Contacts of the helix formed by residues 979 - 1007 (chain C) in PDB entry 1OW8
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 THR 979 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
975C LEU* 4.3 2.3 - - - +
976C PRO* 3.1 25.6 + - + +
977C ALA 3.0 0.6 + - - -
978C SER* 1.3 84.2 - - - +
980C HIS* 1.3 64.5 + - - +
981C ARG 3.3 3.4 + - - -
982C GLU* 3.8 8.2 + - - +
983C ILE* 3.3 24.4 + - - +
1037C VAL* 5.5 0.8 - - - +
1041C ALA* 3.9 30.6 - - + +
1044C LYS* 4.3 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 980 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972C ILE* 2.7 53.4 + - + +
973C PRO* 3.8 13.0 - - + -
975C LEU* 3.2 12.2 + - + -
976C PRO 2.5 32.8 + - - -
977C ALA* 3.0 20.7 + - + +
978C SER 3.4 0.2 - - - -
979C THR* 1.3 82.7 - - - +
981C ARG* 1.3 57.6 + - - +
983C ILE* 3.7 4.6 + - + +
984C GLU* 3.0 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 981 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007B TYR* 5.8 0.4 - - - -
1009B MET 5.0 1.8 + - - -
1010B THR* 3.6 27.9 - - - +
977C ALA 4.8 0.4 + - - -
978C SER 4.6 6.9 + - - +
979C THR 3.3 0.8 - - - -
980C HIS* 1.3 74.4 - - - +
982C GLU* 1.3 61.0 + - - +
983C ILE 3.1 1.8 - - - -
984C GLU* 3.0 13.7 + - - +
985C MET* 2.9 63.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 982 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1011B SER* 5.5 6.5 - - - +
979C THR* 3.8 9.3 + - - +
980C HIS 3.6 0.2 - - - -
981C ARG* 1.3 76.9 - - - +
983C ILE* 1.3 56.6 + - - +
985C MET* 3.5 6.5 + - + +
986C ALA* 2.9 30.0 + - - +
1037C VAL* 4.1 31.5 - - + +
1040C GLN* 5.2 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 983 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968C VAL* 3.8 27.4 - - + -
972C ILE* 4.0 13.7 - - + -
975C LEU* 4.0 23.6 - - + -
979C THR* 3.3 20.8 + - - +
980C HIS* 3.9 9.0 - - - +
981C ARG 3.1 0.6 - - - -
982C GLU* 1.3 73.5 - - - +
984C GLU* 1.3 64.8 + - - +
986C ALA* 3.9 6.4 - - - +
987C GLN* 3.2 22.9 + - - +
1034C LEU* 4.0 3.3 - - + +
1037C VAL* 4.0 18.4 - - + -
1038C ILE* 3.8 26.5 - - + -
1041C ALA* 4.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 984 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972C ILE* 4.1 23.2 - - - +
980C HIS* 3.0 29.9 + - - +
981C ARG* 3.0 16.1 + - - +
983C ILE* 1.3 76.3 - - - +
985C MET* 1.3 76.1 + - + +
987C GLN* 3.3 17.7 - - - +
988C LYS* 3.1 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 985 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007B TYR* 4.3 15.9 - - + -
1010B THR* 4.4 8.5 - - - +
1011B SER* 2.9 29.4 - - - +
1012B LEU* 3.6 24.7 - - + +
981C ARG* 2.9 53.3 + - + +
982C GLU* 3.7 6.7 - - + +
984C GLU* 1.3 85.2 - - + +
986C ALA* 1.3 67.4 + - - +
987C GLN 3.0 1.6 - - - -
988C LYS* 2.9 29.8 + - + +
989C LEU* 2.9 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 986 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012B LEU* 5.3 1.1 - - - +
982C GLU 2.9 19.1 + - - +
