0 + - - +
913D LEU* 3.3 15.2 + - + +
915D GLU* 1.3 78.4 - - + +
917D ILE* 1.3 55.3 + - - +
919D GLU* 3.3 28.3 + - - +
920D THR* 2.9 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 917 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913D LEU* 2.8 20.3 + - + +
914D VAL* 3.1 31.6 + - + +
916D LYS* 1.3 76.1 - - - +
918D SER* 1.3 57.9 + - - +
920D THR* 2.7 22.5 + - - +
921D ALA* 2.8 15.6 + - - +
67Q VAL* 5.2 7.9 - - + -
71Q ASP* 5.8 2.0 - - + -
74Q GLU* 3.8 26.8 - - - +
76Q LEU* 4.6 20.0 - - + -
80Q VAL* 6.1 2.0 - - + -
81Q GLU* 6.1 0.9 - - + -
84Q LEU* 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 918 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914D VAL 2.8 15.2 + - - -
915D GLU* 2.5 29.6 + - - +
917D ILE* 1.3 70.8 - - - +
919D GLU* 1.3 61.7 + - - +
921D ALA* 3.2 9.0 + - - +
922D GLN* 2.9 34.9 + - - +
70Q VAL* 4.7 16.4 - - - -
71Q ASP* 5.1 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 919 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C TYR* 4.9 3.6 + - + -
99C LEU* 3.3 29.8 - - - +
915D GLU* 3.0 21.9 + - - +
916D LYS* 3.3 35.9 + - - +
918D SER* 1.3 79.2 + - - +
920D THR* 1.3 58.7 + - + +
922D GLN* 3.2 16.7 + - - +
923D GLN* 2.9 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 920 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C LEU* 5.3 3.6 - - + -
916D LYS* 2.9 18.1 + - + +
917D ILE* 2.7 29.2 + - - +
919D GLU* 1.3 76.2 - - + +
921D ALA* 1.3 57.0 + - - +
923D GLN* 3.2 29.7 - - - +
924D LYS* 2.9 33.3 + - - +
74Q GLU* 4.9 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 921 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
917D ILE 2.8 17.0 + - - +
918D SER* 3.5 8.1 - - - +
919D GLU 3.2 0.6 - - - -
920D THR* 1.3 72.8 - - - +
922D GLN* 1.3 62.0 + - - +
924D LYS* 3.2 14.4 + - + +
925D ASN* 2.8 34.1 + - - +
71Q ASP* 3.3 26.2 - - - +
74Q GLU* 3.8 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 922 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C TYR* 4.6 3.9 + - - +
95C GLU* 4.3 26.9 - - - +
918D SER* 2.9 19.9 + - - +
919D GLU* 3.2 16.1 + - - +
921D ALA* 1.3 73.2 - - - +
923D GLN* 1.3 61.6 + - - +
925D ASN* 3.1 35.8 + - + +
926D PHE* 3.7 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 923 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C TYR* 3.3 49.9 - - + +
82C LEU* 3.3 37.6 - - + +
83C TYR* 4.7 9.7 + - + +
919D GLU* 2.9 19.4 + - - +
920D THR* 3.2 33.5 - - - +
922D GLN* 1.3 76.6 - - - +
924D LYS* 1.3 60.2 + - - +
925D ASN 3.4 0.3 + - - -
926D PHE* 3.5 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 924 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
920D THR* 2.9 23.3 + - - +
921D ALA* 3.2 12.1 + - + +
923D GLN* 1.3 74.4 - - - +
925D ASN* 1.3 58.7 + - - +
926D PHE* 3.2 7.4 + - - +
74Q GLU* 3.4 28.4 + - + +
75Q GLN* 2.8 31.6 + - + +
76Q LEU* 4.0 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 925 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921D ALA* 2.8 24.7 + - - +
922D GLN* 3.1 28.2 + - + +
924D LYS* 1.3 77.8 - - - +
926D PHE* 1.3 61.4 + - - +
927D SER* 3.1 8.0 + - - -
----------------------------------------------------------
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