Contacts of the helix formed by residues 949 - 972 (chain F) 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 GLU 949 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941E LYS* 3.1 32.9 + - - +
946F PRO* 2.9 41.6 + - + +
947F PRO 3.1 1.0 + - - -
948F GLU* 1.3 72.4 - - - +
950F TYR* 1.3 62.8 + - - +
951F VAL 3.1 2.5 - - - -
952F PRO* 3.2 22.9 - - + +
953F MET* 3.2 17.0 - - + +
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Residues in contact with TYR 950 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938E MET* 6.2 0.2 - - + -
942E ILE* 3.7 22.5 - - + +
945F ALA* 3.0 45.8 + - + +
946F PRO 4.2 1.6 - - - -
947F PRO* 3.8 25.7 - - + +
948F GLU 3.2 4.0 - - - +
949F GLU* 1.3 77.5 - - - +
951F VAL* 1.3 64.8 + - + +
953F MET* 2.9 32.2 + - + +
954F VAL* 3.0 13.7 + - + +
1001F MET* 3.7 22.2 - - + -
1004F ALA* 4.0 9.6 - - + -
1005F GLN* 5.0 0.4 - - + -
1017F LYS* 3.3 28.2 - - + +
1020F MET* 3.6 35.4 - - + -
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Residues in contact with VAL 951 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ASP* 4.6 1.1 - - - +
63B ASP* 3.8 32.3 - - + +
64B LYS* 4.0 27.6 - - + +
67B LEU* 4.4 10.8 - - + +
948F GLU* 3.6 14.4 - - - +
950F TYR* 1.3 76.2 - - - +
952F PRO* 1.3 70.9 - - + +
954F VAL* 3.5 1.9 + - - +
955F LYS* 3.0 21.7 + - - +
1001F MET* 4.0 18.4 - - + -
1005F GLN* 3.6 24.9 - - - +
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Residues in contact with PRO 952 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ASP* 3.3 28.7 - - - +
948F GLU 4.2 3.1 - - - +
949F GLU* 3.2 23.3 - - + +
951F VAL* 1.3 94.7 - - + +
953F MET* 1.3 61.8 - - + +
955F LYS* 3.4 13.9 + - + +
956F GLU* 3.1 32.6 + - - +
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Residues in contact with MET 953 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934E ALA 5.0 0.7 - - - +
937E GLU* 4.9 2.2 - - + +
938E MET* 3.8 34.4 - - + +
941E LYS* 3.5 53.6 - - + +
942E ILE* 5.0 0.2 - - - -
945F ALA* 5.5 2.2 - - + -
949F GLU* 3.2 32.1 - - + +
950F TYR* 2.9 30.2 + - + +
952F PRO* 1.3 80.9 - - + +
954F VAL* 1.3 62.0 + - - +
956F GLU* 3.4 7.9 + - - +
957F VAL* 3.3 24.1 + - - +
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Residues in contact with VAL 954 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 3.7 21.4 - - + +
938E MET* 3.7 23.1 - - + -
950F TYR* 3.0 11.0 + - + +
951F VAL 4.1 1.1 - - - +
953F MET* 1.3 72.6 - - - +
955F LYS* 1.3 65.5 + - - +
957F VAL* 3.2 9.2 + - - +
958F GLY* 3.0 18.0 + - - -
994F LEU* 4.7 2.6 - - + +
997F LEU* 4.0 20.4 - - + -
998F ILE* 4.1 15.9 - - + -
1001F MET* 3.7 32.5 - - + -
1020F MET* 4.2 7.9 - - + -
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Residues in contact with LYS 955 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 4.1 20.8 + - - -
63B ASP* 2.9 32.3 + - - +
66B LEU* 3.6 37.7 - - + +
67B LEU* 3.8 24.6 - - + +
70B THR* 4.4 1.0 - - - +
951F VAL 3.0 18.5 + - - +
952F PRO* 3.5 18.8 - - + +
953F MET 3.2 0.2 - - - -
954F VAL* 1.3 77.5 - - - +
956F GLU* 1.3 72.5 + - - +
958F GLY* 2.9 4.0 + - - -
959F LEU* 2.8 41.6 + - + +
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Residues in contact with GLU 956 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A THR* 5.1 14.2 - - + +
73A ASN* 5.8 0.3 - - - +
934E ALA* 3.9 12.9 - - + +
937E GLU* 5.4 8.0 - - - +
952F PRO* 3.1 19.1 + - - +
953F MET* 3.8 8.0 - - - +
954F VAL 3.3 0.2 - - - -
955F LYS* 1.3 93.2 + - - +
957F VAL* 1.3 62.0 + - - +
959F LEU* 3.8 11.0 - - + +
