Contacts of the helix formed by residues 935 - 969 (chain A) in PDB entry 3MPX
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 ASP 935 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932A GLU* 5.6 4.7 - - - +
936A THR* 1.4 67.1 + - - +
937A LEU* 3.2 9.5 - - - +
938A ALA* 3.4 17.0 + - - +
939A ARG* 3.3 32.5 + - - +
1007A ASN* 4.7 5.2 + - - +
1010A HIS* 6.6 0.2 - - - -
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Residues in contact with THR 936 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935A ASP* 1.4 77.7 - - - +
937A LEU* 1.3 52.6 + - - +
939A ARG* 3.2 34.1 + - - +
940A GLU* 2.8 49.8 + - + +
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Residues in contact with LEU 937 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935A ASP 4.6 7.4 - - - +
936A THR* 1.3 78.8 - - - +
938A ALA* 1.4 62.8 + - - +
940A GLU* 3.3 7.5 + - + +
941A GLU* 3.1 53.4 + - + +
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Residues in contact with ALA 938 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935A ASP 3.4 15.7 + - - +
936A THR 3.4 0.6 - - - -
937A LEU* 1.4 78.8 - - - +
939A ARG* 1.3 52.9 + - - +
941A GLU* 3.5 0.6 + - - -
942A LEU* 2.9 40.6 + - - +
1003A LEU* 3.5 23.0 - - + +
1007A ASN* 3.5 36.8 - - - +
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Residues in contact with ARG 939 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926A LEU* 3.8 27.1 + - + +
929A MSE 3.2 46.0 + - + +
930A ASP* 3.1 36.9 + - - +
932A GLU* 4.5 8.1 + - - +
935A ASP* 3.3 10.8 + - - +
936A THR* 3.2 47.3 + - - +
938A ALA* 1.3 78.9 - - + +
940A GLU* 1.4 55.5 + - - +
942A LEU* 3.2 10.9 + - + +
943A ARG* 2.8 48.4 + - - +
1007A ASN* 5.5 4.3 - - - +
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Residues in contact with GLU 940 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930A ASP* 4.7 2.9 - - - +
936A THR* 2.8 39.0 + - + +
937A LEU* 3.3 8.0 + - + +
939A ARG* 1.4 72.6 + - - +
941A GLU* 1.3 59.2 + - + +
943A ARG* 3.2 37.8 + - - +
944A GLN* 3.1 27.0 + - - +
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Residues in contact with GLU 941 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937A LEU* 3.1 41.1 + - + +
938A ALA* 5.4 0.2 - - - -
940A GLU* 1.3 72.4 - - + +
942A LEU* 1.4 65.9 + - - +
944A GLN* 3.2 8.0 + - - +
945A GLY* 3.2 20.3 + - - -
996A GLN* 4.9 0.9 - - - +
999A ARG* 3.9 18.4 - - + +
1000A TYR* 4.1 5.7 - - + +
1003A LEU* 3.5 30.7 - - + +
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Residues in contact with LEU 942 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922A VAL* 5.3 0.2 - - + -
926A LEU* 3.8 29.6 - - + -
938A ALA 2.9 25.1 + - - +
939A ARG* 3.4 6.5 - - + +
941A GLU* 1.4 76.4 - - - +
943A ARG* 1.3 55.9 + - - +
945A GLY* 3.5 0.7 + - - -
946A LEU* 2.9 47.9 + - + +
1000A TYR* 3.4 34.1 - - + +
1003A LEU* 4.2 15.4 - - + +
1004A LEU* 3.8 25.6 - - + -
1007A ASN* 4.8 7.4 - - + +
1014A LEU* 4.4 16.2 - - + -
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Residues in contact with ARG 943 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923A MSE 4.1 30.3 + - + +
926A LEU* 3.3 33.9 + - + +
927A ASP* 3.2 21.8 + - - +
930A ASP* 2.7 38.3 + - - -
939A ARG* 2.8 33.1 + - - +
940A GLU* 3.2 37.8 + - - +
942A LEU* 1.3 73.4 - - - +
944A GLN* 1.4 56.7 + - - +
946A LEU* 3.6 5.8 + - - +
947A SER* 3.1 27.7 + - - -
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Residues in contact with GLN 944 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
940A GLU 3.1 16.3 + - - +
941A GLU* 3.2 7.7 + - - +
943A ARG* 1.4 73.1 - - - +
945A GLY* 1.3 64.2 + - - +
