Contacts of the helix formed by residues 968 - 1002 (chain D) in PDB entry 3U3F
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 LEU 968 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963D ASN* 3.5 36.1 - - - +
966D THR* 2.5 16.7 + - - +
967D SER* 1.3 83.7 - - - +
969D SER* 1.3 51.0 + - - +
970D GLU 3.3 2.7 - - - -
971D GLU* 3.1 19.5 + - + +
972D CYS* 2.8 32.2 + - - +
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Residues in contact with SER 969 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906D TYR* 6.1 0.2 - - - -
960D ALA 5.5 1.8 - - - -
963D ASN 3.4 17.4 + - - -
964D ALA* 4.1 15.1 + - - -
966D THR 3.3 11.2 + - - -
967D SER* 4.8 0.2 - - - -
968D LEU* 1.3 71.2 - - - +
970D GLU* 1.3 83.0 + - - +
972D CYS* 4.2 7.0 - - - -
973D LYS* 2.8 44.9 + - - +
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Residues in contact with GLU 970 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967D SER* 4.1 18.7 - - - +
968D LEU 3.3 0.2 - - - -
969D SER* 1.3 93.2 + - - +
971D GLU* 1.3 58.4 + - - +
973D LYS* 4.1 11.2 - - - +
974D ARG* 3.0 50.5 + - - +
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Residues in contact with GLU 971 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968D LEU* 3.1 22.0 + - + +
969D SER 3.1 0.4 - - - -
970D GLU* 1.3 76.9 - - - +
972D CYS* 1.3 57.4 + - - +
974D ARG* 2.6 45.7 + - - +
975D GLN* 2.7 65.3 + - - +
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Residues in contact with CYS 972 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956D LYS 4.3 4.1 - - - +
959D LEU* 4.3 11.4 - - + +
960D ALA* 3.4 34.1 - - + +
963D ASN* 4.4 8.3 - - + +
968D LEU 2.8 19.3 + - - +
969D SER* 3.7 9.0 - - - +
971D GLU* 1.3 71.9 - - - +
973D LYS* 1.3 58.3 + - - +
975D GLN* 3.1 23.6 + - - +
976D MET* 3.2 13.7 + - - +
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Residues in contact with LYS 973 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898D LEU* 4.6 27.3 + - + +
899D SER* 5.5 5.7 + - - +
906D TYR* 3.6 30.1 + - + +
960D ALA* 4.4 14.6 - - + +
969D SER* 2.8 36.1 + - - +
970D GLU* 4.1 8.5 - - - +
972D CYS* 1.3 72.4 - - - +
974D ARG* 1.3 64.1 + - - +
975D GLN 2.8 6.3 + - - -
976D MET* 2.9 20.7 + - + +
977D LEU* 2.9 20.5 + - + +
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Residues in contact with ARG 974 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970D GLU* 3.0 47.7 + - - +
971D GLU* 2.6 40.9 + - - +
973D LYS* 1.3 74.4 - - - +
975D GLN* 1.3 56.4 + - - +
977D LEU* 4.0 12.0 - - - +
978D THR* 2.9 27.5 + - - +
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Residues in contact with GLN 975 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956D LYS* 3.4 37.9 + - + +
959D LEU* 5.3 6.5 - - + +
971D GLU* 2.7 54.3 + - - +
972D CYS* 3.3 10.5 - - - +
973D LYS 2.9 0.6 - - - -
974D ARG* 1.3 77.0 - - - +
976D MET* 1.3 66.2 + - - +
977D LEU 3.2 0.7 - - - -
978D THR* 3.3 7.7 + - - +
979D ALA* 2.9 24.8 + - - +
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Residues in contact with MET 976 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894D LEU* 4.3 11.4 - - + -
898D LEU* 4.0 27.8 - - + -
906D TYR* 4.9 5.2 - - - +
910D VAL* 3.6 15.5 - - + -
953D LEU* 3.6 24.6 - - + +
956D LYS* 3.7 27.8 - - - +
957D MET* 3.5 35.4 - - + -
960D ALA* 4.1 12.8 - - + -
972D CYS 3.2 9.5 + - - +
973D LYS* 2.9 9.8 + - - +
975D GLN* 1.3 71.8 - - - +
977D LEU* 1.3 60.1 + - - +
979D ALA* 3.1 3.3 + - - +
980D SER* 2.7 34.8 + - - -
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Residues in contact with LEU 977 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894D LEU* 3.7 15.5 - - + -