983C ILE* 3.9 2.2 - - - +
985C MET* 1.3 75.4 - - - +
987C GLN* 1.3 59.9 + - - +
989C LEU* 3.5 12.6 + - - +
990C LEU* 3.4 23.9 + - - +
1030C ASP* 5.3 1.6 - - - +
1033C ASN* 5.6 0.4 - - + -
1034C LEU* 3.4 36.1 - - + +
1037C VAL* 4.7 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 987 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965C LEU* 3.3 46.5 + - + +
968C VAL* 3.6 23.3 - - + +
969C ASP* 3.3 22.5 + - - +
972C ILE* 3.9 12.8 - - - +
983C ILE 3.2 17.9 + - - +
984C GLU* 3.3 22.5 - - - +
985C MET 3.0 0.6 - - - -
986C ALA* 1.3 74.6 - - - +
988C LYS* 1.3 66.4 + - - +
989C LEU 3.1 1.3 - - - -
990C LEU* 3.1 18.0 + - - +
991C ASN* 3.3 14.5 + - - +
1034C LEU* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 988 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003B LEU* 4.5 7.8 - - - +
1006B GLN* 3.5 17.2 - - - +
1007B TYR* 3.0 42.4 + - + +
1012B LEU* 4.5 2.9 - - + -
1016B TYR* 4.2 12.6 - - - +
984C GLU 3.1 9.4 + - - +
985C MET* 2.9 20.5 + - + +
987C GLN* 1.3 77.5 - - - +
989C LEU* 1.3 63.8 + - - +
991C ASN* 2.9 43.8 + - + +
992C SER* 3.2 12.8 + - - +
4F GLU* 5.9 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 989 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012B LEU* 4.4 11.6 - - + +
1015B GLU* 4.0 25.1 - - + -
1016B TYR* 3.9 10.1 - - + +
1019B GLN* 3.7 26.5 - - - +
985C MET 2.9 11.8 + - - +
986C ALA* 3.6 14.6 - - - +
987C GLN 3.1 0.2 - - - -
988C LYS* 1.3 77.4 - - - +
990C LEU* 1.3 61.4 + - - +
992C SER* 2.8 25.5 + - - +
993C ASP* 3.0 20.5 + - - +
1030C ASP* 3.6 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 990 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961C LEU* 3.9 29.7 - - + +
964C LEU* 4.1 10.5 - - + -
965C LEU* 4.6 6.7 - - + -
986C ALA 3.4 11.4 + - - +
987C GLN* 3.1 9.7 + - - +
989C LEU* 1.3 77.9 - - - +
991C ASN* 1.3 57.0 + - - +
993C ASP* 3.3 6.1 + - - +
994C LEU* 3.0 25.3 + - - +
1027C LEU* 3.5 21.1 - - + +
1030C ASP* 3.5 18.6 - - + +
1031C ALA* 3.4 31.6 - - + +
1034C LEU* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 991 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961C LEU* 4.7 0.8 - - - +
965C LEU* 3.5 18.3 - - - +
987C GLN* 3.3 6.5 + - - +
988C LYS* 2.9 38.2 + - + +
990C LEU* 1.3 80.2 - - - +
992C SER* 1.3 57.9 + - - +
994C LEU* 3.3 8.1 + - - +
995C GLY* 3.0 21.5 + - - -
2F LEU* 5.9 5.5 - - - +
5F LEU* 3.3 33.7 - - - +
8F LEU* 4.6 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 992 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000B LYS* 5.4 3.0 + - - -
1003B LEU* 4.0 17.0 - - - -
1016B TYR* 2.6 42.1 + - - -
1019B GLN* 5.1 1.5 + - - -
988C LYS* 3.2 9.0 + - - +
989C LEU* 2.8 16.8 + - - +
991C ASN* 1.3 75.8 - - - +
993C ASP* 1.3 61.6 + - - +
994C LEU 3.1 0.2 - - - -
995C GLY* 2.9 4.4 + - - +
996C GLU* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 993 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019B GLN* 4.2 10.0 + - - +
