Contacts of the helix formed by residues 979 - 1007 (chain G) in PDB entry 5F28
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 979 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
975G LEU* 3.8 8.1 - - - +
976G PRO* 2.7 26.8 + - + +
977G ALA 3.1 0.2 - - - -
978G SER* 1.3 87.2 - - - +
980G HIS* 1.3 69.9 + - - +
981G ARG 3.2 3.4 + - - -
982G GLU* 3.3 10.9 + - - +
983G ILE* 3.1 40.1 + - - +
1037G VAL* 5.6 4.3 - - + +
1041G ALA* 3.9 23.5 - - + +
1044G LYS* 6.0 4.5 - - + +
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Residues in contact with HIS 980 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972G ILE* 3.1 44.1 + - + +
973G PRO* 4.8 5.8 - - + -
975G LEU* 3.1 26.8 + - + -
976G PRO 3.1 14.5 + - - -
977G ALA* 3.3 23.5 + - + +
979G THR* 1.3 84.1 - - - +
981G ARG* 1.3 61.3 + - - +
983G ILE* 4.2 7.4 - - + +
984G GLU* 3.1 25.3 + - - +
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Residues in contact with ARG 981 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
977G ALA 4.8 1.6 + - - -
978G SER 4.8 4.4 + - - +
979G THR 3.2 0.8 - - - -
980G HIS* 1.3 76.6 - - - +
982G GLU* 1.3 65.7 + - - +
984G GLU* 3.2 23.2 + - - +
985G MET* 3.0 43.2 + - + +
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Residues in contact with GLU 982 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978G SER 5.3 1.7 + - - +
979G THR* 3.3 13.8 + - - +
981G ARG* 1.3 79.8 - - - +
983G ILE* 1.3 57.7 + - - +
985G MET* 3.5 8.5 + - + +
986G ALA* 3.0 26.8 + - + +
1037G VAL* 4.1 32.4 - - + +
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Residues in contact with ILE 983 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968G VAL* 3.7 22.9 - - + -
972G ILE* 4.0 10.3 - - + -
975G LEU* 3.6 31.0 - - + -
979G THR* 3.1 29.6 + - - +
980G HIS* 4.2 6.3 - - + +
981G ARG 3.2 0.2 - - - -
982G GLU* 1.3 73.9 - - - +
984G GLU* 1.3 59.2 + - - +
985G MET 3.1 1.3 - - - -
986G ALA* 3.2 5.6 + - - +
987G GLN* 2.8 46.5 + - - +
1034G LEU* 3.9 10.8 - - + -
1037G VAL* 3.9 21.8 - - + -
1038G ILE* 4.2 10.1 - - + -
1041G ALA* 5.0 2.9 - - + -
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Residues in contact with GLU 984 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972G ILE* 5.3 2.4 - - + +
980G HIS 3.1 16.9 + - - +
981G ARG* 3.2 33.1 + - - +
983G ILE* 1.3 77.7 - - - +
985G MET* 1.3 68.9 + - + +
987G GLN* 3.4 15.2 + - - +
988G LYS* 3.0 26.7 + - - +
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Residues in contact with MET 985 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981G ARG* 3.0 41.8 + - + +
982G GLU* 3.6 8.5 - - + +
983G ILE 3.1 0.2 - - - -
984G GLU* 1.3 85.3 - - + +
986G ALA* 1.3 60.4 + - - +
988G LYS* 3.2 33.6 + - + +
989G LEU* 2.9 27.7 + - - +
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Residues in contact with ALA 986 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982G GLU* 3.0 18.6 + - + +
983G ILE 3.2 4.5 + - - +
985G MET* 1.3 75.7 - - - +
987G GLN* 1.3 62.5 + - - +
989G LEU* 3.2 12.3 + - + +
990G LEU* 3.1 28.7 + - - +
1030G ASP* 5.6 2.1 - - - +
1033G ASN* 6.3 1.1 - - + -
1034G LEU* 3.7 31.9 - - + +
1037G VAL* 5.8 4.9 - - + -
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Residues in contact with GLN 987 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965G LEU* 3.6 33.9 + - + +
968G VAL* 3.4 29.8 - - + +
969G ASP* 2.6 31.0 + - - +
972G ILE* 3.5 17.0 - - - +
983G ILE 2.8 22.3 + - - +
984G GLU* 3.4 16.1 - - - +
986G ALA* 1.3 72.6 - - - +
988G LYS* 1.3 65.6 + - - +
990G LEU* 3.3 12.5 + - - +
991G ASN* 3.3 19.1 + - - -
1034G LEU* 4.2 5.4 - - + -
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Residues in contact with LYS 988 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984G GLU 3.0 18.9 + - - +
985G MET* 3.4 32.4 - - + +
987G GLN* 1.3 75.0 - - - +
989G LEU* 1.3 63.5 + - - +
991G ASN* 3.4 9.7 + - - +
992G SER* 3.1 22.7 + - - -