895D LYS* 3.8 40.9 - - + +
898D LEU* 3.5 26.7 - - + -
973D LYS* 2.9 21.7 + - + +
974D ARG* 4.0 8.7 - - - +
976D MET* 1.3 78.7 - - - +
978D THR* 1.3 57.7 + - - +
980D SER* 2.7 17.3 + - - -
981D HIS* 2.8 20.2 + - - +
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Residues in contact with THR 978 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
974D ARG* 2.9 18.8 + - - +
975D GLN* 3.3 11.5 + - - -
976D MET 3.1 0.4 - - - -
977D LEU* 1.3 79.5 - - - +
979D ALA* 1.3 58.8 + - - +
981D HIS* 3.2 7.2 + - - +
982D THR* 3.0 38.2 + - + +
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Residues in contact with ALA 979 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
949D ASP* 4.6 4.9 - - - +
952D GLU* 4.5 11.9 - - + +
953D LEU* 3.8 32.8 - - - +
956D LYS* 4.4 9.2 - - + -
975D GLN 2.9 17.1 + - - +
976D MET 3.6 3.4 - - - +
978D THR* 1.3 73.8 - - - +
980D SER* 1.3 60.2 + - - +
982D THR* 3.0 11.2 + - - -
983D LEU* 2.9 28.5 + - - +
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Residues in contact with SER 980 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891D VAL* 3.3 30.6 - - - +
894D LEU* 3.9 16.8 - - - +
895D LYS* 4.3 2.1 - - - -
913D VAL* 6.2 0.2 - - - -
953D LEU* 4.2 21.9 - - - +
976D MET 2.7 15.9 + - - -
977D LEU* 2.7 26.5 + - - -
979D ALA* 1.3 74.5 - - - +
981D HIS* 1.3 61.1 + - - +
983D LEU* 3.3 10.5 - - - +
984D ALA 3.0 16.3 + - - -
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Residues in contact with HIS 981 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891D VAL* 4.3 0.2 - - - +
895D LYS* 3.4 27.2 + - - +
977D LEU 2.8 14.7 + - - +
978D THR* 3.4 11.2 - - - +
979D ALA 3.1 0.2 - - - -
980D SER* 1.3 77.8 - - - +
982D THR* 1.3 63.6 + - + +
984D ALA* 2.9 11.6 + - + +
985D VAL* 2.7 63.7 + - + +
----------------------------------------------------------
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Residues in contact with THR 982 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
949D ASP* 3.8 15.1 + - - +
978D THR* 3.0 23.2 + - + +
979D ALA* 3.0 17.8 + - - -
981D HIS* 1.3 81.3 - - + +
983D LEU* 1.3 56.0 + - - +
985D VAL* 3.6 10.4 - - + +
986D ASP* 2.8 36.7 + - - -
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Residues in contact with LEU 983 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887D LEU* 4.3 17.9 - - + -
891D VAL* 4.7 1.1 - - + -
913D VAL* 3.9 25.6 - - + -
917D LEU* 4.7 9.0 - - + -
946D LEU* 3.2 30.9 - - + +
949D ASP* 3.7 17.5 - - + -
950D LEU* 4.1 22.7 - - + -
953D LEU* 4.0 15.7 - - + -
979D ALA 2.9 13.4 + - - +
980D SER* 3.3 11.9 - - - +
981D HIS 3.1 0.2 - - - -
982D THR* 1.3 78.8 + - - +
984D ALA* 1.3 56.8 + - - +
986D ASP 3.4 0.3 + - - -
987D ALA* 3.0 22.3 + - - +
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Residues in contact with ALA 984 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887D LEU* 5.2 1.3 - - - -
888D VAL* 4.6 24.0 - - + +
891D VAL* 4.2 22.0 - - + -
980D SER 3.0 10.5 + - - +
981D HIS* 2.9 12.4 + - + +
983D LEU* 1.3 75.3 - - - +
985D VAL* 1.3 65.9 + - + +
987D ALA* 3.1 9.2 + - - +
988D LYS* 3.1 22.0 + - - +
----------------------------------------------------------
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Residues in contact with VAL 985 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981D HIS* 2.7 55.3 + - + +
982D THR* 3.3 10.1 + - + +
984D ALA* 1.3 74.2 - - + +
986D ASP* 1.3 63.7 + - - +
988D LYS* 3.3 7.9 + - - +
989D ASN* 2.8 38.2 + - - +
----------------------------------------------------------
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Residues in contact with ASP 986 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942D THR* 5.0 4.3 - - - +
