Contacts of the helix formed by residues 959 - 986 (chain A) in PDB entry 5NC5
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 GLY 959 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953A MET* 4.3 0.9 - - - -
957A GLY 3.4 1.6 + - - -
958A LYS* 1.3 76.4 - - - +
960A LEU* 1.3 67.4 + - - -
961A ILE 3.5 1.3 - - - -
962A GLU* 3.2 11.1 + - - +
963A ALA* 2.9 19.6 + - - +
1038A GLU 4.3 3.1 - - - -
1039A ASP 3.0 20.6 - - - -
1040A ILE 4.2 1.3 - - - -
1041A GLU* 3.9 18.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 960 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953A MET* 3.6 23.5 - - + +
959A GLY* 1.3 70.7 - - - +
961A ILE* 1.3 69.8 + - + +
963A ALA* 3.1 2.1 + - - +
964A THR* 2.9 27.2 + - - +
1026A PHE* 3.9 14.4 - - + -
1027A VAL* 3.7 25.4 - - + +
1030A ARG* 3.5 30.3 - - + -
1031A ARG* 3.7 40.6 - - + +
1038A GLU* 4.1 18.0 + - - +
1039A ASP* 3.1 15.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 961 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A GLY* 6.0 1.6 - - - +
535A LEU* 4.2 26.9 - - + +
959A GLY 3.5 0.6 - - - -
960A LEU* 1.3 86.7 - - + +
962A GLU* 1.3 66.4 + - - +
964A THR* 3.1 8.1 + - - -
965A LEU* 2.9 42.7 + - + +
1027A VAL* 4.5 5.4 - - + -
1031A ARG* 3.3 39.3 - - - +
1039A ASP* 5.0 3.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 962 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958A LYS* 3.3 42.6 + - + +
959A GLY* 3.2 13.0 + - - +
961A ILE* 1.3 81.3 - - - +
963A ALA* 1.3 57.5 + - - +
965A LEU* 3.3 7.8 + - + +
966A ASP* 2.9 44.3 + - - +
1041A GLU* 5.2 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 963 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
949A ALA* 3.6 16.3 - - + +
952A LEU* 3.7 21.0 - - + +
953A MET* 3.6 25.6 - - + -
958A LYS* 3.9 7.5 - - + +
959A GLY 2.9 15.4 + - - +
960A LEU 3.6 3.4 - - - +
962A GLU* 1.3 77.5 - - - +
964A THR* 1.3 56.7 + - - +
966A ASP* 4.5 0.4 - - - -
967A ALA* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 964 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A VAL* 5.5 0.4 - - + -
535A LEU* 4.2 10.8 - - + -
945A ILE* 6.0 3.6 - - + -
949A ALA* 4.1 8.3 - - + +
960A LEU 2.9 14.6 + - - -
961A ILE 3.6 6.3 - - - -
963A ALA* 1.3 77.1 - - - +
965A LEU* 1.3 58.0 + - - +
967A ALA* 3.7 1.7 - - + +
968A VAL* 3.0 29.4 + - + +
1023A PRO* 3.6 43.5 - - + +
1026A PHE* 3.5 24.5 - - + -
1027A VAL* 3.6 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 965 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A THR* 4.0 19.9 - - + +
531A VAL* 3.9 16.6 - - + -
532A GLY* 3.7 34.5 - - - +
535A LEU* 4.4 4.0 - - + -
961A ILE* 2.9 37.4 + - + +
962A GLU* 3.8 7.4 - - + +
964A THR* 1.3 73.8 - - - +
966A ASP* 1.3 66.0 + - - +
968A VAL* 3.6 7.0 + - + +
969A ARG* 3.2 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 966 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952A LEU* 3.6 17.7 - - + +
958A LYS* 3.7 18.0 + - - +
962A GLU* 2.9 40.3 + - - +
965A LEU* 1.3 75.4 - - - +
967A ALA* 1.3 64.0 + - - +
