Contacts of the helix formed by residues 112 - 137 (chain A) in PDB entry 5HKZ
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 ASN 112 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A THR 3.5 9.7 + - - +
109A LEU* 3.1 19.1 + - + +
111A GLU* 1.3 75.6 - - - +
113A GLU* 1.3 64.6 + - - +
114A TYR* 3.1 12.9 + - - +
115A PHE* 2.9 31.3 + - + +
116A ARG* 3.0 24.3 + - - +
169A PHE* 4.7 2.0 - - - -
174A PHE* 3.6 41.7 - - - -
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Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PRO* 5.8 2.0 - - + +
111A GLU 3.3 3.0 + - - -
112A ASN* 1.3 75.3 - - - +
114A TYR* 1.3 64.7 + - - +
116A ARG* 3.3 29.8 + - - +
117A VAL* 3.0 29.1 + - + +
199A ILE* 4.0 23.3 - - + +
201A PRO* 5.4 4.7 - - - +
235A TYR* 4.2 19.9 + - - -
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Residues in contact with TYR 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASN* 3.1 8.5 + - - +
113A GLU* 1.3 78.4 - - - +
115A PHE* 1.3 60.7 + - - +
117A VAL* 3.3 1.4 + - - +
118A PHE* 2.8 51.8 + + + +
164A GLU* 2.7 46.8 + - + +
165A LEU* 3.4 16.4 + - + -
168A ILE* 3.9 19.1 - - + -
169A PHE* 3.8 28.9 - + - -
174A PHE* 4.4 4.0 - - + -
198A THR* 4.0 29.2 - - + -
199A ILE* 3.9 32.0 - - + +
233A ASN* 6.2 0.4 - - - -
237A SER* 4.5 3.8 - - - -
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Residues in contact with PHE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL* 3.7 23.3 - - + -
56A VAL* 4.7 7.9 - - + -
95A LEU* 3.8 24.7 - - + -
98A ILE* 4.4 12.8 - - + -
99A LEU* 5.6 2.7 - - + -
106A MET* 5.7 0.2 - - + -
109A LEU* 3.7 51.6 - - + +
110A GLY* 5.2 0.2 - - - -
112A ASN* 2.9 20.5 + - + +
113A GLU 3.2 0.2 - - - -
114A TYR* 1.3 79.6 - - - +
116A ARG* 1.3 58.9 + - - +
118A PHE* 3.6 4.2 - + + +
119A MET* 2.9 61.6 + - + +
165A LEU* 4.8 7.4 - - + -
169A PHE* 4.0 20.9 - + + -
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Residues in contact with ARG 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PRO* 3.0 32.7 + - + +
49A GLY 3.3 27.6 - - - +
50A THR* 3.7 5.8 - - - +
51A VAL* 3.9 10.6 - - + +
55A MET* 5.5 0.3 - - - +
110A GLY 3.2 26.5 - - - +
111A GLU* 2.4 36.3 + - - +
112A ASN 3.0 16.5 + - - +
113A GLU* 3.6 33.1 - - - +
115A PHE* 1.3 75.0 - - - +
117A VAL* 1.3 62.0 + - - +
119A MET* 4.0 1.0 - - - +
120A GLU* 3.1 25.5 + - - +
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Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PRO* 3.6 24.0 - - + -
113A GLU* 3.0 26.5 + - + +
114A TYR* 3.7 3.4 - - + +
116A ARG* 1.3 71.5 - - - +
118A PHE* 1.3 67.9 + - - +
120A GLU* 3.4 6.1 + - - +
121A ASN* 3.0 22.3 + - - +
199A ILE* 3.8 13.7 - - + -
233A ASN* 3.6 27.4 - - + +
235A TYR* 3.7 40.2 - - + +
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Residues in contact with PHE 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A THR* 4.7 9.6 - - + -
95A LEU* 4.5 5.6 - - + -
114A TYR* 2.8 45.5 + - + +
115A PHE* 3.6 7.6 - + + +
117A VAL* 1.3 77.5 - - - +
119A MET* 1.3 70.2 + - + +
121A ASN* 3.1 7.6 + - - +
122A LEU* 2.8 47.3 + - + +
161A MET* 3.4 52.0 - - + +
162A LEU* 5.3 0.2 - - - -
164A GLU* 4.0 6.7 - - - -
165A LEU* 3.9 38.1 - - + -
233A ASN* 5.6 2.0 - - - +
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Residues in contact with MET 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL* 3.8 19.3 - - + -
55A MET* 3.7 13.2 - - + +
56A VAL* 4.2 23.6 - - + -
59A CYS* 3.9 34.5 - - + -
