Contacts of the helix formed by residues 1012 - 1044 (chain A) in PDB entry 3H2V
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 SER1012 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010A ASN 3.4 3.6 + - - -
1011A ILE* 1.3 78.8 - - - +
1013A ASP* 1.3 57.5 + - - +
1014A GLU* 3.0 17.8 + - - +
1015A GLU* 3.0 20.4 + - - +
1016A SER* 2.6 33.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1013 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1011A ILE 3.9 0.2 + - - -
1012A SER* 1.3 71.6 + - - +
1014A GLU* 1.3 77.6 + - - +
1016A SER* 3.2 7.8 + - - -
1017A GLU* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1014 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012A SER* 3.0 7.4 + - - +
1013A ASP* 1.3 90.1 - - - +
1015A GLU* 1.3 61.4 + - - +
1017A GLU* 3.7 7.8 + - - +
1018A GLN* 3.2 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1015 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005A MET* 4.1 17.2 - - + +
1011A ILE* 3.3 29.0 - - + +
1012A SER* 3.0 26.1 + - - +
1014A GLU* 1.3 77.8 - - - +
1016A SER* 1.3 57.5 + - - +
1018A GLN* 3.3 5.9 + - - +
1019A ALA* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1016 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002A LYS* 3.2 26.1 + - - -
1005A MET* 3.9 17.3 - - - -
1011A ILE* 4.0 6.0 + - - +
1012A SER 2.6 18.6 + - - -
1013A ASP* 3.2 8.0 + - - -
1015A GLU* 1.3 76.7 - - - +
1017A GLU* 1.3 63.4 + - - +
1019A ALA 3.2 6.8 + - - -
1020A THR* 3.2 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1017 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013A ASP 3.1 15.4 + - - +
1014A GLU* 4.6 9.0 - - - +
1016A SER* 1.3 76.8 - - - +
1018A GLN* 1.3 59.6 + - - +
1020A THR* 3.9 17.7 - - - +
1021A GLU* 3.0 66.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1018 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014A GLU 3.2 19.3 + - - +
1015A GLU* 3.6 6.1 - - - +
1016A SER 3.1 0.4 - - - -
1017A GLU* 1.3 79.9 + - - +
1019A ALA* 1.3 62.3 + - - +
1020A THR 3.1 0.2 - - - -
1021A GLU* 3.3 17.4 + - - +
1022A MET* 2.8 49.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1019 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998A LEU* 5.3 3.8 - - - +
1001A VAL* 4.0 19.7 - - + -
1002A LYS* 3.7 17.7 - - + +
1005A MET* 3.7 17.5 - - + -
1015A GLU 3.0 14.2 + - - +
1016A SER 3.2 8.7 + - - +
1018A GLN* 1.3 78.7 - - - +
1020A THR* 1.3 63.7 + - - +
1022A MET* 3.2 24.2 + - + +
1023A LEU* 3.3 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1020 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895A ASN* 4.3 17.5 - - - +
937A VAL* 4.8 14.1 + - + +
1002A LYS* 3.1 32.0 + - - +
1016A SER 3.2 8.5 + - - -
1017A GLU* 3.8 26.7 - - - +
1019A ALA* 1.3 81.1 - - - +
1021A GLU* 1.3 58.6 + - + +
1023A LEU* 3.4 6.8 - - - +
1024A VAL* 3.2 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1021 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017A GLU* 3.0 49.0 + - - +
1018A GLN* 3.3 20.6 + - - +
1019A ALA 3.3 0.4 - - - -
1020A THR* 1.3 77.2 - - + +
1022A MET* 1.3 60.3 + - - +
