Contacts of the helix formed by residues 940 - 972 (chain A) in PDB entry 6J8H
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 940 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
936A MET* 2.9 19.7 + - - -
937A GLU 4.4 1.0 + - - -
938A VAL 3.6 1.8 + - - -
939A ALA* 1.3 81.4 - - - +
941A GLN* 1.3 65.5 + - - -
942A ALA 3.6 2.0 - - - -
943A MET 4.0 0.6 + - - -
944A CYS* 3.5 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 941 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A TYR* 3.3 34.8 + - + +
349A TRP* 4.0 24.3 - - - -
936A MET* 4.1 17.3 + - + +
940A GLY* 1.3 71.4 - - - -
942A ALA* 1.3 65.7 + - - +
945A LEU* 3.1 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 942 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
940A GLY 3.6 0.6 - - - -
941A GLN* 1.3 79.2 - - - +
943A MET* 1.3 61.1 + - - +
945A LEU* 4.2 1.8 - - - +
946A ILE* 3.0 38.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 943 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887A LEU* 4.7 24.7 - - + +
888A PHE* 3.8 26.5 - - + -
939A ALA* 3.4 29.8 - - + +
940A GLY 4.0 1.6 + - - -
941A GLN 3.4 0.2 - - - -
942A ALA* 1.3 77.4 - - - +
944A CYS* 1.3 65.9 + - - +
945A LEU 3.4 0.2 + - - -
946A ILE* 3.4 5.7 + - - +
947A VAL* 3.3 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 944 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A PHE* 4.1 4.9 - - - -
932A MET* 3.9 9.0 - - + -
935A CYS* 2.0 66.0 - - - -
936A MET* 3.4 15.3 - - + +
939A ALA* 5.0 0.2 - - + -
940A GLY 3.5 17.4 + - - +
943A MET* 1.3 79.5 - - - +
945A LEU* 1.3 62.9 + - - +
948A TYR* 3.1 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 945 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A TRP* 5.5 7.0 - - + -
352A LEU* 4.6 9.9 - - + -
932A MET* 4.4 7.0 - - - -
936A MET* 2.8 34.8 - - + -
941A GLN* 3.1 24.7 + - + +
942A ALA* 4.2 2.9 - - - +
944A CYS* 1.3 81.1 - - - +
946A ILE* 1.3 61.8 + - + +
948A TYR* 4.3 0.2 - - - +
949A MET* 2.8 69.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 946 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942A ALA* 3.0 25.4 + - + +
943A MET* 3.9 5.6 - - - +
944A CYS 3.4 0.2 - - - -
945A LEU* 1.3 77.7 - - + +
947A VAL* 1.3 64.1 + - + +
949A MET* 4.0 4.1 - - - +
950A MET* 3.2 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 947 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A PHE* 5.5 5.8 - - + +
883A VAL* 5.4 7.4 - - + -
884A GLY* 5.1 9.0 - - - +
887A LEU* 4.1 17.7 - - + -
888A PHE* 3.6 31.9 - - + -
910A MET* 5.6 4.0 - - + -
943A MET* 3.3 18.8 + - + +
944A CYS 4.1 1.6 - - - +
946A ILE* 1.3 78.8 - - + +
948A TYR* 1.3 68.7 + - + +
950A MET* 3.4 13.3 + - + +
951A VAL* 2.9 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 948 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A PHE* 4.9 3.4 - + - -
892A TYR* 4.4 0.2 + - - -
910A MET* 4.2 17.4 - - + -
919A ILE* 3.8 12.1 - - + +
923A VAL* 4.5 23.6 - - + +
928A TRP* 4.1 21.8 - - + +
931A THR* 2.9 38.7 + - + +
932A MET* 4.0 32.8 - - + -