95A LEU* 4.0 22.4 - - + -
115A PHE* 2.9 57.7 + - + +
118A PHE* 1.3 77.3 - - + +
120A GLU* 1.3 67.1 + - - +
122A LEU* 3.9 5.6 - - + +
123A MET* 3.0 26.3 + - - +
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PRO* 3.6 36.1 - - + +
49A GLY 4.8 1.5 + - - +
55A MET* 3.9 12.8 - - + +
116A ARG 3.1 18.4 + - - +
117A VAL* 3.8 6.9 - - - +
119A MET* 1.3 75.9 - - - +
121A ASN* 1.3 57.2 + - - +
123A MET* 3.5 3.4 + - - +
124A LYS* 3.0 29.7 + - + +
235A TYR* 5.6 3.3 - - - -
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Residues in contact with ASN 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A VAL 3.0 17.9 + - - +
118A PHE* 3.6 6.4 - - - +
120A GLU* 1.3 74.9 + - - +
122A LEU* 1.3 60.9 + - - +
124A LYS* 3.3 5.4 + - - +
125A LYS* 2.7 62.0 + - - +
161A MET* 3.6 22.4 - - + +
231A THR* 2.9 29.1 + - - -
232A CYS 3.7 0.3 - - - +
233A ASN* 3.6 26.5 - - + +
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A CYS* 3.7 21.1 - - - -
63A MET* 4.0 9.9 - - - -
88A LEU* 4.7 3.6 - - + -
91A THR* 4.0 16.2 - - + -
95A LEU* 3.7 30.7 - - + -
118A PHE* 2.8 29.1 + - + +
119A MET* 3.9 8.3 - - - +
121A ASN* 1.3 73.1 - - - +
123A MET* 1.3 65.9 + - - +
125A LYS* 4.2 0.8 - - - +
126A THR* 2.7 34.4 + - - +
158A PHE* 3.9 24.5 - - + -
161A MET* 3.6 17.7 - - + +
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Residues in contact with MET 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A MET* 3.8 45.1 - - + +
58A LYS* 3.8 27.6 - - + -
59A CYS* 4.0 24.8 - - + +
62A LEU* 4.3 5.3 - - + +
119A MET 3.0 17.6 + - - +
120A GLU* 3.8 4.0 - - - +
122A LEU* 1.3 77.9 - - - +
124A LYS* 1.3 64.0 + - - +
126A THR* 3.3 3.4 + - - -
127A LYS* 3.0 52.8 + - + +
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Residues in contact with LYS 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLU* 3.0 19.8 + - + +
121A ASN* 3.7 9.2 - - - +
123A MET* 1.3 77.4 - - - +
125A LYS* 1.3 59.0 + - + +
127A LYS* 3.2 10.5 + - - +
128A GLN* 2.9 41.2 + - - +
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Residues in contact with LYS 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ASN* 2.7 53.9 + - - +
122A LEU* 4.2 0.7 - - - +
124A LYS* 1.3 75.4 - - + +
126A THR* 1.3 60.6 + - - +
128A GLN* 3.4 23.0 + - - +
129A THR* 2.9 27.7 + - - -
154A LEU* 3.9 21.8 - - + +
157A ILE* 3.8 19.5 - - + -
158A PHE* 3.8 21.3 - - + -
161A MET* 4.5 5.2 - - - -
231A THR 3.7 11.7 - - - -
232A CYS* 2.8 29.2 + - - +
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Residues in contact with THR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A CYS* 4.7 1.5 - - - -
62A LEU* 3.5 44.6 - - + +
63A MET* 3.6 21.3 - - + +
66A VAL* 3.7 10.5 - - + -
88A LEU* 4.9 2.1 - - + +
122A LEU* 2.7 30.7 + - - +
123A MET* 3.7 5.8 - - - -
125A LYS* 1.3 76.0 - - - +
127A LYS* 1.3 62.0 + - - +
129A THR* 3.1 6.5 + - - -
130A ILE* 3.1 22.7 + - + +
158A PHE* 3.9 10.7 - - - -
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Residues in contact with LYS 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LYS* 3.7 22.4 - - - +
62A LEU* 3.9 26.0 - - + -
123A MET* 3.0 38.7 + - + +
124A LYS* 3.2 9.8 + - - +
126A THR* 1.3 76.9 - - - +
128A GLN* 1.3 56.3 + - + +
130A ILE* 3.3 10.1 + - + +
131A SER* 2.9 33.3 + - - +
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Residues in contact with GLN 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LYS* 2.9 31.9 + - - +
125A LYS* 3.6 24.0 + - - +
126A THR 3.3 0.2 - - - -