1023A LEU 3.2 0.7 - - - -
1024A VAL* 3.9 8.2 - - + +
1025A HIS* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1022 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998A LEU* 3.2 40.9 - - + +
1001A VAL* 5.7 5.2 - - + -
1018A GLN* 2.8 42.8 - - + +
1019A ALA* 3.2 16.4 + - + +
1021A GLU* 1.3 74.8 - - - +
1023A LEU* 1.3 62.6 + - - +
1025A HIS* 3.7 7.9 - - - +
1026A ASN* 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1023 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898A MET* 5.0 7.4 - - - -
933A MET* 5.1 8.3 - - - -
937A VAL* 4.3 15.7 - - + -
947A LEU* 5.2 4.0 - - + -
995A LEU* 3.7 31.4 - - + +
998A LEU* 3.9 25.3 - - + +
999A SER* 4.2 9.6 - - - +
1002A LYS* 3.7 40.4 - - + -
1019A ALA 3.3 6.9 + - - +
1020A THR* 3.4 11.2 - - - +
1022A MET* 1.3 78.4 - - - +
1024A VAL* 1.3 54.0 + - + +
1026A ASN* 2.9 5.4 + - - +
1027A ALA* 2.7 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1024 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895A ASN* 3.6 30.5 - - - +
897A PRO* 3.6 33.7 - - + -
898A MET* 3.9 9.6 - - + +
937A VAL* 6.4 0.7 - - + -
1020A THR* 3.2 19.9 + - + +
1021A GLU* 4.0 9.4 - - + +
1023A LEU* 1.3 80.2 - - - +
1025A HIS* 1.3 58.7 + - - +
1027A ALA* 3.8 7.5 - - - +
1028A GLN* 2.9 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1025 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021A GLU 3.1 19.3 + - - +
1022A MET* 3.8 8.5 - - - +
1023A LEU 3.0 1.0 + - - -
1024A VAL* 1.3 77.6 - - - +
1026A ASN* 1.3 65.5 + - - +
1028A GLN* 3.3 13.8 + - - +
1029A ASN* 2.9 54.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1026 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991A ILE* 2.8 39.8 - - - +
994A GLN* 2.7 41.6 + - - +
995A LEU* 3.5 16.0 + - + +
998A LEU* 3.2 20.8 - - + +
1022A MET 3.0 16.4 + - - +
1023A LEU 2.9 4.0 + - - +
1025A HIS* 1.3 80.8 - - - +
1027A ALA* 1.3 57.6 + - - +
1029A ASN* 3.2 3.6 + - - -
1030A LEU* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1027 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898A MET* 4.1 19.3 - - + -
901A ALA* 4.7 1.3 - - + -
930A MET* 3.9 27.6 - - + -
933A MET* 6.2 0.2 - - - -
995A LEU* 4.0 12.0 - - + +
1023A LEU* 2.7 19.7 + - + +
1024A VAL* 3.8 6.5 - - - +
1026A ASN* 1.3 70.0 - - - +
1028A GLN* 1.3 66.5 + - - +
1030A LEU* 3.2 5.2 + - - +
1031A MET* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1028 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897A PRO* 4.2 14.6 + - - +
901A ALA* 4.1 20.6 - - + +
1024A VAL* 2.9 42.5 + - + +
1025A HIS* 3.4 18.9 + - - +
1027A ALA* 1.3 77.8 - - + +
1029A ASN* 1.3 66.8 + - - +
1031A MET* 3.5 2.8 + - - +
1032A GLN* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1029 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991A ILE* 4.3 13.5 - - + -
1025A HIS* 2.9 46.5 + - - +
1026A ASN* 3.9 4.5 - - - +
1028A GLN* 1.3 86.3 + - - +
1030A LEU* 1.3 60.2 + - - +
1032A GLN* 3.7 7.3 - - - +
1033A SER* 2.8 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1030 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926A MET* 3.8 11.4 - - + -