935A CYS* 3.9 10.8 - - + +
944A CYS* 3.1 47.0 + - - +
945A LEU 4.3 0.4 - - - +
947A VAL* 1.3 84.2 - - + +
949A MET* 1.3 65.3 + - + +
951A VAL* 3.3 7.0 + - + +
952A MET* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 949 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LEU* 4.1 19.1 - - + -
355A PHE* 4.1 24.0 - - + -
928A TRP* 4.1 11.7 - - + -
932A MET* 4.1 16.2 - - - -
945A LEU* 2.8 52.9 + - + +
946A ILE* 4.0 3.8 - - - +
948A TYR* 1.3 76.5 - - + +
950A MET* 1.3 59.0 + - + +
952A MET* 3.5 5.1 + - - +
953A VAL* 3.0 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 950 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A PHE* 4.5 17.0 - - + -
946A ILE* 3.2 34.3 + - + +
947A VAL* 3.8 12.8 - - + +
948A TYR 3.2 0.2 - - - -
949A MET* 1.3 77.2 - - + +
951A VAL* 1.3 59.4 + - - +
953A VAL* 4.5 2.7 - - - +
954A ILE* 2.8 47.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 951 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A PHE* 3.9 37.7 - - + -
920A VAL* 4.2 27.8 - - + -
923A VAL* 4.2 22.4 - - + -
924A LEU* 4.7 7.4 - - + -
947A VAL* 2.9 26.8 + - + +
948A TYR* 3.7 8.3 - - + +
950A MET* 1.3 76.3 - - - +
952A MET* 1.3 59.8 + - - +
955A GLY* 2.7 30.1 + - - -
956A ASN* 3.8 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 952 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A PHE* 4.8 19.3 - - + -
359A THR* 5.2 9.9 - - + -
923A VAL* 3.9 22.9 - - + +
926A GLY* 4.5 10.3 - - - -
928A TRP* 3.2 47.8 - - + +
948A TYR 3.0 15.0 + - - +
949A MET* 3.7 7.6 - - - +
951A VAL* 1.3 80.3 - - - +
953A VAL* 1.3 61.1 + - + +
956A ASN* 3.0 62.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 953 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A MET* 6.2 4.5 - - + -
355A PHE* 5.8 5.8 - - + -
949A MET* 3.0 22.5 + - + +
950A MET* 4.3 2.2 - - - +
952A MET* 1.3 80.7 - - + +
954A ILE* 1.3 71.7 + - + +
956A ASN* 4.4 1.0 - - - +
957A LEU* 3.2 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 954 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A LEU* 6.1 1.6 - - + -
242A VAL* 6.4 0.7 - - + -
876A ILE* 4.1 23.6 - - + -
880A PHE* 4.4 15.0 - - + -
950A MET* 2.8 34.2 + - + +
953A VAL* 1.3 78.6 - - + +
955A GLY* 1.3 64.3 + - - +
957A LEU* 3.4 15.7 + - + +
958A VAL* 3.1 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 955 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873A LEU* 5.0 2.7 - - - +
876A ILE* 4.8 10.5 - - - -
880A PHE* 4.7 3.1 - - - -
924A LEU* 4.5 10.7 - - - +
951A VAL* 2.7 24.7 + - - +
954A ILE* 1.3 75.1 - - - +
956A ASN* 1.3 63.3 + - - +
958A VAL* 3.4 9.4 + - - +
959A VAL* 3.2 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 956 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923A VAL 4.0 4.8 + - - -
924A LEU* 3.9 36.6 + - - +
926A GLY* 5.9 0.2 - - - -
952A MET* 3.0 46.5 + - - +
953A VAL* 4.4 1.1 - - - +
955A GLY* 1.3 76.6 - - - +
957A LEU* 1.3 60.4 + - - +
959A VAL* 3.2 8.0 + - - +
960A LEU* 2.7 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 957 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A LEU* 3.9 28.0 - - + +