989C LEU* 3.0 29.6 + - - +
990C LEU* 3.3 10.5 - - - +
991C ASN 3.2 0.2 - - - -
992C SER* 1.3 77.0 + - - +
994C LEU* 1.3 64.4 + - - +
996C GLU* 3.3 10.8 + - - +
997C LEU* 3.2 19.8 + - - +
1023C ALA 4.2 8.4 - - - +
1026C ALA* 3.7 7.7 - - - +
1027C LEU* 3.6 32.7 + - + +
1030C ASP* 2.7 36.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 994 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
954C VAL* 5.3 2.7 - - + +
957C VAL* 4.2 8.7 - - + -
958C GLY* 4.0 28.0 - - - +
961C LEU* 3.9 14.8 - - + -
990C LEU 3.0 12.9 + - - +
991C ASN 3.4 8.3 - - - +
993C ASP* 1.3 77.6 - - - +
995C GLY* 1.3 62.9 + - - +
997C LEU* 3.2 26.0 + - + +
998C ILE* 3.0 42.6 + - + +
1027C LEU* 4.1 5.1 - - + +
5F LEU* 3.5 28.9 - - + -
8F LEU* 4.4 6.1 - - + -
9F LEU* 5.1 4.5 - - + -
12F LEU* 6.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 995 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991C ASN 3.0 11.7 + - - -
992C SER* 2.9 9.8 + - - -
994C LEU* 1.3 77.1 - - - +
996C GLU* 1.3 59.2 + - - +
998C ILE* 3.3 12.3 + - - +
999C ASN* 3.0 32.3 + - - +
8F LEU* 4.6 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 996 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996B GLU* 4.9 11.4 - - + +
1000B LYS* 3.0 38.8 - - - +
1019B GLN* 3.6 7.4 - - - +
992C SER 2.8 11.8 + - - +
993C ASP* 3.5 13.6 - - - +
994C LEU 3.2 0.2 - - - -
995C GLY* 1.3 73.9 - - - +
997C LEU* 1.3 64.4 + - - +
999C ASN* 3.0 11.8 + - - +
1000C LYS* 2.9 42.4 + - - +
1019C GLN 4.9 0.9 - - - +
1022C THR* 4.4 8.5 - - - +
1023C ALA* 3.4 27.6 + - + +
1026C ALA* 5.4 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 997 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938C MET* 4.1 15.5 - - + -
954C VAL* 4.2 27.4 - - + -
957C VAL* 4.1 25.4 - - + -
993C ASP 3.2 10.2 + - - +
994C LEU* 3.2 18.3 + - + +
996C GLU* 1.3 79.7 - - - +
998C ILE* 1.3 61.2 + - - +
1000C LYS* 3.5 3.7 + - - +
1001C MET* 3.1 20.8 + - - +
1020C MET* 3.7 37.4 - - + +
1023C ALA* 3.7 10.9 - - + +
1024C ALA* 4.0 17.7 - - + +
1027C LEU* 4.9 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 998 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
954C VAL* 4.7 15.3 - - + -
994C LEU* 3.0 38.3 + - + +
995C GLY* 3.5 6.5 - - - +
997C LEU* 1.3 75.8 - - - +
999C ASN* 1.3 56.9 + - - +
1001C MET* 2.7 33.0 + - + +
1002C LYS* 2.7 46.9 + - + +
8F LEU* 3.8 41.1 - - + +
11F GLU* 3.6 12.6 - - + +
12F LEU* 5.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 999 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999B ASN* 3.0 31.6 - - - +
1000B LYS* 5.5 1.8 - - - +
995C GLY 3.0 23.4 + - - +
996C GLU* 3.4 10.9 - - - +
998C ILE* 1.3 75.8 - - - +
1000C LYS* 1.3 71.1 + - + +
1002C LYS* 3.6 20.4 + - - +
1003C LEU* 3.2 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1000 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
992B SER* 4.9 4.9 + - - -
996B GLU* 2.5 49.0 + - - +
999B ASN* 5.9 1.0 - - - +
996C GLU* 2.9 29.8 + - + +