930A MET* 4.8 0.4 - - + -
954A ILE* 3.5 32.8 - - + -
958A SER* 4.6 0.4 - - - +
988A ILE* 4.0 28.7 - - + +
991A ILE* 3.7 16.7 - - + +
992A SER* 4.2 12.6 - - - +
995A LEU* 3.8 17.0 - - + -
1026A ASN* 2.9 17.4 + - - +
1027A ALA* 3.2 6.7 + - - +
1029A ASN* 1.3 73.2 - - - +
1031A MET* 1.3 80.7 + - + +
1033A SER* 3.3 3.5 + - - -
1034A VAL* 2.9 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1031 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901A ALA* 3.8 37.0 - - + +
902A ALA* 4.4 1.8 - - - -
904A GLN* 6.1 0.4 - - + -
905A LEU* 3.7 24.6 - - + +
926A MET* 3.7 28.7 - - + -
927A ALA* 4.9 0.9 - - - -
930A MET* 3.3 49.1 - - + -
1027A ALA 3.0 17.1 + - - +
1028A GLN 3.8 3.6 - - - +
1030A LEU* 1.3 86.3 - - + +
1032A GLN* 1.3 62.3 + - - +
1034A VAL* 3.2 3.9 + - - +
1035A LYS* 3.1 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1032 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904A GLN* 5.6 3.8 - - - +
1028A GLN 3.0 18.8 + - - +
1029A ASN* 3.7 9.4 - - - +
1030A LEU 3.3 0.2 - - - -
1031A MET* 1.3 77.1 - - - +
1033A SER* 1.3 58.5 + - - +
1035A LYS* 3.5 29.8 + - + +
1036A GLU* 2.4 74.1 + - - +
1039A ARG* 5.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1033 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984A VAL 4.5 4.2 - - - +
987A ARG* 3.1 27.9 + - - +
988A ILE* 4.1 19.5 - - - +
991A ILE* 3.6 14.0 - - - +
1029A ASN* 2.8 21.7 + - - +
1030A LEU* 3.6 5.6 - - - -
1032A GLN* 1.3 76.1 - - - +
1034A VAL* 1.3 65.8 + - - +
1036A GLU* 3.1 7.3 + - - +
1037A THR* 3.0 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1034 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905A LEU* 3.8 20.2 - - + -
923A ALA* 4.2 13.2 - - + -
926A MET* 3.3 41.5 - - + -
961A VAL* 4.2 19.5 - - + -
988A ILE* 4.2 19.3 - - + -
1030A LEU* 2.9 22.7 + - + +
1031A MET* 3.2 0.9 + - - +
1033A SER* 1.3 75.0 - - - +
1035A LYS* 1.3 59.9 + - - +
1037A THR* 3.2 4.9 + - - -
1038A VAL* 3.0 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1035 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904A GLN* 3.9 41.6 + - + +
905A LEU* 3.6 15.9 - - + +
908A GLU* 4.2 22.2 + - + +
1031A MET 3.1 15.5 + - - +
1032A GLN* 3.6 28.9 - - + +
1034A VAL* 1.3 74.4 - - - +
1036A GLU* 1.3 66.1 + - - +
1037A THR 3.2 0.4 + - - -
1038A VAL* 3.6 10.8 + - - +
1039A ARG* 3.1 50.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1036 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984A VAL* 4.5 19.0 - - + +
987A ARG* 4.1 17.0 + - - -
1032A GLN* 2.4 57.3 + - - +
1033A SER* 3.1 8.5 + - - +
1035A LYS* 1.3 77.2 - - - +
1037A THR* 1.3 66.5 + - - +
1039A ARG* 3.2 18.2 + - - +
1040A GLU* 3.1 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1037 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919A ILE* 4.4 8.3 - - + -
961A VAL* 3.9 22.4 - - + -
965A ALA* 4.0 23.6 - - + -
981A LEU* 4.2 7.1 - - + +
984A VAL* 4.3 11.8 + - - +
985A CYS* 4.0 11.8 - - - +
988A ILE* 3.6 15.2 - - - +
1033A SER 3.0 14.9 + - - -
1034A VAL 3.3 10.8 - - - -