969A ARG* 3.2 20.7 + - - +
970A MET* 2.9 33.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 967 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
945A ILE* 3.5 15.9 - - + +
948A PHE* 3.8 11.2 - - + -
949A ALA* 3.3 32.1 - - + +
952A LEU* 4.0 1.1 - - + +
963A ALA 2.9 18.2 + - - +
964A THR 3.7 2.9 - - - +
966A ASP* 1.3 76.7 - - - +
968A VAL* 1.3 64.7 + - - +
970A MET* 3.1 8.1 + - - +
971A ARG* 3.1 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 968 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A TYR* 2.9 43.1 + - + +
528A THR* 4.7 4.7 - - + -
531A VAL* 4.6 13.0 - - + -
945A ILE* 4.4 22.6 - - + +
964A THR 3.0 15.9 + - - +
965A LEU* 3.6 14.4 - - + +
967A ALA* 1.3 77.7 - - - +
969A ARG* 1.3 60.5 - - + +
971A ARG* 3.4 6.0 + - - +
972A LEU* 3.0 27.0 + - - +
975A ILE* 5.9 0.2 - - - +
1019A ILE 3.9 1.3 - - - +
1023A PRO* 3.7 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 969 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A GLU* 5.2 6.3 + - - -
505A HIS* 5.9 3.6 + - - -
521A GLU* 5.5 4.4 + - - -
524A THR* 3.5 27.8 - - + +
525A HIS* 5.9 2.5 - - - +
527A TYR* 4.9 0.4 - - - -
528A THR* 3.6 23.1 - - + -
965A LEU 3.2 14.5 + - - +
966A ASP* 3.8 19.0 + - - +
967A ALA 3.1 0.8 - - - -
968A VAL* 1.3 79.3 - - - +
970A MET* 1.3 77.6 + - - +
971A ARG 3.1 2.1 + - - -
972A LEU* 3.5 15.0 + - - +
973A ARG* 4.7 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 970 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A GLU* 3.9 8.1 - - - +
418A ARG* 3.0 61.4 - - - +
422A GLU* 4.8 5.2 - - - +
948A PHE* 3.7 27.6 - - + -
952A LEU* 4.6 16.8 - - + -
966A ASP* 2.9 30.8 + - + +
967A ALA* 3.1 4.9 + - - +
969A ARG* 1.3 89.9 - - - +
971A ARG* 1.3 64.9 + - - +
973A ARG* 4.6 1.4 + - - +
974A PRO* 3.5 15.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 971 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A VAL* 3.8 31.7 + - - +
414A GLU* 3.6 12.1 + - - -
415A ASN* 4.0 6.3 - - - +
418A ARG* 4.9 1.4 - - - +
438A ILE* 6.1 0.6 - - - +
941A ASN 5.2 0.2 - - - +
944A LEU* 3.8 29.0 + - + +
945A ILE* 3.7 33.2 - - + +
948A PHE* 3.7 44.5 - - + -
967A ALA 3.1 15.9 + - - +
968A VAL 3.7 4.0 - - - +
969A ARG 3.1 0.2 - - - -
970A MET* 1.3 81.4 + - - +
972A LEU* 1.3 65.0 + - - +
973A ARG 3.3 2.5 - - - -
974A PRO* 3.2 41.7 - - - +
975A ILE* 3.2 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 972 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A PHE* 5.3 2.9 - - + -
523A SER 5.5 0.4 - - - -
524A THR* 3.7 32.5 - - + +
527A TYR* 3.1 44.4 - - + -
968A VAL 3.0 13.1 + - - +
969A ARG 3.5 10.8 + - - +
971A ARG* 1.3 78.3 - - - +
973A ARG* 1.3 65.1 + - - +
975A ILE* 3.4 6.2 + - - +
976A LEU* 3.1 49.7 + - + +
1019A ILE* 4.9 15.3 - - + -
26G ILE* 5.0 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 973 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A PHE* 4.1 25.2 + - + -
359A LEU* 3.8 26.7 - - - +
414A GLU* 3.5 31.9 + - + +
417A GLU* 3.9 22.8 + - - +
418A ARG* 5.0 3.0 - - - +