960F ALA* 3.1 25.6 + - - +
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Residues in contact with VAL 957 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931E LEU* 3.6 10.2 - - + +
934E ALA* 3.8 33.4 - - + +
935E VAL* 4.0 15.9 - - + +
938E MET* 4.4 11.9 - - + -
953F MET 3.3 14.6 + - - +
954F VAL* 3.2 13.6 + - - +
955F LYS 3.1 0.6 - - - -
956F GLU* 1.3 78.7 - - - +
958F GLY* 1.3 57.3 + - - +
961F LEU* 3.0 27.2 + - + +
994F LEU* 4.4 6.3 - - + -
997F LEU* 4.2 8.7 - - + -
1027F LEU* 4.1 27.4 - - + -
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Residues in contact with GLY 958 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B THR* 3.6 18.4 - - - -
954F VAL 3.0 9.6 + - - -
955F LYS 2.9 7.1 + - - -
957F VAL* 1.3 77.8 - - - +
959F LEU* 1.3 61.5 + - - +
961F LEU* 3.4 3.8 + - - +
962F ARG* 3.1 21.8 + - - +
994F LEU* 3.8 28.4 - - - +
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Residues in contact with LEU 959 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 4.7 26.2 - - + -
69A TYR* 5.1 5.4 - - + -
70A THR* 3.6 33.0 - - + -
66B LEU* 4.9 13.9 - - + +
69B TYR* 5.0 4.3 - - + -
70B THR* 3.7 19.7 - - + -
955F LYS* 2.8 48.3 + - + +
956F GLU* 4.0 8.7 - - + +
957F VAL 3.3 0.2 - - - -
958F GLY* 1.3 70.4 - - - +
960F ALA* 1.3 65.7 + - - +
962F ARG* 3.0 17.8 + - + +
963F THR* 3.3 17.6 + - - +
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Residues in contact with ALA 960 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A THR* 5.8 0.2 - - - +
927E ASN* 4.5 3.1 - - - +
930E GLY 3.9 23.3 - - - +
931E LEU* 4.0 17.0 - - + +
934E ALA* 4.4 4.7 - - + -
956F GLU 3.1 18.5 + - - +
957F VAL 4.0 2.7 - - - +
959F LEU* 1.3 76.2 - - - +
961F LEU* 1.3 59.5 + - - +
963F THR* 3.2 17.5 + - - -
964F LEU* 3.6 12.1 + - - +
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Residues in contact with LEU 961 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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931E LEU* 3.7 28.2 - - + +
957F VAL* 3.0 17.9 + - + +
958F GLY 3.6 5.6 - - - +
959F LEU 3.1 0.4 - - - -
960F ALA* 1.3 75.5 - - - +
962F ARG* 1.3 64.8 + - - +
964F LEU* 3.3 5.1 + - + +
965F LEU* 3.0 40.0 + - + +
990F LEU* 3.8 43.5 - - + +
991F ASN* 4.4 8.5 - - - +
994F LEU* 3.8 29.6 - - + -
1027F LEU* 4.8 6.7 - - + -
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Residues in contact with ARG 962 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 5.9 0.6 - - - +
63A ASP* 5.8 4.3 - - - +
69B TYR* 3.7 41.6 + - - -
70B THR* 3.4 32.4 + - - +
72B TYR* 2.0 38.0 + - - +
73B ASN* 3.9 10.5 + - - +
74B GLU 4.5 2.6 + - - +
76B HIS* 5.3 8.9 - - - -
958F GLY 3.1 7.5 + - - +
959F LEU* 3.0 13.5 + - + +
961F LEU* 1.3 77.6 - - - +
963F THR* 1.3 65.2 + - + +
965F LEU* 3.2 9.3 + - + +
966F ALA* 2.9 25.8 + - + +
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Residues in contact with THR 963 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ASP* 4.9 22.9 - - + +
66A LEU* 6.5 0.7 - - + -
67A LEU* 4.9 20.4 - - + +
927E ASN* 4.1 14.1 + - - -
959F LEU 3.3 11.4 + - - +
960F ALA* 3.2 15.8 + - - -
962F ARG* 1.3 75.9 - - + +
964F LEU* 1.3 53.9 + - - +
966F ALA* 3.9 5.6 - - - +
967F THR* 2.7 38.1 + - - -
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Residues in contact with LEU 964 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924E VAL* 4.1 8.7 - - + +
927E ASN* 3.6 29.1 + - + +
928E VAL* 3.7 33.4 - - + +
931E LEU* 3.7 26.9 - - + -
960F ALA 3.6 10.3 + - - +