1036A GLU* 1.3 73.0 - - - +
1038A VAL* 1.2 58.7 + - + +
1039A ARG 2.4 17.1 + - - -
1040A GLU* 2.7 1.8 + - - +
1041A ALA* 2.6 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1038 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905A LEU* 5.7 0.4 - - + -
908A GLU* 4.9 13.0 - - + +
909A ALA* 5.8 1.3 - - + -
912A TRP* 5.0 5.6 + - + +
919A ILE* 4.0 20.4 - - + -
920A ILE* 4.4 20.2 - - + -
923A ALA* 4.9 13.9 - - + -
1034A VAL* 3.0 21.8 - - + +
1035A LYS* 3.7 11.4 - - - +
1037A THR* 1.2 78.4 - - - +
1039A ARG* 1.3 59.8 + - + +
1041A ALA* 3.8 8.1 - - - -
1042A GLU* 3.7 4.5 + - - +
1058A TRP* 3.7 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1039 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908A GLU* 3.0 43.5 + - - +
1035A LYS* 3.1 44.0 + - - +
1036A GLU* 3.6 17.6 + - - +
1037A THR 2.4 2.2 + - - -
1038A VAL* 1.3 80.9 - - + +
1040A GLU* 1.3 69.8 + - + +
1041A ALA 3.2 0.2 - - - -
1042A GLU* 3.9 7.4 - - - +
1043A ALA* 3.6 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1040 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
977A ILE* 3.7 22.3 - - - +
980A ASN* 3.6 33.2 - - + +
981A LEU* 4.0 19.1 - - + +
984A VAL* 4.7 11.4 - - + -
1036A GLU* 3.1 14.7 + - + +
1037A THR 2.7 3.1 + - - +
1039A ARG* 1.3 88.2 - - + +
1041A ALA* 1.3 58.9 + - - +
1042A GLU 3.3 0.4 - - - -
1043A ALA* 3.8 7.0 - - - +
1044A ALA* 3.4 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1041 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919A ILE* 4.1 20.0 - - + -
965A ALA* 5.5 0.4 - - - -
968A VAL* 3.9 11.6 - - + +
981A LEU* 3.9 18.1 - - + +
1037A THR* 2.6 19.0 + - + +
1038A VAL* 4.1 6.7 - - - -
1040A GLU* 1.3 75.7 - - - +
1042A GLU* 1.3 63.9 + - - +
1044A ALA* 3.5 3.1 + - - -
1045A SER* 3.1 24.3 + - - -
1058A TRP* 3.8 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1042 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912A TRP* 3.1 29.1 - - + -
1038A VAL 3.7 8.8 + - - +
1039A ARG* 4.2 7.0 - - - +
1040A GLU 3.3 0.2 - - - -
1041A ALA* 1.3 78.6 - - - +
1043A ALA* 1.3 73.1 + - - +
1045A SER* 3.1 16.6 + - - -
1046A ILE* 3.9 9.4 - - - +
1058A TRP* 3.4 49.9 - - + -
915B LYS* 3.4 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1043 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
977A ILE* 4.3 16.6 - - + -
1039A ARG 3.6 11.6 + - - +
1040A GLU* 3.5 15.4 + - - +
1041A ALA 3.3 0.2 - - - -
1042A GLU* 1.3 88.3 + - - +
1044A ALA* 1.3 50.4 + - - +
1045A SER 3.1 0.2 - - - -
1046A ILE* 3.0 15.8 - - - +
1047A LYS* 2.6 30.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1044 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968A VAL* 4.0 22.2 - - + +
972A CYS* 3.8 23.7 - - + +
977A ILE* 3.5 21.1 - - + +
981A LEU* 4.2 9.6 - - + -
1040A GLU 3.4 11.1 + - - +
1041A ALA 3.7 5.6 - - - +
1042A GLU 3.2 0.8 - - - -
1043A ALA* 1.3 75.3 - - - +
1045A SER* 1.3 56.9 + - - +
1047A LYS* 3.0 23.4 + - - +
1048A ILE* 4.5 4.5 - - - +
----------------------------------------------------------
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