Contacts of the helix formed by residues 109 - 144 in PDB entry 2IIL
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 GLY 109
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28 PHE* 3.9 17.7 - - - -
106 TRP* 2.9 37.8 + - - -
107 VAL 3.1 6.1 - - - -
108 PHE* 1.3 76.9 - - - +
110 GLU* 1.3 64.5 + - - -
111 ALA 3.3 1.2 + - - -
113 CYS* 3.2 2.6 + - - +
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Residues in contact with GLU 110
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13 SER* 5.1 13.7 - - - +
28 PHE* 4.3 15.0 - - + -
109 GLY* 1.3 71.3 - - - -
111 ALA* 1.3 51.8 + - - +
113 CYS* 3.0 18.9 + - - -
114 LYS* 2.7 53.9 + - - +
178 VAL* 5.5 7.8 - - - +
179 MET 4.9 5.7 - - - +
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Residues in contact with ALA 111
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108 PHE* 4.1 11.4 + - + +
109 GLY 3.3 0.6 - - - -
110 GLU* 1.3 75.0 - - - +
112 MET* 1.3 61.0 + - - +
114 LYS* 3.2 12.3 + - - +
115 LEU* 3.1 20.4 + - - +
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Residues in contact with MET 112
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96 PHE* 3.2 56.5 - - + +
99 VAL* 3.3 8.3 - - - -
100 TYR* 3.7 17.3 - - + +
106 TRP* 2.9 55.5 + - + +
107 VAL* 4.0 2.7 - - + +
108 PHE* 3.2 51.1 - - + +
109 GLY 3.5 1.2 + - - -
110 GLU 3.5 0.4 - - - -
111 ALA* 1.3 78.3 - - - +
113 CYS* 1.3 52.4 + - - +
115 LEU* 3.2 3.2 + - - +
116 ASN* 2.8 30.8 + - - +
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Residues in contact with CYS 113
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28 PHE* 3.9 11.7 - - + -
106 TRP* 2.8 17.3 - - + +
109 GLY 3.2 12.0 + - - +
110 GLU* 3.0 19.9 + - - +
112 MET* 1.3 73.4 - - - +
114 LYS* 1.3 57.5 + - - +
117 PRO* 2.9 29.5 - - - +
179 MET* 3.3 27.1 - - - +
180 THR* 4.5 0.4 - - - -
181 ASP* 3.6 13.2 - - - +
187 VAL* 3.4 21.7 - - + +
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Residues in contact with LYS 114
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110 GLU* 2.7 42.2 + - + +
111 ALA* 3.2 11.4 + - - +
113 CYS* 1.3 74.0 - - - +
115 LEU* 1.3 58.4 + - + +
117 PRO* 3.8 0.9 - - - +
118 PHE* 2.8 34.9 + - + +
173 PHE 4.3 2.7 - - - -
174 LEU* 3.3 51.3 + - + +
175 ILE* 5.5 1.4 - - - +
178 VAL* 5.9 4.3 - - - +
179 MET* 3.3 33.0 - - + +
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Residues in contact with LEU 115
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92 MET* 3.0 43.7 - - + +
93 CYS* 3.5 2.3 - - - +
96 PHE* 3.2 28.7 - - + -
111 ALA 3.1 12.9 + - - +
112 MET* 3.2 7.4 + - - +
114 LYS* 1.3 81.0 - - + +
116 ASN* 1.3 62.2 + - - +
118 PHE* 4.5 8.3 - - + -
119 VAL* 3.0 48.1 + - + +
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Residues in contact with ASN 116
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93 CYS* 2.9 41.4 - - - +
96 PHE* 4.5 3.5 - - + +
97 THR* 3.5 31.2 + - - -
106 TRP* 3.2 40.5 - - + -
112 MET 2.8 12.7 + - - +
115 LEU* 1.3 69.8 - - - +
117 PRO* 1.3 65.9 - - + +
120 GLN* 3.1 18.1 + - - +
186 ASN* 4.0 6.6 - - - +
187 VAL 3.9 8.2 - - - +
306 HIS* 4.9 2.9 + - - -
310 MET* 4.7 6.4 - - - +
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Residues in contact with PRO 117
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113 CYS 2.9 30.3 - - - +
114 LYS 3.8 0.2 - - - +
116 ASN* 1.3 86.8 - - + +
118 PHE* 1.3 57.1 + - - +
119 VAL 3.2 2.0 - - - -
120 GLN* 4.0 5.8 - - + -
121 CYS* 2.7 38.4 + - + +
179 MET* 3.5 16.8 - - + -
187 VAL* 3.1 46.2 - - + +
188 THR* 3.7 10.8 - - + -
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Residues in contact with PHE 118
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92 MET* 5.5 4.9 - - - -
114 LYS* 2.8 27.5 + - + +
115 LEU* 4.2 9.9 - - + +