961F LEU* 3.3 9.8 + - + +
962F ARG 3.1 0.6 - - - -
963F THR* 1.3 81.6 + - - +
965F LEU* 1.3 58.8 + - + +
967F THR* 3.2 3.9 + - - -
968F VAL* 2.9 45.0 + - + +
990F LEU* 4.4 7.4 - - + -
1031F ALA* 5.0 0.9 - - + -
1034F LEU* 4.1 19.5 - - + -
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Residues in contact with LEU 965 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ASN* 5.1 2.5 - - - +
961F LEU* 3.0 39.4 + - + +
962F ARG* 3.8 7.2 - - + +
964F LEU* 1.3 77.6 - - + +
966F ALA* 1.3 58.0 + - - +
968F VAL* 3.2 3.9 + - + +
969F ASP* 2.8 36.4 + - - +
987F GLN* 3.7 41.4 + - + +
990F LEU* 4.6 8.1 - - + -
991F ASN* 3.2 33.9 - - - +
1034F LEU* 4.7 6.3 - - + -
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Residues in contact with ALA 966 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ASP* 4.0 23.8 - - - +
962F ARG* 2.9 17.4 + - + +
963F THR* 4.0 6.7 - - - +
965F LEU* 1.3 73.4 - - - +
967F THR* 1.3 64.2 + - - +
969F ASP* 3.4 10.8 + - - +
970F GLU* 3.3 24.7 + - - +
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Residues in contact with THR 967 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923E LYS* 3.7 32.6 + - + -
924E VAL* 4.1 21.8 - - + +
927E ASN* 2.6 28.1 + - + +
963F THR* 2.7 20.2 + - - -
964F LEU* 3.2 5.8 + - + -
966F ALA* 1.3 76.6 - - - +
968F VAL* 1.3 56.8 + - + +
970F GLU* 3.3 17.2 + - - +
971F THR* 2.6 36.8 + - - +
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Residues in contact with VAL 968 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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924E VAL* 4.5 6.3 - - + -
964F LEU* 2.9 33.5 + - + +
965F LEU* 3.2 7.6 + - + +
967F THR* 1.3 73.9 - - - +
969F ASP* 1.3 62.0 + - - +
971F THR* 2.9 7.4 + - - -
972F ILE* 2.8 48.3 + - + +
983F ILE* 3.9 14.8 - - + -
987F GLN* 3.4 22.4 - - + +
1034F LEU* 4.4 9.4 - - + -
1038F ILE* 3.9 23.8 - - + -
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Residues in contact with ASP 969 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965F LEU* 2.8 21.8 + - - +
966F ALA* 3.7 10.1 - - - +
967F THR 3.3 0.2 - - - -
968F VAL* 1.3 77.8 - - - +
970F GLU* 1.3 59.7 + - - +
972F ILE* 4.4 7.6 - - - +
973F PRO* 3.5 17.5 - - - +
987F GLN* 3.1 24.9 + - - +
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Residues in contact with GLU 970 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923E LYS* 5.3 5.5 + - - +
966F ALA 3.3 10.2 + - - +
967F THR* 3.3 27.6 + - - +
969F ASP* 1.3 78.1 - - - +
971F THR* 1.3 62.0 + - - +
973F PRO* 4.0 8.6 - - - +
974F ALA* 5.3 2.4 + - - +
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Residues in contact with THR 971 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923E LYS* 6.0 0.3 - - - +
924E VAL* 4.6 15.2 - - + +
967F THR* 2.6 29.6 + - - +
968F VAL* 2.9 9.7 + - - -
970F GLU* 1.3 81.8 - - - +
972F ILE* 1.3 67.2 + - + +
973F PRO* 3.4 0.9 - - - -
974F ALA* 3.1 22.4 + - + +
975F LEU* 3.9 21.3 + - + +
1038F ILE* 5.6 4.0 - - + -
1042F ARG* 5.5 7.6 - - - +
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Residues in contact with ILE 972 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968F VAL* 2.8 41.4 + - + +
969F ASP* 4.4 7.2 - - - +
971F THR* 1.3 75.0 - - - +
973F PRO* 1.3 66.2 - - + +
975F LEU* 2.8 38.2 + - + +
980F HIS* 3.5 34.8 + - + +
983F ILE* 3.9 24.0 - - + -
984F GLU* 4.3 17.3 - - + +
987F GLN* 4.0 15.5 - - - +
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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