997C LEU 3.8 4.7 - - - +
999C ASN* 1.3 81.3 - - + +
1001C MET* 1.3 62.7 + - - +
1003C LEU* 3.8 19.5 - - + +
1004C ALA* 3.2 15.9 + - - +
1016C TYR* 3.6 16.9 - - + +
1019C GLN* 3.1 42.4 + - + +
1020C MET* 3.7 21.3 - - + +
1023C ALA* 4.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1001 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950C TYR* 4.4 20.0 - - + -
951C VAL* 3.9 24.7 - - + -
954C VAL* 3.9 17.3 - - + -
997C LEU 3.1 12.6 + - - +
998C ILE* 2.7 21.7 + - + +
1000C LYS* 1.3 76.0 - - - +
1002C LYS* 1.3 77.8 + - + +
1003C LEU 2.7 6.1 + - - -
1004C ALA* 2.8 12.6 + - - +
1005C GLN* 2.9 31.7 + - + +
1020C MET* 3.7 13.7 - - + -
11F GLU* 5.6 4.3 - - + +
12F LEU* 3.4 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1002 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998C ILE* 2.7 34.0 + - + +
999C ASN* 3.9 18.3 + - - +
1001C MET* 1.3 84.8 - - + +
1003C LEU* 1.3 57.8 + - + +
1005C GLN* 3.6 15.2 - - - +
1006C GLN* 3.1 26.5 + - - +
8F LEU* 6.3 0.2 - - - +
11F GLU* 2.5 44.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1003 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
992B SER* 4.1 14.8 - - - +
999C ASN* 3.2 23.6 + - + +
1000C LYS* 3.9 20.2 - - + +
1001C MET 2.7 4.9 + - - -
1002C LYS* 1.3 73.4 - - + +
1004C ALA* 1.3 64.1 + - - +
1005C GLN 2.9 2.6 + - - -
1006C GLN* 3.1 21.4 + - - +
1007C TYR* 3.0 38.9 + - + -
1016C TYR* 3.4 42.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1004 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950C TYR* 3.4 24.2 + - + +
1000C LYS 3.2 12.3 + - - +
1001C MET* 2.8 11.5 + - - +
1003C LEU* 1.3 75.8 - - - +
1005C GLN* 1.3 61.4 + - - +
1007C TYR 3.6 16.4 - - - +
1008C VAL* 3.9 2.6 + - - +
1013C GLN* 4.0 12.4 - - + +
1016C TYR* 3.7 21.7 - - + +
1017C LYS* 4.7 5.6 - - + +
1020C MET* 4.2 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1005 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947C PRO* 4.3 12.2 + - + +
950C TYR* 4.2 19.3 - - + -
951C VAL* 3.8 23.1 - - + +
1001C MET* 2.9 32.6 + - + +
1002C LYS* 3.6 15.6 - - - +
1004C ALA* 1.3 75.4 - - - +
1006C GLN* 1.3 54.4 + - - +
1007C TYR 2.7 10.7 + - - -
1008C VAL* 2.7 32.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1006 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002C LYS 3.1 14.6 + - - +
1003C LEU* 3.1 19.0 + - - +
1005C GLN* 1.3 77.7 - - - +
1007C TYR* 1.3 91.8 + - + +
1008C VAL 3.8 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1007 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985B MET* 4.2 10.1 - - + -
988B LYS* 3.5 39.4 + - + +
1003C LEU* 3.0 24.9 + - + +
1004C ALA 3.6 4.2 - - - +
1005C GLN 2.7 1.6 + - - -
1006C GLN* 1.3 115.2 + - + +
1008C VAL* 1.3 57.7 + - - +
1010C THR* 3.4 14.2 + - + +
1012C LEU* 4.0 27.6 - - + -
1013C GLN* 3.0 26.0 - - - +
1016C TYR* 3.7 22.0 - + + -
----------------------------------------------------------
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