Contacts of the helix formed by residues 91 - 114 (chain 2) in PDB entry 5LN3
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 91 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902 GLY* 1.4 70.3 - - - -
922 ALA* 1.3 66.4 - - - +
932 ALA 3.8 4.3 - - - +
942 ASP* 3.3 38.2 + - - +
952 THR* 2.9 25.0 + - - -
1382 GLY* 3.0 17.7 + - - -
993 ARG* 4.0 11.2 - - - +
1273 ILE* 4.0 13.7 - - + -
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Residues in contact with ALA 92 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762 LYS* 4.3 20.2 + - - +
902 GLY 3.3 5.8 + - - +
912 THR* 1.3 74.2 - - - +
932 ALA* 1.3 57.0 + - - +
952 THR* 3.2 12.7 + - - -
962 ASP* 2.8 25.3 + - - +
1273 ILE* 4.6 3.4 - - + +
1293 CYS* 3.8 23.8 - - + -
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Residues in contact with ALA 93 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912 THR* 3.4 0.6 - - + -
922 ALA* 1.3 74.4 - - - +
942 ASP* 1.3 63.1 + - - +
962 ASP* 2.8 29.6 - - - +
972 MET* 3.5 8.0 + - - +
963 TYR* 5.0 4.2 - - + -
993 ARG* 4.1 15.2 + - - +
1273 ILE* 3.1 53.0 - - + +
1283 GLY 4.7 0.4 - - - -
1293 CYS* 3.8 6.6 - - - +
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Residues in contact with ASP 94 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912 THR* 3.3 26.9 + - - +
932 ALA* 1.3 78.6 - - - +
952 THR* 1.3 62.5 + - - +
972 MET* 3.3 12.5 + - - +
982 THR* 3.4 15.5 + - - +
1362 TYR* 3.7 6.3 - - - +
1372 ILE* 3.5 46.5 - - + +
1382 GLY 3.3 16.6 + - - +
1392 ALA* 4.6 4.5 - - + -
963 TYR* 5.5 0.5 + - - -
993 ARG* 3.2 29.9 + - - +
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Residues in contact with THR 95 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762 LYS* 3.9 11.3 + - - +
782 HIS* 3.8 28.0 - - + +
882 GLY* 3.8 20.6 - - - -
892 ALA 3.6 20.1 + - - -
912 THR 2.9 15.4 + - - -
922 ALA 3.2 9.1 + - - -
942 ASP* 1.3 73.4 - - - +
962 ASP* 1.4 66.2 + - - +
982 THR* 3.2 10.7 - - - +
992 THR* 3.0 25.8 + - - +
1392 ALA* 3.7 8.4 - - - +
1412 LEU* 4.7 6.3 - - + -
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Residues in contact with ASP 96 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762 LYS* 5.7 2.9 - - - +
782 HIS* 6.0 4.5 - - + -
922 ALA 2.8 20.1 + - - +
932 ALA* 2.8 27.7 - - - +
952 THR* 1.4 77.0 - - - +
972 MET* 1.4 71.8 + - - +
992 THR* 3.2 8.3 + - - +
1002 GLN* 3.2 22.9 + - - +
963 TYR* 5.7 2.4 - - - -
1283 GLY 5.0 3.6 - - - +
1293 CYS* 3.5 17.9 - - - +
1303 PRO* 4.4 8.9 - - + +
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Residues in contact with MET 97 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932 ALA 3.7 9.2 - - - +
942 ASP* 3.3 11.4 + - - +
952 THR 3.3 0.4 - - - -
962 ASP* 1.4 82.6 + - - +
982 THR* 1.3 65.9 + - - +
1002 GLN* 3.3 6.7 + - - +
1012 LEU* 3.1 47.1 + - + +
1292 MET* 5.4 3.4 - - + -
1332 TYR* 4.3 17.7 - - + +
963 TYR* 3.4 47.1 - - + +
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Residues in contact with THR 98 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942 ASP 3.4 10.2 + - - +
952 THR* 3.2 20.6 - - - +
972 MET* 1.3 81.1 - - - +
992 THR* 1.3 63.1 + - - +
1012 LEU* 3.8 5.4 - - - +
1022 ILE* 3.0 25.0 + - - +
1262 LEU* 3.2 24.3 - - + +
1292 MET* 3.5 28.6 - - + +
1372 ILE* 6.3 2.2 - - + -
1392 ALA* 5.4 2.2 - - + -
1412 LEU* 4.5 25.6 - - + -
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Residues in contact with THR 99 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782 HIS* 3.9 37.3 - - + -