947A SER* 2.5 41.6 + - - -
948A GLU* 3.9 11.6 + - - +
992A THR* 6.0 0.3 - - - +
996A GLN* 3.8 18.0 + - - +
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Residues in contact with GLY 945 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941A GLU 3.2 10.2 + - - -
942A LEU 3.9 1.6 - - - -
944A GLN* 1.3 75.8 - - - +
946A LEU* 1.3 59.6 + - - +
947A SER 3.5 0.5 + - - -
948A GLU* 3.6 17.9 + - - +
949A LEU* 4.6 1.0 + - - +
993A HIS* 4.0 4.7 - - - -
996A GLN* 3.5 20.2 + - - -
1000A TYR* 3.9 37.2 - - - -
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Residues in contact with LEU 946 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918A PHE* 3.4 39.9 - - + -
919A HIS* 3.0 40.6 + - - +
922A VAL* 3.7 29.2 - - + -
923A MSE 4.6 8.7 - - - -
926A LEU* 4.3 4.9 - - + -
942A LEU* 2.9 41.2 + - + +
943A ARG* 3.8 5.8 - - - +
945A GLY* 1.3 73.6 - - - +
947A SER* 1.4 61.6 + - - +
948A GLU 3.2 2.0 + - - -
949A LEU* 3.4 22.5 + - + +
950A PRO* 3.5 0.2 - - - +
1000A TYR* 4.1 10.1 - - + -
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Residues in contact with SER 947 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919A HIS* 4.7 5.2 - - - -
923A MSE 6.6 0.2 - - - -
943A ARG 3.1 13.5 + - - -
944A GLN* 2.5 35.8 + - - -
946A LEU* 1.4 76.8 - - - +
948A GLU* 1.3 64.8 + - - +
949A LEU 3.4 0.4 - - - -
950A PRO* 3.2 18.9 - - - +
951A ALA* 4.0 9.0 + - - +
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Residues in contact with GLU 948 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944A GLN* 4.3 12.2 - - - +
945A GLY 3.6 15.3 - - - +
946A LEU 3.2 0.2 - - - -
947A SER* 1.3 89.0 + - - +
949A LEU* 1.4 57.4 + - - +
951A ALA* 3.3 4.9 + - - +
952A ILE* 2.9 34.5 + - + +
989A HIS* 2.9 41.7 + - - +
992A THR* 3.3 29.3 - - + +
993A HIS* 4.0 29.4 - - + -
996A GLN* 4.3 4.2 + - - +
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Residues in contact with LEU 949 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911A LEU* 5.6 3.2 - - + +
914A LEU* 4.2 16.4 - - + -
915A ASN* 3.6 19.6 + - - +
918A PHE* 3.6 37.0 - - + -
919A HIS* 4.1 9.9 - - + -
945A GLY 4.8 0.2 - - - +
946A LEU* 3.7 21.1 - - + +
948A GLU* 1.4 75.8 - - - +
950A PRO* 1.4 64.1 - - + +
952A ILE* 3.2 10.7 + - + +
953A HIS 2.9 23.7 + - - -
993A HIS* 3.9 24.5 - - + +
1000A TYR* 4.1 1.6 - - - +
1036A LEU* 3.8 21.3 - - + -
1039A VAL* 4.8 4.3 - - + -
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Residues in contact with PRO 950 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915A ASN* 3.2 20.4 - - - +
919A HIS* 3.5 22.2 - - + +
946A LEU 3.5 8.7 - - - +
947A SER* 3.2 15.7 - - - +
949A LEU* 1.4 91.9 - - + +
951A ALA* 1.3 54.7 + - - +
953A HIS* 3.3 4.2 + - + +
954A ASP* 3.0 41.2 + - - +
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Residues in contact with ALA 951 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947A SER 4.0 6.7 + - - +
948A GLU* 3.3 12.1 + - - +
950A PRO* 1.3 79.0 - - - +
952A ILE* 1.4 57.5 + - - +
954A ASP* 3.7 7.6 + - - +
955A LEU* 3.2 25.6 + - - +
989A HIS* 3.6 41.9 - - + +
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Residues in contact with ILE 952 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A UNX 4.2 5.8 - - - -
907A TYR* 4.2 2.9 - - - +
911A LEU* 3.8 17.0 - - + -
948A GLU* 2.9 30.8 + - + +
949A LEU* 3.6 7.0 - - + +
951A ALA* 1.4 73.1 - - - +
953A HIS* 1.3 66.4 + - - +
955A LEU* 3.0 16.1 + - + +
956A HIS* 3.0 38.1 + - + -
989A HIS* 4.1 18.8 - - + +
990A HIS* 3.7 24.0 - - + +
993A HIS* 3.9 35.0 - - + +
1039A VAL* 4.5 6.5 - - + -
----------------------------------------------------------