945D LEU* 3.2 32.4 - - + +
946D LEU* 3.6 14.1 - - + +
949D ASP* 2.5 35.0 - - - +
982D THR* 2.8 19.0 + - - +
985D VAL* 1.3 77.1 - - - +
987D ALA* 1.3 67.2 + - - +
989D ASN* 3.1 19.6 + - + +
990D LEU* 2.9 22.3 + - - +
----------------------------------------------------------
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Residues in contact with ALA 987 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884D VAL* 3.8 23.5 - - + +
887D LEU* 4.5 21.8 - - + -
888D VAL* 4.7 6.3 - - + -
920D LEU* 4.8 4.7 - - + -
946D LEU* 3.8 12.3 - - + +
983D LEU 3.0 14.7 + - - +
984D ALA* 3.1 14.1 + - - +
986D ASP* 1.3 75.7 - - - +
988D LYS* 1.3 63.6 + - - +
990D LEU* 3.2 6.5 + - - +
991D LEU 3.2 16.1 + - - -
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Residues in contact with LYS 988 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881D TYR* 6.1 1.4 - - - -
884D VAL* 4.6 6.7 - - + +
888D VAL* 5.6 2.9 - - + +
984D ALA 3.1 7.6 + - - +
985D VAL* 3.4 13.0 - - + +
986D ASP 3.2 0.2 - - - -
987D ALA* 1.3 79.2 - - - +
989D ASN* 1.3 66.8 + - - +
991D LEU* 3.2 28.0 + - + +
992D ASP* 3.1 45.3 + - - +
----------------------------------------------------------
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Residues in contact with ASN 989 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942D THR* 4.7 10.2 - - + +
945D LEU* 6.0 1.2 - - + +
985D VAL* 2.8 25.0 + - - +
986D ASP* 3.1 23.3 + - + +
988D LYS* 1.3 80.2 - - - +
990D LEU* 1.3 65.5 + - - +
992D ASP* 3.1 13.4 + - - +
993D ALA* 3.1 22.9 + - - +
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Residues in contact with LEU 990 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880D VAL* 4.8 2.7 - - + -
884D VAL* 4.8 2.2 - - + -
920D LEU* 4.2 29.8 - - + -
921D ILE* 6.1 2.0 - - + -
924D VAL* 4.0 22.7 - - + -
939D ILE* 4.1 20.0 - - + +
942D THR* 2.7 36.4 - - - +
943D GLN* 4.3 16.2 - - + +
946D LEU* 4.4 11.0 - - + -
986D ASP 2.9 12.2 + - - +
987D ALA 3.4 8.5 - - - +
989D ASN* 1.3 75.9 - - - +
991D LEU* 1.3 65.5 + - - +
992D ASP 3.1 0.3 + - - -
993D ALA* 3.2 2.6 + - - +
994D VAL* 3.0 29.8 + - + +
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Residues in contact with LEU 991 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878D ASP* 5.1 0.9 - - - +
880D VAL* 4.2 15.0 - - + -
881D TYR* 3.6 49.8 - - + +
884D VAL* 4.0 21.1 - - + -
885D MET* 6.0 0.7 - - - -
987D ALA 3.2 9.3 + - - +
988D LYS* 3.2 30.7 + - + +
990D LEU* 1.3 79.8 - - - +
992D ASP* 1.3 59.8 + - - +
994D VAL* 4.5 4.3 - - + -
995D ASP* 3.0 51.7 + - - +
----------------------------------------------------------
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Residues in contact with ASP 992 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
988D LYS* 3.1 38.7 + - - +
989D ASN* 3.1 17.1 + - - +
991D LEU* 1.3 77.9 - - - +
993D ALA* 1.3 65.7 + - - +
995D ASP* 3.1 8.7 + - - +
996D GLN* 3.0 23.8 + - - +
----------------------------------------------------------
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Residues in contact with ALA 993 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938D GLU* 3.8 34.7 - - + +
939D ILE* 4.1 17.3 - - + -
942D THR* 5.0 6.7 - - + -
989D ASN 3.1 12.2 + - - +
990D LEU* 3.7 8.1 - - - +
992D ASP* 1.3 75.9 - - - +
994D VAL* 1.3 57.5 + - - +
996D GLN* 3.3 9.8 + - - +
997D ALA* 3.0 27.2 + - - +
----------------------------------------------------------
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Residues in contact with VAL 994 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880D VAL* 4.4 23.6 - - + -