127A LYS* 1.3 76.3 - - + +
129A THR* 1.3 62.7 + - - +
131A SER* 3.4 7.1 + - - -
132A LEU* 3.0 24.8 + - - +
154A LEU* 4.1 24.5 - - + +
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Residues in contact with THR 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 3.8 29.6 - - + -
84A ILE* 4.2 4.3 - - + -
125A LYS 2.9 16.2 + - - -
126A THR* 3.1 8.2 + - - -
128A GLN* 1.3 73.0 - - - +
130A ILE* 1.3 66.2 + - - +
132A LEU* 3.2 12.6 + - + +
133A PHE* 3.2 25.4 - - + -
151A LEU* 3.8 28.3 - - + -
154A LEU* 3.6 15.3 - - + +
158A PHE* 3.5 17.4 - - - -
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Residues in contact with ILE 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 3.9 44.4 - - + +
65A LYS* 4.4 17.9 - - + -
66A VAL* 3.6 14.1 - - + -
69A LEU* 4.5 15.7 - - + -
126A THR 3.1 14.3 + - - +
127A LYS* 3.6 11.7 - - + +
129A THR* 1.3 75.8 - - - +
131A SER* 1.3 63.2 + - - +
133A PHE* 2.9 15.4 + - - +
134A LYS* 3.1 38.0 + - + +
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Residues in contact with SER 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LYS* 2.9 18.7 + - - +
128A GLN* 3.7 8.2 - - - -
129A THR 3.3 0.2 - - - -
130A ILE* 1.3 76.3 - - - +
132A LEU* 1.3 57.1 + - - +
134A LYS* 4.4 11.4 - - - +
135A GLU* 2.8 53.3 + - - +
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A GLN 3.0 10.8 + - - +
129A THR* 3.3 11.9 - - - +
130A ILE 3.1 0.2 - - - -
131A SER* 1.3 78.5 - - - +
133A PHE* 1.3 59.2 + - + +
135A GLU* 4.5 6.2 - - - +
136A GLY* 2.8 27.3 + - - +
140A MET* 4.1 7.8 - - - +
147A PRO* 3.5 34.7 - - + +
150A ASN* 3.7 30.7 - - + +
151A LEU* 3.6 25.6 - - + +
154A LEU* 3.8 20.9 - - + -
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Residues in contact with PHE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 5.1 1.6 - - + -
69A LEU* 3.8 49.6 - - + -
70A CYS* 3.7 31.9 - - - -
72A ASN* 6.0 0.4 - - + -
75A LEU* 3.8 24.2 - - + -
129A THR* 3.2 33.6 + - + -
130A ILE 2.9 6.9 + - - +
132A LEU* 1.3 76.2 - - + +
134A LYS* 1.3 64.0 + - + +
137A LYS* 3.0 27.5 + - - +
140A MET* 4.0 28.5 - - + -
141A TYR* 6.3 1.8 - + - -
151A LEU* 4.2 15.0 - - + -
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Residues in contact with LYS 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 5.8 2.9 - - + -
130A ILE* 3.1 37.1 + - + +
131A SER* 3.3 9.2 + - - +
133A PHE* 1.3 79.7 - - + +
135A GLU* 1.3 63.3 + - + +
137A LYS* 4.3 7.3 + - - +
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Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A SER* 2.8 34.3 + - - +
132A LEU* 4.5 6.7 + - + +
134A LYS* 1.3 79.4 - - + +
136A GLY* 1.3 62.6 + - - +
137A LYS* 3.5 2.8 - - - +
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Residues in contact with GLY 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LEU 2.8 20.0 + - - -
134A LYS 3.4 0.2 - - - -
135A GLU* 1.3 77.9 - - - +
137A LYS* 1.3 73.3 + - - +
139A ARG* 2.9 20.9 + - - +
140A MET* 4.3 3.1 - - - -
147A PRO* 4.0 23.6 - - - -
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Residues in contact with LYS 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PHE 3.0 16.8 + - - +
134A LYS 4.7 6.3 - - - +
135A GLU 3.5 4.7 - - - +
136A GLY* 1.3 77.2 - - - +
138A GLU* 1.3 64.4 + - - +
139A ARG 3.1 0.7 + - - -
140A MET* 3.1 20.5 + - - +
141A TYR* 4.6 6.7 + - - -
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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