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Residues in contact with LEU 989 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985G MET 2.9 13.4 + - - +
986G ALA* 3.2 13.2 + - + +
988G LYS* 1.3 76.7 - - - +
990G LEU* 1.3 58.6 + - + +
992G SER* 3.2 10.3 + - - +
993G ASP* 2.8 44.8 + - - +
1030G ASP* 3.2 30.5 - - + +
1033G ASN* 6.2 0.9 - - - +
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Residues in contact with LEU 990 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961G LEU* 3.6 29.5 - - + +
964G LEU* 4.0 11.0 - - + -
965G LEU* 3.9 17.3 - - + -
986G ALA 3.1 15.9 + - - +
987G GLN 3.7 6.3 - - - +
988G LYS 3.3 0.4 - - - -
989G LEU* 1.3 77.3 - - - +
991G ASN* 1.3 56.5 + - - +
993G ASP* 3.3 0.9 + - - -
994G LEU* 2.9 25.6 + - - +
1027G LEU* 3.4 25.4 - - + +
1030G ASP* 3.6 41.5 - - + +
1031G ALA* 3.6 9.0 - - + +
1034G LEU* 3.9 23.8 - - + -
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Residues in contact with ASN 991 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961G LEU* 3.8 6.9 - - - +
965G LEU* 3.2 28.0 - - - +
987G GLN 3.3 12.3 + - - -
988G LYS* 3.7 10.5 - - + +
989G LEU 3.3 0.2 - - - -
990G LEU* 1.3 77.4 - - - +
992G SER* 1.3 56.2 + - - +
994G LEU* 3.2 12.5 + - + +
995G GLY* 2.9 24.9 + - - -
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Residues in contact with SER 992 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
988G LYS* 3.1 17.0 + - - -
989G LEU* 3.5 17.1 - - - +
991G ASN* 1.3 77.0 - - - +
993G ASP* 1.3 64.7 + - - +
995G GLY* 3.2 3.3 + - - +
996G GLU* 3.0 21.9 + - - +
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Residues in contact with ASP 993 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989G LEU* 2.8 32.1 + - - +
990G LEU* 3.7 5.2 - - - +
992G SER* 1.3 78.0 + - - +
994G LEU* 1.3 62.0 + - - +
996G GLU* 3.2 8.7 + - - +
997G LEU* 3.1 22.9 + - - +
1023G ALA 4.4 7.8 - - - +
1026G ALA* 3.3 24.3 - - - +
1027G LEU* 3.7 23.1 + - + +
1030G ASP* 2.7 22.8 - - - +
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Residues in contact with LEU 994 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
954G VAL* 5.1 3.1 - - + +
957G VAL* 4.6 11.0 - - + -
958G GLY* 3.8 26.2 - - - +
961G LEU* 3.8 23.1 - - + -
962G ARG* 3.9 25.4 - - + +
990G LEU 2.9 14.2 + - - +
991G ASN* 3.2 14.6 + - - +
993G ASP* 1.3 76.8 - - - +
995G GLY* 1.3 59.1 + - - +
997G LEU* 3.4 10.9 + - + +
998G ILE* 3.2 40.4 + - + +
1027G LEU* 4.2 5.3 - - + +
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Residues in contact with GLY 995 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991G ASN 2.9 13.8 + - - -
992G SER* 3.2 4.9 + - - -
994G LEU* 1.3 77.4 - - - +
996G GLU* 1.3 58.1 + - - +
998G ILE* 3.4 9.7 + - - +
999G SER* 3.0 30.8 + - - -
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Residues in contact with GLU 996 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1018F LYS* 5.8 3.9 + - - -
992G SER 3.0 12.9 + - - +
993G ASP* 3.2 11.6 + - - +
995G GLY* 1.3 75.2 - - - +
997G LEU* 1.3 65.2 + - - +
999G SER* 3.2 10.4 + - - -
1000G LYS* 3.0 48.1 + - + +
1023G ALA* 4.2 15.7 - - + -
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Residues in contact with LEU 997 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938G MET* 4.0 17.7 - - + -
954G VAL* 3.9 26.2 - - + -
957G VAL* 4.1 18.4 - - + -
993G ASP 3.1 12.9 + - - +
994G LEU* 3.7 14.1 - - + +
996G GLU* 1.3 76.0 - - - +
998G ILE* 1.3 56.9 + - - +
1000G LYS* 3.4 2.5 + - - +
1001G MET* 2.9 26.3 + - - +
1020G MET* 3.4 46.7 - - + +
1023G ALA* 3.8 13.4 - - + +
1024G ALA* 4.2 14.8 - - + +
1027G LEU* 5.4 2.9 - - + -
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Residues in contact with ILE 998 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
954G VAL* 4.5 13.7 - - + -
994G LEU* 3.2 37.5 + - + +
995G GLY* 3.8 8.1 - - - +
997G LEU* 1.3 74.2 - - - +
999G SER* 1.3 60.5 + - - +
1001G MET* 3.0 17.2 + - + +
1002G LYS* 2.9 66.0 + - + +
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Residues in contact with SER 999 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025F HIS* 3.8 21.2 + - - -