239A ILE* 6.2 0.9 - - + -
241A SER* 5.1 8.1 - - - -
242A VAL* 3.4 34.3 - - + +
245A LEU* 4.9 15.3 - - + -
401A VAL* 5.1 10.3 - - + -
953A VAL* 3.2 20.1 + - + +
954A ILE* 3.7 16.6 - - + +
955A GLY 3.3 0.2 - - - -
956A ASN* 1.3 76.3 - - - +
958A VAL* 1.3 57.5 + - - +
960A LEU* 3.3 7.4 + - + +
961A ASN* 2.9 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 958 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A LEU* 3.9 23.3 - - + -
869A LEU* 4.4 14.3 - - + +
872A VAL* 4.4 13.7 - - + -
873A LEU* 4.0 32.8 - - + +
876A ILE* 4.0 23.1 - - + -
954A ILE* 3.1 18.6 - - + +
955A GLY* 3.7 6.5 - - - +
956A ASN 3.2 0.6 - - - -
957A LEU* 1.3 77.6 - - - +
959A VAL* 1.3 61.8 + - - +
961A ASN* 3.2 6.1 + - - +
962A LEU* 3.0 23.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 959 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873A LEU* 3.9 19.7 - - + -
924A LEU* 3.8 36.6 - - + +
955A GLY 3.2 13.4 + - - +
956A ASN* 3.2 12.0 + - - +
958A VAL* 1.3 76.2 - - - +
960A LEU* 1.3 63.1 + - - +
962A LEU* 3.3 6.9 + - - +
963A PHE* 3.0 23.0 + - + +
1446A PHE* 4.1 22.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
397A ILE* 4.3 17.7 - - + -
398A LEU* 3.6 30.1 - - + -
401A VAL* 3.7 27.4 - - + -
956A ASN 2.7 20.9 + - - +
957A LEU* 3.7 8.7 - - + +
959A VAL* 1.3 77.1 - - - +
961A ASN* 1.3 55.8 + - - +
963A PHE* 3.4 3.9 + - + +
964A LEU* 2.7 63.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 961 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ALA 5.1 1.0 + - - -
238A LEU* 3.5 33.3 - - + +
241A SER* 3.9 19.7 + - - -
401A VAL* 3.5 23.7 - - - +
405A TYR* 5.0 12.9 - - - +
869A LEU* 4.5 9.8 - - + +
957A LEU* 2.9 27.2 + - - +
958A VAL 3.2 6.3 + - - +
960A LEU* 1.3 75.0 - - - +
962A LEU* 1.3 56.3 + - - +
964A LEU* 4.1 2.4 - - - +
965A ALA* 2.7 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 962 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862A SER* 5.4 3.8 - - - -
866A LEU* 4.1 19.3 - - + -
869A LEU* 4.2 21.2 - - + +
870A THR* 4.3 27.6 - - - +
873A LEU* 4.1 23.6 - - + -
958A VAL* 3.0 15.9 + - + +
959A VAL* 3.7 6.3 - - - +
961A ASN* 1.3 74.9 - - - +
963A PHE* 1.3 60.5 + - - +
965A ALA* 4.4 2.2 - - - -
966A LEU* 2.8 52.2 + - + +
1446A PHE* 4.6 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 963 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959A VAL* 3.0 17.4 + - + +
960A LEU* 3.8 6.3 - - - +
962A LEU* 1.3 77.0 - - - +
964A LEU* 1.3 72.9 + - + +
966A LEU* 4.5 0.2 - - - -
967A LEU* 2.9 51.1 + - + +
1446A PHE* 3.9 33.1 - + + -
1449A LEU* 3.4 34.1 - - + -
1450A ASN* 3.6 36.6 - - + +
1453A ILE* 4.2 13.9 - - + -
1755A TYR* 5.3 4.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 964 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A LEU* 4.8 13.7 - - + +
401A VAL* 5.2 2.5 - - + -
402A ALA* 3.9 35.2 - - + +
405A TYR* 5.2 5.8 - - + -
960A LEU* 2.7 52.9 + - + +
961A ASN* 4.1 3.1 - - - +
963A PHE* 1.3 90.0 - - + +