792 PHE 4.2 9.0 - - - +
802 ILE* 4.0 11.6 - - + +
862 CYS* 4.2 9.3 - - - -
952 THR* 3.0 15.5 + - - +
962 ASP* 3.2 13.5 + - - +
982 THR* 1.3 77.2 - - - +
1002 GLN* 1.4 60.5 + - - +
1022 ILE* 3.5 9.5 - - - +
1032 SER* 3.1 29.8 + - - -
1412 LEU* 5.1 0.5 - - - +
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Residues in contact with GLN 100 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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962 ASP 3.2 8.7 + - - +
972 MET* 3.6 10.2 - - - +
992 THR* 1.4 80.5 - - + +
1012 LEU* 1.3 64.1 + - - +
1032 SER* 3.9 4.9 - - - -
1042 SER* 3.0 25.2 + - - +
933 ASN* 5.3 2.8 - - - +
99B LEU* 2.8 38.4 + - + +
100B VAL* 3.5 23.1 + - - +
102B GLN* 3.6 15.4 - - - +
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Residues in contact with LEU 101 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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972 MET* 3.1 37.3 + - + +
982 THR* 3.3 7.6 + - - +
1002 GLN* 1.3 76.8 - - - +
1022 ILE* 1.3 56.2 + - - +
1042 SER* 3.1 11.8 + - - -
1052 ASN* 2.7 53.6 + - - +
1292 MET* 4.2 16.4 - - - -
1322 ARG* 4.1 22.4 - - - +
1332 TYR* 5.2 1.1 - - - +
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Residues in contact with ILE 102 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802 ILE* 3.9 28.3 - - + -
982 THR* 3.0 18.2 + - - +
992 THR* 3.5 8.5 - - - +
1012 LEU* 1.3 78.0 - - + +
1032 SER* 1.3 66.7 - - - +
1052 ASN* 2.9 19.8 + - + +
1062 LEU* 2.9 25.8 + - + +
1222 ALA* 3.9 31.2 - - + +
1252 MET* 4.2 22.2 - - + -
1262 LEU* 4.0 28.3 - - + -
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Residues in contact with SER 103 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792 PHE* 4.3 8.8 + - - -
802 ILE* 3.3 33.9 + - - +
992 THR* 3.1 20.1 + - - -
1002 GLN* 3.9 5.8 - - - -
1022 ILE* 1.3 75.8 - - - +
1042 SER* 1.4 62.7 + - - +
1062 LEU* 3.6 3.0 + - - +
1072 GLU* 3.1 29.7 + - - +
99B LEU* 4.7 9.1 - - - +
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Residues in contact with SER 104 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002 GLN* 3.0 13.6 + - - +
1012 LEU* 3.1 13.8 + - - -
1032 SER* 1.4 81.0 - - - +
1052 ASN* 1.4 64.9 + - - +
1062 LEU 3.3 0.5 + - - -
1072 GLU* 3.3 6.6 + - - +
1082 LEU* 3.3 10.6 + - - +
95B GLN* 3.5 13.1 + - - +
96B GLN* 5.3 6.0 - - - -
99B LEU* 2.9 37.4 - - - +
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Residues in contact with ASN 105 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012 LEU* 2.7 39.8 + - - +
1022 ILE* 2.9 18.8 + - + +
1042 SER* 1.4 76.7 - - - +
1062 LEU* 1.3 61.4 + - - +
1082 LEU* 3.4 10.8 - - - +
1092 HIS* 3.3 20.4 + - - +
1252 MET* 5.1 27.0 - - + +
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Residues in contact with LEU 106 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802 ILE* 3.9 12.8 - - + +
812 SER* 3.5 33.9 - - - +
842 ILE* 4.3 11.9 - - + -
1022 ILE* 2.9 29.7 + - + +
1032 SER 3.9 3.6 - - - +
1052 ASN* 1.3 78.0 - - - +
1072 GLU* 1.4 58.6 + - - +
1092 HIS* 3.1 12.1 + - + +
1102 SER* 2.9 35.8 + - - +
1172 PRO* 4.4 16.4 - - + -
1182 ARG 4.4 12.3 - - - +
1212 THR* 5.0 9.9 - - + -
1222 ALA* 4.7 13.9 - - + +
1252 MET* 6.3 1.6 - - + -
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Residues in contact with GLU 107 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032 SER* 3.1 22.2 + - - +