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Residues in contact with HIS 953 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908A VAL* 4.0 6.7 + - + -
911A LEU* 3.8 16.7 - - + +
912A GLN* 3.2 56.0 + - - +
915A ASN* 3.6 31.4 + - + +
949A LEU 2.9 6.0 + - - +
950A PRO* 3.5 9.5 + - + +
952A ILE* 1.3 77.0 - - - +
954A ASP* 1.4 55.7 + - - +
956A HIS* 3.4 1.6 + - - +
957A GLN* 2.8 65.2 + - + +
----------------------------------------------------------
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Residues in contact with ASP 954 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950A PRO* 3.0 26.6 + - - +
951A ALA* 3.9 7.7 - - - +
953A HIS* 1.4 74.9 + - - +
955A LEU* 1.4 65.9 + - - +
957A GLN* 3.3 20.4 + - - +
958A GLY* 3.1 18.7 + - - -
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Residues in contact with LEU 955 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951A ALA 3.2 13.5 + - - +
952A ILE* 3.0 9.8 + - - +
954A ASP* 1.4 78.0 - - - +
956A HIS* 1.3 80.9 + - + +
958A GLY* 3.4 2.3 + - - -
959A ILE* 3.1 39.0 + - + +
983A ARG* 4.0 23.2 + - + -
986A GLY* 3.4 44.4 - - - +
987A PHE* 4.0 7.2 - - + +
989A HIS* 5.9 0.2 - - + -
990A HIS* 3.7 15.0 - - + -
----------------------------------------------------------
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Residues in contact with HIS 956 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904A GLU* 2.8 24.3 + - - +
907A TYR* 3.4 20.5 - + + -
908A VAL* 3.5 15.1 - - + +
911A LEU* 3.8 9.9 - - + -
952A ILE* 3.0 38.5 + - + +
953A HIS 4.0 0.2 - - - +
955A LEU* 1.3 78.9 - - + +
957A GLN* 1.4 66.2 + - - +
958A GLY 3.2 1.6 - - - -
959A ILE* 3.7 13.1 - - + +
960A LEU* 2.9 25.8 + - - +
987A PHE* 4.5 1.6 - + - -
990A HIS* 2.8 28.3 + - - -
1042A ARG* 4.6 0.7 - - + -
1046A TYR* 2.9 29.4 + + - -
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Residues in contact with GLN 957 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908A VAL* 3.9 18.7 - - + +
912A GLN* 4.0 10.5 + - - +
953A HIS* 2.8 54.5 + - - +
954A ASP* 3.3 25.9 + - - +
956A HIS* 1.4 73.9 - - - +
958A GLY* 1.3 57.1 + - - +
960A LEU* 3.5 4.7 - - - +
961A GLU* 3.1 26.7 + - - +
----------------------------------------------------------
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Residues in contact with GLY 958 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
954A ASP 3.1 13.0 + - - -
955A LEU 3.7 4.0 - - - -
956A HIS 3.2 0.2 - - - -
957A GLN* 1.3 73.9 - - - +
959A ILE* 1.4 58.8 + - - +
961A GLU* 3.2 8.0 + - - +
962A GLU* 3.0 29.6 + - - +
983A ARG* 3.8 14.4 + - - -
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Residues in contact with ILE 959 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904A GLU* 3.6 17.3 - - - +
955A LEU* 3.1 26.2 + - + +
956A HIS* 3.2 21.7 + - - +
958A GLY* 1.4 72.0 - - - +
960A LEU* 1.3 52.3 + - - +
962A GLU* 3.3 3.3 + - - +
963A LEU* 2.8 60.7 + - + +
979A VAL* 4.2 15.7 - - + +
980A PHE* 4.8 11.7 - - + -
983A ARG* 3.6 22.8 - - - +
987A PHE* 3.9 29.6 - - + -
1046A TYR* 4.1 4.0 - - - +
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Residues in contact with LEU 960 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901A LEU* 3.7 16.4 - - + +
904A GLU* 4.3 7.6 - - + -
905A LYS* 3.6 42.8 - - + +
908A VAL* 3.8 35.0 - - + -
956A HIS 2.9 17.9 + - - +
957A GLN* 3.5 5.6 - - - +
959A ILE* 1.3 76.2 - - - +
961A GLU* 1.3 54.3 + - - +
963A LEU* 3.2 2.9 + - - -
964A GLU* 2.7 41.5 + - + +
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Residues in contact with GLU 961 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957A GLN 3.1 14.4 + - - +
