Contacts of the helix formed by residues 946 - 972 (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 PRO 946 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944G PRO 4.3 3.4 - - - +
945G ALA* 1.3 87.8 - - - +
947G PRO* 1.3 77.0 - - + +
948G GLU* 3.4 31.0 - - - +
949G GLU* 3.0 39.7 + - + +
950G TYR* 3.3 10.4 + - - -
1013G GLN* 5.2 2.0 - - - +
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Residues in contact with PRO 947 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946G PRO* 1.3 88.0 - - + +
948G GLU* 1.3 63.9 + - - +
949G GLU 3.0 2.0 + - - -
950G TYR* 3.4 32.8 - - + +
951G VAL* 3.3 29.4 + - - +
1005G GLN* 4.5 15.7 - - + +
1008G VAL* 3.8 28.7 - - + -
1013G GLN* 3.9 10.5 - - - +
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Residues in contact with GLU 948 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946G PRO* 3.4 29.0 - - + +
947G PRO* 1.3 79.3 - - - +
949G GLU* 1.3 64.7 + - + +
951G VAL* 5.6 0.4 - - - -
952G PRO* 3.5 19.4 - - - +
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Residues in contact with GLU 949 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941G LYS* 5.2 1.6 - - - +
944G PRO 4.9 1.0 - - - +
945G ALA* 3.5 14.7 - - + +
946G PRO* 3.0 39.6 + - + +
948G GLU* 1.3 85.2 - - + +
950G TYR* 1.3 60.5 + - - +
951G VAL 3.5 0.7 - - - -
952G PRO* 3.2 16.2 - - - +
953G MET* 3.4 19.5 + - + +
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Residues in contact with TYR 950 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938G MET* 5.9 0.2 - - + -
942G ILE* 3.9 19.7 - - + -
945G ALA* 3.7 15.3 - - + -
946G PRO 3.3 13.2 + - - -
947G PRO* 3.3 34.3 + - + +
949G GLU* 1.3 77.0 - - - +
951G VAL* 1.3 77.4 + - + +
953G MET* 3.2 25.4 + - + +
954G VAL* 2.8 32.1 + - + +
1001G MET* 3.9 21.1 - - + -
1004G ALA* 3.6 20.5 + - + -
1005G GLN* 3.4 22.0 - - + +
1013G GLN* 3.9 3.0 + - + -
1017G LYS* 4.0 20.6 - - + -
1020G MET* 4.4 6.1 - - + -
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Residues in contact with VAL 951 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947G PRO 3.3 15.2 + - - +
948G GLU* 5.5 0.4 - - - -
950G TYR* 1.3 79.6 - - + +
952G PRO* 1.3 67.0 - - + +
954G VAL* 3.3 1.6 + - - +
955G LYS* 2.8 32.9 + - + +
1001G MET* 3.8 26.0 - - + -
1005G GLN* 3.5 26.7 - - - +
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Residues in contact with PRO 952 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948G GLU* 3.5 22.7 - - - +
949G GLU* 3.2 13.5 - - - +
951G VAL* 1.3 95.0 - - + +
953G MET* 1.3 55.6 + - + +
955G LYS* 3.7 9.7 - - + +
956G GLU* 2.8 36.1 + - + +
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Residues in contact with MET 953 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934G ALA 4.9 1.2 - - - +
937G GLU 4.3 2.9 - - - +
938G MET* 3.9 32.0 - - + +
941G LYS* 4.0 20.9 - - + +
942G ILE* 3.9 31.0 - - + +
945G ALA* 4.6 4.3 - - + -
949G GLU* 3.4 14.4 - - + +
950G TYR* 3.2 31.0 + - + +
952G PRO* 1.3 73.2 - - + +
954G VAL* 1.3 64.6 + - - +
956G GLU* 3.4 9.6 + - - +
957G VAL* 3.2 23.9 + - - +
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Residues in contact with VAL 954 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938G MET* 3.6 23.8 - - + -
950G TYR* 2.8 21.3 + - + +
951G VAL 3.8 3.6 - - - +
953G MET* 1.3 72.5 - - - +
955G LYS* 1.3 66.9 + - - +
957G VAL* 3.1 5.7 + - - +
958G GLY* 3.0 18.4 + - - -
994G LEU* 5.1 2.9 - - + +
997G LEU* 3.9 22.4 - - + -
998G ILE* 4.5 14.8 - - + -
1001G MET* 4.0 21.8 - - + -
1020G MET* 3.6 27.8 - - + -