965A ALA* 1.3 65.9 + - - +
967A LEU* 3.9 14.7 - - + +
968A LEU* 3.0 36.6 + - + +
1755A TYR* 4.7 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 965 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A TYR* 3.3 38.8 + - + +
866A LEU* 3.9 16.7 - - + +
869A LEU* 4.2 11.7 - - + -
961A ASN* 2.7 25.8 + - - +
962A LEU 3.9 2.0 - - - +
964A LEU* 1.3 73.9 - - - +
966A LEU* 1.3 63.1 + - - +
969A SER* 3.2 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 966 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858A ILE* 3.5 32.1 - - + +
861A ASN* 3.6 20.9 - - + +
862A SER* 4.0 15.0 - - - +
866A LEU* 3.7 16.4 - - + +
962A LEU* 2.8 30.5 + - + +
963A PHE 3.6 3.4 - - - +
965A ALA* 1.3 78.6 - - - +
967A LEU* 1.3 60.6 + - - +
969A SER* 4.0 1.3 - - - -
970A SER* 3.1 27.6 + - - -
1446A PHE* 4.5 8.1 - - + -
1447A PHE* 3.8 28.3 - - + -
1450A ASN* 3.9 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 967 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963A PHE* 2.9 41.5 + - + +
964A LEU* 3.9 12.8 - - + +
966A LEU* 1.3 78.1 - - - +
968A LEU* 1.3 92.5 + - + +
970A SER* 3.8 3.1 - - - -
971A PHE* 3.0 25.9 + - + +
1450A ASN* 3.7 20.8 + - - +
1453A ILE* 4.2 18.8 - - + -
1454A GLY* 4.3 19.5 - - - +
1457A ILE* 5.5 9.2 - - + -
1755A TYR* 5.0 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 968 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ALA* 4.5 9.2 - - + +
405A TYR* 4.2 24.5 - - + -
406A LYS* 3.9 39.7 - - + +
964A LEU* 3.0 29.6 + - + +
967A LEU* 1.3 101.1 - - + +
969A SER* 1.3 65.0 + - - +
971A PHE* 3.3 13.4 + - + +
972A SER* 3.1 22.9 + - - -
1457A ILE* 6.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 969 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A TYR* 4.6 7.7 + - - -
409A ASN* 5.4 5.4 - - - +
861A ASN* 3.4 16.7 + - - -
866A LEU* 5.2 10.3 - - - +
965A ALA 3.2 19.4 + - - -
966A LEU* 4.0 3.6 - - - -
968A LEU* 1.3 77.0 - - - +
970A SER* 1.3 62.8 + - - +
972A SER 3.4 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 970 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854A MET* 4.2 11.0 - - - +
857A LYS* 4.0 27.6 + - - +
858A ILE* 3.8 30.5 - - - +
861A ASN* 4.0 14.8 - - - +
966A LEU* 3.1 21.3 + - - -
967A LEU* 3.8 5.2 - - - -
969A SER* 1.3 77.7 + - - +
971A PHE* 1.3 63.5 + - - +
972A SER* 3.5 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 971 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854A MET* 6.1 2.2 - - - -
967A LEU* 3.0 22.7 + - + +
968A LEU* 3.6 14.6 - - + +
969A SER 3.3 0.2 - - - -
970A SER* 1.3 79.3 + - - +
972A SER* 1.3 72.6 + - - +
1454A GLY* 4.9 6.1 - - - -
1457A ILE* 4.7 11.0 - - + -
1458A ASP* 2.6 46.0 - - + -
1461A ASN* 5.3 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 972 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968A LEU 3.1 10.6 + - - -
969A SER* 3.4 17.5 - - - +
970A SER 3.3 1.6 - - - +
971A PHE* 1.3 96.3 - - - +
----------------------------------------------------------
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