958A GLY* 3.2 10.7 + - - +
960A LEU* 1.3 75.5 - - - +
962A GLU* 1.3 60.9 + - - +
964A GLU* 3.7 5.8 + - - +
965A GLU* 3.4 22.3 + - - +
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Residues in contact with GLU 962 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958A GLY 3.0 15.9 + - - +
959A ILE 3.7 3.4 - - - +
961A GLU* 1.3 72.4 - - - +
963A LEU* 1.4 60.2 + - - +
965A GLU* 3.5 4.9 + - - +
966A ARG* 3.0 41.4 + - - +
979A VAL* 4.2 20.6 - - + -
983A ARG* 4.1 16.4 - - - +
----------------------------------------------------------
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Residues in contact with LEU 963 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900A LEU* 4.0 33.2 - - + +
901A LEU* 3.7 15.0 - - + -
904A GLU* 4.1 22.2 - - + +
959A ILE* 2.8 47.0 + - + +
960A LEU 3.7 3.6 - - - +
962A GLU* 1.4 69.0 - - - +
964A GLU* 1.4 65.3 + - - +
966A ARG* 3.3 3.0 + - - +
967A LEU* 3.1 35.3 + - + +
976A VAL* 3.9 30.5 - - + +
979A VAL* 4.8 12.6 - - + -
980A PHE* 5.3 2.9 - - + -
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Residues in contact with GLU 964 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901A LEU* 3.5 21.0 - - + +
905A LYS* 5.8 3.1 - - - -
960A LEU* 2.7 25.5 + - + +
961A GLU* 3.9 7.6 - - - +
963A LEU* 1.4 73.2 - - - +
965A GLU* 1.4 58.3 + - - +
967A LEU* 3.6 3.3 + - - +
968A SER* 3.0 25.2 + - - -
----------------------------------------------------------
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Residues in contact with GLU 965 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961A GLU 3.4 14.4 + - - +
962A GLU* 3.8 5.4 - - - +
963A LEU 3.3 0.4 - - - -
964A GLU* 1.4 76.4 - - - +
966A ARG* 1.3 64.2 + - + +
968A SER* 3.2 16.7 + - - -
969A ASN* 3.3 22.5 + - - +
----------------------------------------------------------
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Residues in contact with ARG 966 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A UNX 2.2 33.7 - - - -
962A GLU* 3.0 22.2 + - - +
963A LEU 3.9 3.8 - - - +
965A GLU* 1.3 76.9 - - + +
967A LEU* 1.3 59.8 + - - +
969A ASN* 3.6 1.1 - - - +
970A TRP* 3.5 13.1 + - - -
975A LYS* 3.0 30.1 + - - +
976A VAL* 4.3 9.2 - - + +
978A ASP* 2.7 40.1 + - - -
979A VAL* 3.4 30.0 - - - +
983A ARG* 6.0 0.2 - - - +
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Residues in contact with LEU 967 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A LEU* 4.3 14.4 - - + +
897A ALA* 3.5 39.3 - - + +
898A GLN* 3.7 30.3 - - + -
901A LEU* 3.7 26.2 - - + -
963A LEU* 3.1 30.1 + - + +
964A GLU 4.0 3.8 - - - +
966A ARG* 1.3 74.1 - - - +
968A SER* 1.3 63.4 + - - +
969A ASN 3.4 0.7 - - - -
970A TRP* 3.8 23.1 - - + +
976A VAL* 4.8 6.5 - - + -
----------------------------------------------------------
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Residues in contact with SER 968 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964A GLU 3.0 15.7 + - - -
965A GLU* 3.2 13.7 + - - -
967A LEU* 1.3 77.5 - - - +
969A ASN* 1.3 67.0 + - - +
970A TRP 3.4 2.6 + - - -
971A GLU 5.3 0.3 + - - -
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Residues in contact with ASN 969 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A UNX 3.1 10.6 - - - -
965A GLU* 3.3 17.4 + - - +
966A ARG* 3.6 0.6 + - - +
968A SER* 1.3 85.6 - - - +
970A TRP* 1.4 58.2 + - - -
971A GLU 3.3 2.7 - - - -
972A SER* 3.4 12.8 + - - +
973A GLN* 3.0 25.4 + - + +
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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