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Residues in contact with LYS 955 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951G VAL* 2.8 26.5 + - + +
952G PRO* 3.7 9.4 - - + +
954G VAL* 1.3 71.8 - - - +
956G GLU* 1.3 61.2 + - - +
958G GLY* 3.2 2.7 + - - +
959G LEU* 2.8 43.9 + - - +
962G ARG* 4.3 10.7 + - - +
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Residues in contact with GLU 956 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934G ALA* 4.4 11.1 - - + +
952G PRO* 2.8 22.5 + - + +
953G MET* 3.5 9.4 - - - +
955G LYS* 1.3 75.2 - - - +
957G VAL* 1.3 58.0 + - - +
959G LEU* 3.5 16.5 + - - +
960G ALA* 2.9 29.5 + - - +
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Residues in contact with VAL 957 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931G LEU* 3.7 4.7 - - + +
934G ALA* 3.7 33.4 - - + +
935G VAL* 4.1 9.6 - - + +
938G MET* 3.6 26.9 - - + -
953G MET 3.2 4.7 + - - +
954G VAL 3.1 9.5 + - - +
956G GLU* 1.3 76.2 - - - +
958G GLY* 1.3 62.5 + - - +
960G ALA* 3.0 4.8 + - - +
961G LEU* 2.8 27.7 + - - +
994G LEU* 4.6 2.2 - - + -
997G LEU* 4.1 14.6 - - + -
1027G LEU* 3.5 30.1 - - + -
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Residues in contact with GLY 958 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
954G VAL 3.0 12.9 + - - -
955G LYS* 3.2 2.2 + - - -
957G VAL* 1.3 76.5 - - - +
959G LEU* 1.3 58.1 + - - +
961G LEU* 3.4 3.8 + - - +
962G ARG* 3.0 50.5 + - - +
994G LEU* 3.8 24.4 - - - +
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Residues in contact with LEU 959 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955G LYS* 2.8 30.9 + - - +
956G GLU* 3.8 18.8 - - - +
958G GLY* 1.3 73.2 - - - +
960G ALA* 1.3 61.8 + - - +
962G ARG* 3.2 21.1 + - + +
963G THR* 2.9 40.0 + - - +
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Residues in contact with ALA 960 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927G ASN* 4.8 2.6 - - - +
930G GLY 4.6 2.2 - - - +
931G LEU* 3.8 33.9 - - + +
934G ALA* 4.3 7.6 - - + -
956G GLU 2.9 18.4 + - - +
957G VAL 3.4 4.9 - - - +
959G LEU* 1.3 76.3 - - - +
961G LEU* 1.3 58.0 + - - +
963G THR* 3.3 8.5 + - - -
964G LEU* 3.0 26.9 + - - +
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Residues in contact with LEU 961 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931G LEU* 3.9 24.4 - - + +
957G VAL 2.8 15.8 + - - +
958G GLY* 3.6 5.4 - - - +
959G LEU 3.2 0.2 - - - -
960G ALA* 1.3 77.7 - - - +
962G ARG* 1.3 58.3 + - + +
964G LEU* 3.1 4.5 + - + +
965G LEU* 2.8 38.3 + - + +
990G LEU* 3.6 55.2 - - + +
991G ASN* 3.8 12.3 - - - +
994G LEU* 3.8 29.6 - - + -
1027G LEU* 4.3 8.1 - - + -
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Residues in contact with ARG 962 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955G LYS* 4.3 14.8 + - - +
958G GLY* 3.0 40.2 + - - +
959G LEU* 3.2 21.7 + - + +
961G LEU* 1.3 77.2 - - + +
963G THR* 1.3 62.0 + - - +
965G LEU* 4.3 9.8 - - + +
966G ALA* 3.2 23.9 + - - +
991G ASN* 6.2 0.2 - - - +
994G LEU* 3.9 22.4 - - + +
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Residues in contact with THR 963 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923G LYS* 6.1 1.8 - - - -
927G ASN* 3.5 21.5 - - - +
959G LEU* 2.9 24.6 + - - +
960G ALA* 3.6 11.0 - - - -
962G ARG* 1.3 78.8 - - - +
964G LEU* 1.3 58.8 + - - +
966G ALA* 3.9 4.1 - - - +
967G THR* 3.1 28.3 + - - +
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Residues in contact with LEU 964 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924G VAL* 4.1 9.0 - - + +