520A PHE* 3.8 35.6 - - + -
969A ARG 4.7 2.1 + - - +
970A MET 4.6 2.1 + - - +
972A LEU* 1.3 78.5 - - - +
974A PRO* 1.3 73.0 - - + +
976A LEU* 3.1 4.1 + - - +
977A MET* 2.9 41.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 974 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ASP* 4.6 1.3 - - - +
410A ILE* 4.0 18.0 - - + +
411A VAL* 4.8 7.2 - - + -
414A GLU* 3.4 30.5 - - + +
941A ASN* 5.4 1.6 - - - +
970A MET 3.5 9.6 - - - +
971A ARG* 3.2 42.0 - - - +
973A ARG* 1.3 97.0 - - + +
975A ILE* 1.3 61.0 + - + +
977A MET* 3.6 4.9 + - + +
978A THR* 3.2 28.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 975 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941A ASN* 3.5 42.8 + - + +
945A ILE* 3.8 28.7 - - + -
968A VAL 5.9 0.2 - - - +
971A ARG* 3.2 27.3 + - + +
972A LEU* 3.5 5.6 - - - +
973A ARG 3.2 0.2 - - - -
974A PRO* 1.3 82.5 - - + +
976A LEU* 1.3 65.4 + - + +
978A THR* 3.9 2.4 - - - -
979A SER* 3.1 22.9 + - - -
1015A THR* 3.9 23.1 - - + -
1019A ILE* 4.1 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 976 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A PHE* 4.7 9.6 - - + -
520A PHE* 3.8 23.1 - - + -
972A LEU* 3.1 35.3 + - + +
973A ARG* 3.1 7.2 + - - +
975A ILE* 1.3 75.2 - - + +
977A MET* 1.3 67.6 + - - +
979A SER* 3.3 3.2 + - - +
980A LEU* 2.9 31.3 + - + +
1015A THR* 3.9 23.1 - - + -
1019A ILE* 5.3 1.8 - - + -
19G MET* 6.1 1.3 - - - -
22G ILE* 4.0 25.4 - - + -
23G LEU* 4.4 7.0 - - + -
26G ILE* 4.3 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 977 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A VAL* 4.0 3.6 - - - +
355A MET* 3.7 28.1 - - + +
358A PHE* 3.6 53.4 - - + -
359A LEU* 4.2 20.0 - - + -
410A ILE* 3.9 26.7 - - + -
413A VAL* 5.9 2.7 - - + -
414A GLU* 4.5 11.2 - - + -
973A ARG* 2.9 38.3 + - - +
974A PRO 3.8 4.3 - - - +
976A LEU* 1.3 76.7 - - - +
978A THR* 1.3 56.6 + - - +
980A LEU* 4.0 1.2 - - - +
981A ALA* 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 978 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A GLY 4.1 9.4 - - - +
406A VAL* 4.4 5.2 - - + -
407A ASP* 2.7 50.5 + - + +
410A ILE* 3.9 13.1 - - - +
937A LEU* 4.4 15.5 - - + -
941A ASN* 5.5 5.8 - - - +
974A PRO 3.2 14.7 + - - -
975A ILE* 3.9 4.5 - - - -
977A MET* 1.3 75.1 - - - +
979A SER* 1.3 64.6 + - - +
981A ALA* 3.4 3.4 + - - +
982A PHE* 2.9 24.5 + - + +
1011A MET* 5.6 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 979 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941A ASN* 5.5 2.3 + - - -
975A ILE* 3.1 15.9 + - - +
976A LEU* 3.3 4.2 + - - -
978A THR* 1.3 77.0 - - - +
980A LEU* 1.3 61.3 + - - +
982A PHE* 4.1 0.4 - - - +
983A ILE* 2.8 41.7 + - - +
1011A MET* 3.2 23.1 - - - +
1015A THR* 2.3 41.0 + - - +
22G ILE* 6.2 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 980 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A VAL* 4.1 15.3 - - + -
358A PHE* 4.0 10.8 - - + -
976A LEU* 2.9 20.4 + - + +
977A MET 4.0 2.7 - - - +
979A SER* 1.3 76.1 - - - +