995G GLY 3.0 19.7 + - - -
996G GLU* 3.2 16.7 + - - -
998G ILE* 1.3 78.1 - - - +
1000G LYS* 1.3 61.6 + - - +
1002G LYS* 3.7 5.8 + - - +
1003G LEU* 3.4 22.0 + - - +
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Residues in contact with LYS1000 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943E GLN* 6.1 3.1 - - - +
1021F LEU* 4.9 7.3 + - - +
1025F HIS* 3.1 35.4 + - + +
996G GLU* 3.0 38.4 + - - +
997G LEU* 3.9 2.5 - - - +
999G SER* 1.3 73.9 - - - +
1001G MET* 1.3 62.6 + - - +
1003G LEU* 4.0 7.0 - - + +
1004G ALA* 3.2 22.9 + - - +
1016G TYR* 3.9 6.4 - - + +
1019G GLN* 2.9 48.0 + - + +
1020G MET* 3.6 26.3 - - + +
1023G ALA* 4.7 3.6 - - + -
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Residues in contact with MET1001 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950G TYR* 3.9 13.3 + - + -
951G VAL* 3.8 29.6 - - + -
954G VAL* 4.0 25.8 - - + -
997G LEU 2.9 17.7 + - - +
998G ILE* 3.0 21.5 + - + +
1000G LYS* 1.3 75.2 - - - +
1002G LYS* 1.3 97.8 + - + +
1004G ALA* 3.2 5.5 + - - +
1005G GLN* 3.2 24.3 + - - +
1020G MET* 3.6 27.8 - - + +
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Residues in contact with LYS1002 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998G ILE* 2.9 36.4 + - + +
999G SER* 4.1 5.8 - - - +
1001G MET* 1.3 94.6 - - + +
1003G LEU* 1.3 59.1 + - - +
1005G GLN* 3.0 37.5 + - - +
1006G GLN* 3.1 21.0 + - - +
----------------------------------------------------------
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Residues in contact with LEU1003 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025F HIS* 3.5 34.3 - - + +
1028F ALA* 4.5 9.0 - - + -
1029F VAL* 4.3 14.4 - - + +
999G SER 3.4 14.4 + - - +
1000G LYS* 4.0 7.2 - - + +
1001G MET 3.2 0.6 - - - -
1002G LYS* 1.3 77.2 - - - +
1004G ALA* 1.3 59.4 + - - +
1006G GLN* 3.0 39.2 + - - +
1007G TYR* 3.4 34.7 + - + -
1016G TYR* 3.4 40.2 - - + +
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Residues in contact with ALA1004 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950G TYR* 3.6 12.0 + - + +
1000G LYS 3.2 18.4 + - - +
1001G MET 3.2 5.8 + - - +
1003G LEU* 1.3 75.8 - - - +
1005G GLN* 1.3 58.6 + - - +
1007G TYR 3.9 1.6 + - - +
1008G VAL 3.8 5.4 + - - -
1013G GLN* 3.5 31.7 - - + +
1016G TYR* 3.7 25.0 - - + +
1017G LYS* 4.3 3.6 - - + +
1020G MET* 4.0 16.8 - - - -
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Residues in contact with GLN1005 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947G PRO* 4.5 11.7 - - + +
950G TYR* 3.4 18.3 - - + +
951G VAL* 3.5 30.3 - - - +
1001G MET* 3.2 14.7 + - - +
1002G LYS* 3.0 31.0 + - - +
1004G ALA* 1.3 75.9 - - - +
1006G GLN* 1.3 64.9 + - + +
1007G TYR 3.1 3.3 + - - -
1008G VAL* 3.2 25.9 + - - +
----------------------------------------------------------
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Residues in contact with GLN1006 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1029F VAL* 4.4 20.3 - - - +
1032F LYS* 2.8 58.2 + - + +
1002G LYS* 3.1 14.6 + - - +
1003G LEU* 3.0 33.2 + - - +
1005G GLN* 1.3 75.4 - - + +
1007G TYR* 1.3 68.7 + - + +
1008G VAL* 3.5 1.4 + - - +
1009G MET 5.4 0.3 + - - -
1010G THR* 5.4 0.7 - - - +
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Residues in contact with TYR1007 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928E VAL* 5.0 6.3 - - + +
929E THR* 6.0 0.9 - - - -
932E VAL* 3.2 24.8 - - + +
1028F ALA* 3.0 25.9 + - + -
1032F LYS* 3.8 20.8 + - + +
1003G LEU* 3.4 37.7 + - + +
1004G ALA 3.9 5.1 + - - +
1005G GLN 3.1 0.6 - - - -
1006G GLN* 1.3 86.3 - - + +
1008G VAL* 1.3 61.8 + - - +
1009G MET 3.1 3.1 - - - +
1010G THR* 3.0 35.2 + - + +
1012G LEU* 3.6 39.3 - - + +
1013G GLN* 3.2 17.9 - - - +
1016G TYR* 3.8 14.8 - + + -
----------------------------------------------------------
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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