1042 SER 3.3 5.8 + - - +
1062 LEU* 1.4 73.7 - - - +
1082 LEU* 1.3 64.1 + - - +
1102 SER* 3.3 13.3 + - - -
1112 LEU* 3.0 38.6 + - + +
69B THR* 5.6 1.9 - - - +
70B LYS* 3.6 35.0 + - - +
95B GLN* 3.2 27.9 + - - +
99B LEU* 3.9 20.6 - - - +
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Residues in contact with LEU 108 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1042 SER 3.3 5.4 + - - +
1052 ASN* 3.4 13.2 - - - +
1072 GLU* 1.3 78.5 - - - +
1092 HIS* 1.4 62.9 - - - +
1112 LEU* 3.6 0.5 + - - -
1122 SER* 3.2 21.8 + - - +
105A TYR* 5.7 4.3 - - - +
88B HIS* 5.3 13.7 - - + +
91B ARG* 3.3 21.5 + - + +
92B LYS* 4.0 41.3 - - + +
95B GLN* 3.2 30.4 + - - +
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Residues in contact with HIS 109 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052 ASN 3.3 8.2 + - - +
1062 LEU* 3.1 15.5 + - + +
1082 LEU* 1.4 79.0 - - - +
1102 SER* 1.4 64.4 - - - +
1122 SER* 2.7 25.9 + - - -
1132 THR* 3.1 28.3 + - + +
1172 PRO* 6.5 1.8 - - + -
1212 THR* 5.2 6.1 - - + -
1252 MET* 6.4 0.2 - - + -
101A TRP* 3.1 38.6 - + - -
105A TYR* 3.2 52.3 + + + +
113A MET* 4.2 6.2 - - + +
117A ARG* 5.4 0.4 + - - -
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Residues in contact with SER 110 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812 SER* 5.2 1.4 + - - -
1062 LEU* 2.9 24.3 + - - +
1072 GLU* 3.5 13.9 - - - -
1082 LEU 3.3 0.2 - - - -
1092 HIS* 1.4 73.8 - - - +
1112 LEU* 1.4 64.2 + - - +
1132 THR* 3.3 6.0 + - - -
1142 GLY* 3.3 19.9 + - - -
1152 ARG 3.9 11.5 - - - +
1172 PRO* 4.1 25.2 - - - +
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Residues in contact with LEU 111 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072 GLU* 3.0 40.6 + - + +
1082 LEU 4.2 0.4 - - - +
1102 SER* 1.4 80.1 - - - +
1122 SER* 1.4 66.0 + - - +
1142 GLY* 3.6 8.4 + - - +
116A LYS* 5.6 0.5 + - - -
66B GLU* 5.7 1.0 - - - +
67B PRO* 3.4 38.6 - - + +
68B ILE 3.9 11.2 - - - +
69B THR* 5.3 2.7 - - - -
70B LYS* 5.9 2.2 - - - +
91B ARG* 3.7 25.6 - - - +
95B GLN* 3.9 13.0 - - - +
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Residues in contact with SER 112 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082 LEU* 3.2 12.2 + - - +
1092 HIS* 2.7 33.8 + - - -
1112 LEU* 1.4 76.7 - - - +
1132 THR* 1.3 60.2 + - - +
1142 GLY* 4.8 0.2 - - - -
113A MET* 4.2 20.4 - - - +
116A LYS* 3.9 21.2 + - - +
88B HIS* 5.9 2.0 - - - -
91B ARG* 3.4 28.2 - - - +
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Residues in contact with THR 113 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092 HIS* 3.1 48.7 + - + +
1102 SER* 3.3 5.9 + - - -
1122 SER* 1.3 76.0 - - - +
1142 GLY* 1.3 60.5 + - - +
1152 ARG* 3.4 44.3 + - - +
101A TRP* 4.3 7.2 - - + -
110A PRO* 5.7 4.7 - - + -
112A ASP* 4.9 1.7 - - - +
113A MET* 4.2 17.0 - - + -
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Residues in contact with GLY 114 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102 SER 3.3 10.9 + - - -
1112 LEU* 3.6 5.7 + - - -
1122 SER 3.5 2.4 - - - -
1132 THR* 1.3 76.1 + - - +
1152 ARG* 1.4 61.4 + - - +
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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
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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) + - + + + + + -
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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