981A ALA* 1.3 66.0 + - - +
983A ILE* 4.6 3.1 - - + -
984A LEU* 2.9 30.9 + - + +
15G VAL 5.5 0.4 - - - +
18G VAL* 3.8 28.9 - - + +
19G MET* 3.2 48.9 - - + -
22G ILE* 3.8 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 981 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LEU 5.4 0.2 - - - -
351A VAL* 4.3 29.2 + - + +
354A VAL* 4.1 19.6 - - + +
355A MET* 4.7 8.1 - - + -
402A ILE* 6.0 0.9 - - - +
406A VAL* 4.5 13.7 - - + -
410A ILE* 4.9 0.2 - - + -
977A MET 3.0 19.8 + - - +
978A THR* 3.7 7.2 - - - +
980A LEU* 1.3 75.4 - - - +
982A PHE* 1.3 57.2 + - - +
984A LEU* 3.8 1.6 - - - +
985A GLY* 2.8 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 982 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A VAL 4.0 13.5 - - - -
400A LEU* 3.9 19.3 - - + -
402A ILE* 4.6 8.7 - - + -
403A GLY* 3.5 31.4 - - - -
406A VAL* 5.6 2.2 - - + -
933A THR* 4.0 14.1 - - + -
934A THR* 5.7 0.9 - - - -
937A LEU* 3.6 29.2 - - + -
978A THR* 2.9 18.5 + - + +
979A SER* 4.1 3.1 - - - +
981A ALA* 1.3 74.5 - - - +
983A ILE* 1.3 66.6 + - - +
985A GLY* 2.9 12.0 + - - +
986A VAL* 3.1 26.0 + - + +
1007A VAL* 3.7 25.1 - - + -
1011A MET* 3.7 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 983 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
979A SER* 2.8 30.5 + - - +
980A LEU* 4.2 3.8 - - + +
982A PHE* 1.3 72.2 - - - +
984A LEU* 1.3 64.4 + - + +
986A VAL* 3.4 10.9 - - - +
987A MET* 3.3 19.5 + - + +
1007A VAL* 6.2 0.4 - - - -
1008A MET* 4.2 26.3 - - + +
1011A MET* 3.8 22.4 - - + +
1012A VAL* 3.6 39.3 - - + +
1015A THR* 5.1 0.2 - - - +
18G VAL* 4.1 25.4 - - + -
22G ILE* 4.7 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 984 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LEU* 3.3 33.7 - - + +
354A VAL* 3.7 18.6 - - + -
980A LEU* 2.9 16.1 + - + +
981A ALA 4.0 2.7 - - - +
983A ILE* 1.3 78.4 - - - +
985A GLY* 1.3 61.3 + - - +
987A MET* 3.1 45.8 + - + +
988A PRO* 3.6 0.2 - - - +
14G MET* 4.0 13.0 - - + +
15G VAL* 3.3 39.7 - - + -
18G VAL* 3.5 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 985 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A THR* 4.6 3.8 - - - +
347A ALA* 3.9 31.8 - - - +
350A LEU* 4.3 6.7 - - - -
399A VAL* 6.1 1.2 - - - +
402A ILE* 6.1 2.2 - - - -
981A ALA 2.8 21.0 + - - -
982A PHE* 2.9 9.2 + - - -
984A LEU* 1.3 74.0 - - - +
986A VAL* 1.3 57.4 + - - +
988A PRO* 3.3 14.9 - - - +
989A LEU* 5.1 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 986 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A VAL* 5.0 7.4 - - + -
400A LEU* 5.8 0.4 - - + -
982A PHE* 3.1 23.5 + - + +
983A ILE* 3.4 16.2 - - - +
985A GLY* 1.3 76.0 - - - +
987A MET* 1.3 67.5 + - - +
988A PRO* 3.3 3.1 - - - -
989A LEU* 3.0 36.7 + - + +
990A VAL* 3.3 6.7 + - + +
1003A VAL* 5.8 1.1 - - + -
1004A GLY* 4.0 21.3 - - - +
1007A VAL* 3.8 26.5 - - + -
1008A MET* 4.2 16.4 - - + +
----------------------------------------------------------
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