924D VAL* 4.7 13.5 - - + -
927D LEU* 4.9 11.0 - - + -
931D LEU* 5.7 3.3 - - + +
939D ILE* 3.5 31.4 - - + -
990D LEU* 3.0 31.9 + - + +
991D LEU* 3.9 6.3 - - + +
993D ALA* 1.3 72.6 - - - +
995D ASP* 1.3 72.5 + - - +
996D GLN 3.1 1.8 - - - -
997D ALA* 3.1 2.0 + - - +
998D LYS* 2.8 27.6 + - + +
----------------------------------------------------------
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Residues in contact with ASP 995 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878D ASP* 4.1 15.8 - - - +
881D TYR* 5.9 0.5 - - - -
991D LEU* 3.0 40.7 + - - +
992D ASP* 3.1 8.1 + - - +
994D VAL* 1.3 80.2 - - - +
996D GLN* 1.3 61.5 + - - +
998D LYS* 3.4 6.4 + - - +
999D VAL* 3.3 27.6 + - - +
----------------------------------------------------------
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Residues in contact with GLN 996 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938D GLU* 5.1 8.2 - - - +
992D ASP 3.0 12.9 + - - +
993D ALA* 3.5 11.8 - - - +
995D ASP* 1.3 75.3 - - - +
997D ALA* 1.3 64.6 + - - +
999D VAL* 3.2 7.8 + - - +
1000D LEU* 3.1 24.6 + - + +
----------------------------------------------------------
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Residues in contact with ALA 997 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931D LEU* 4.0 18.3 - - + +
932D PRO* 4.0 5.9 - - - +
935D SER* 3.2 38.6 - - - +
938D GLU* 5.7 0.2 + - - -
939D ILE* 4.2 5.4 - - + -
993D ALA 3.0 15.5 + - - +
994D VAL 3.6 4.0 - - - +
996D GLN* 1.3 75.5 - - - +
998D LYS* 1.3 62.0 + - - +
1000D LEU* 3.7 6.1 + - - +
1001D ALA* 3.2 23.6 + - - +
----------------------------------------------------------
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Residues in contact with LYS 998 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927D LEU* 6.0 4.9 - - + -
931D LEU* 5.3 3.1 - - - +
994D VAL* 2.8 21.9 + - + +
995D ASP* 3.6 9.6 - - - +
997D ALA* 1.3 78.5 - - - +
999D VAL* 1.3 62.5 + - + +
1001D ALA* 3.4 7.4 + - - +
1002D ASN* 3.2 19.2 + - - +
----------------------------------------------------------
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Residues in contact with VAL 999 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
995D ASP 3.3 12.7 + - - +
996D GLN* 3.2 9.9 + - - +
998D LYS* 1.3 73.3 - - + +
1000D LEU* 1.3 60.3 + - - +
1001D ALA 3.1 1.3 - - - -
1002D ASN* 2.7 36.4 + - + +
----------------------------------------------------------
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Residues in contact with LEU1000 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932D PRO* 4.5 15.0 - - + -
996D GLN* 3.1 16.6 + - + +
997D ALA* 4.0 5.8 - - - +
999D VAL* 1.3 79.5 - - - +
1001D ALA* 1.3 60.1 + - - +
1002D ASN 3.6 4.0 + - - -
----------------------------------------------------------
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Residues in contact with ALA1001 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930D SER 4.1 17.3 - - - +
931D LEU* 4.4 1.1 - - + -
932D PRO* 4.0 18.1 - - + +
997D ALA 3.2 17.7 + - - +
998D LYS* 3.6 7.4 - - - +
999D VAL 3.1 1.2 - - - -
1000D LEU* 1.3 73.5 - - - +
1002D ASN* 1.3 64.0 + - - +
----------------------------------------------------------
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Residues in contact with ASN1002 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998D LYS 3.2 10.9 + - - +
999D VAL* 2.7 25.5 + - + +
1000D LEU 4.3 4.0 - - - -
1001D ALA* 1.3 74.6 - - - +
----------------------------------------------------------
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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