927G ASN* 4.0 26.7 - - + +
928G VAL* 3.6 34.8 - - + -
931G LEU* 3.9 22.7 - - + -
960G ALA 3.0 14.3 + - - +
961G LEU* 3.5 8.3 - - + +
963G THR* 1.3 75.0 - - - +
965G LEU* 1.3 61.4 + - - +
967G THR* 3.1 3.6 + - - -
968G VAL* 2.8 48.3 + - + +
990G LEU* 4.0 22.7 - - + -
1031G ALA* 4.5 4.9 - - + -
1034G LEU* 4.9 4.5 - - + -
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Residues in contact with LEU 965 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961G LEU* 2.8 37.2 + - + +
962G ARG* 4.3 9.6 - - + +
964G LEU* 1.3 73.2 - - + +
966G ALA* 1.3 57.5 + - - +
968G VAL* 3.3 3.0 + - - -
969G ASP* 2.9 35.7 + - - +
987G GLN* 3.6 42.0 + - + +
990G LEU* 3.9 22.0 - - + -
991G ASN* 3.2 34.3 - - - +
1034G LEU* 5.0 1.8 - - + -
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Residues in contact with ALA 966 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962G ARG 3.2 16.9 + - - +
963G THR* 3.9 5.8 - - - +
964G LEU 3.2 0.8 - - - -
965G LEU* 1.3 79.2 - - - +
967G THR* 1.3 58.4 + - - +
969G ASP* 3.2 9.5 + - - +
970G GLU* 2.8 29.9 + - - +
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Residues in contact with THR 967 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923G LYS* 3.3 44.7 + - + +
924G VAL* 3.9 23.6 - - + +
927G ASN* 2.6 25.2 + - - +
963G THR* 3.1 6.9 + - - +
964G LEU* 3.1 8.1 + - - -
966G ALA* 1.3 77.8 - - - +
968G VAL* 1.3 58.4 + - - +
970G GLU* 3.2 12.6 + - - +
971G THR* 2.8 34.4 + - - +
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Residues in contact with VAL 968 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924G VAL* 4.8 4.5 - - + -
964G LEU* 2.8 33.8 + - + +
965G LEU* 3.6 8.5 - - - +
967G THR* 1.3 73.8 - - - +
969G ASP* 1.3 59.8 + - - +
971G THR* 2.9 9.0 + - - +
972G ILE* 2.9 33.8 + - + +
983G ILE* 3.7 20.4 - - + -
987G GLN* 3.4 28.5 - - + +
1034G LEU* 3.7 21.3 - - + -
1038G ILE* 4.1 20.0 - - + -
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Residues in contact with ASP 969 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965G LEU* 2.9 19.0 + - - +
966G ALA* 3.5 10.8 - - - +
968G VAL* 1.3 74.4 - - - +
970G GLU* 1.3 61.3 + - - +
972G ILE* 3.6 13.5 + - - +
973G PRO* 3.4 18.2 - - - +
987G GLN* 2.6 29.0 + - - +
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Residues in contact with GLU 970 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923G LYS* 3.2 30.1 + - - +
966G ALA 2.8 16.3 + - - +
967G THR* 3.3 16.4 - - + +
968G VAL 3.1 0.2 - - - -
969G ASP* 1.3 73.7 - - - +
971G THR* 1.3 59.9 + - - +
973G PRO* 3.7 9.7 - - - +
974G ALA* 5.4 1.0 + - - +
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Residues in contact with THR 971 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924G VAL* 3.7 21.4 - - + +
967G THR* 2.8 21.4 + - - +
968G VAL* 2.9 9.9 + - - -
970G GLU* 1.3 78.7 - - - +
972G ILE* 1.3 64.4 + - - +
973G PRO* 3.4 1.6 - - - -
974G ALA* 3.1 19.6 + - + +
975G LEU* 3.4 28.0 - - + +
1038G ILE* 4.8 9.4 - - + -
1042G ARG* 5.1 8.2 + - - +
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Residues in contact with ILE 972 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968G VAL* 2.9 17.5 + - + +
969G ASP* 3.6 21.1 - - - +
971G THR* 1.3 76.3 - - - +
973G PRO* 1.3 71.9 - - + +
975G LEU* 3.0 23.8 + - + +
980G HIS* 3.1 48.9 + - + +
983G ILE* 4.0 20.6 - - + -
984G GLU* 5.3 2.9 - - + +
987G GLN* 3.5 24.9 - - - +
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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