117 PRO* 1.3 71.0 - - - +
119 VAL* 1.3 66.6 + - + +
121 CYS* 3.6 2.2 - - - +
122 VAL* 2.7 49.3 + - + +
167 VAL* 4.8 11.9 - - + -
170 SER* 3.1 53.2 + - - -
171 LEU* 3.4 15.5 - - + -
174 LEU* 3.4 18.4 - - + -
179 MET* 3.7 10.4 - - + +
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Residues in contact with VAL 119
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88 LEU* 3.0 44.0 - - + +
89 VAL* 3.3 9.6 - - - +
92 MET* 3.2 30.7 - - + -
93 CYS* 3.7 6.3 - - + +
115 LEU* 3.0 33.1 + - + +
117 PRO 3.2 0.4 - - - -
118 PHE* 1.3 80.3 - - + +
120 GLN* 1.3 59.0 + - - +
122 VAL* 3.3 8.9 - - + +
123 SER* 2.9 30.7 + - - -
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Residues in contact with GLN 120
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89 VAL* 3.4 15.7 - - - +
93 CYS* 3.6 5.9 - - - -
116 ASN* 3.1 23.6 + - - +
117 PRO* 3.9 7.2 - - + +
119 VAL* 1.3 76.0 - - - +
121 CYS* 1.3 56.4 + - - +
123 SER* 2.8 32.6 + - - -
124 ILE* 3.1 15.9 + - - +
187 VAL 5.3 0.2 - - - +
188 THR* 6.5 0.4 - - + -
276 TRP* 4.0 24.6 - - + -
306 HIS* 4.1 23.7 + - + +
309 ALA 4.9 0.2 + - - -
310 MET* 3.5 46.8 + - - +
312 SER* 5.6 1.2 - - - -
313 THR* 4.7 0.8 + - - -
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Residues in contact with CYS 121
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117 PRO* 2.7 24.9 + - + +
118 PHE* 3.6 2.2 - - - +
120 GLN* 1.3 71.0 - - - +
122 VAL* 1.4 56.0 + - - +
124 ILE* 3.0 13.1 - - - +
125 THR* 2.9 32.1 + - - +
169 SER* 3.1 27.6 - - - -
170 SER* 3.2 18.2 - - - +
173 PHE* 4.0 18.6 - - + -
179 MET* 6.0 0.2 - - + -
188 THR* 6.4 2.0 - - + -
215 LEU* 5.3 1.1 - - - -
219 GLN* 5.1 1.8 - - - -
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Residues in contact with VAL 122
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85 SER* 5.4 3.1 - - - +
88 LEU* 5.1 9.9 - - + -
92 MET* 6.2 1.1 - - - -
118 PHE* 2.7 33.0 + - + +
119 VAL* 3.3 28.9 - - + +
121 CYS* 1.4 67.9 - - - +
123 SER* 1.3 63.8 + - - +
125 THR* 3.2 1.9 - - - +
126 VAL* 2.9 43.2 + - + +
163 TRP* 4.5 21.5 - - + -
166 ALA* 4.2 18.8 - - + -
167 VAL* 4.9 2.5 - - + +
170 SER* 2.9 17.9 + - - +
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Residues in contact with SER 123
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85 SER* 4.3 5.2 - - - -
86 ASP* 5.0 5.7 - - - +
89 VAL* 3.1 33.7 - - - +
119 VAL 2.9 10.5 + - - -
120 GLN* 2.8 34.1 + - - -
122 VAL* 1.3 78.3 - - - +
124 ILE* 1.3 58.7 + - - +
126 VAL* 3.0 26.1 - - - +
127 SER* 3.3 9.5 + - - -
276 TRP* 5.0 1.7 - - - -
312 SER* 4.9 7.5 + - - -
313 THR* 4.9 1.2 + - - -
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Residues in contact with ILE 124
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120 GLN 3.1 10.3 + - - +
121 CYS* 3.0 29.8 - - - +
123 SER* 1.3 81.1 + - - +
125 THR* 1.3 58.5 + - - +
127 SER* 3.0 5.0 + - - -
128 ILE* 2.9 27.4 + - + +
272 PHE* 3.1 32.8 - - + -
276 TRP* 2.9 66.9 - - + +
312 SER* 3.9 7.9 - - - +
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Residues in contact with THR 125
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121 CYS* 2.9 25.0 + - - +
122 VAL* 3.2 15.0 - - - +
124 ILE* 1.3 76.9 - - - +
126 VAL* 1.3 62.9 + - - +
128 ILE* 3.0 12.0 - - - +
129 PHE* 3.0 56.3 + - - -
166 ALA* 3.3 31.4 - - + +
169 SER* 3.8 16.6 - - - -
170 SER* 3.7 2.5 - - - +
219 GLN* 5.0 1.6 - - - +
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Residues in contact with VAL 126
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81 ASN* 4.3 4.3 - - - +
82 LEU* 4.3 9.0 - - + -
85 SER* 3.1 40.2 - - - +
86 ASP* 5.7 0.7 - - - +
122 VAL* 2.9 31.6 + - + +
123 SER 3.0 20.2 - - - +
125 THR* 1.3 75.7 - - - +
127 SER* 1.3 51.1 + - - +
130 SER* 2.8 42.0 + - - -
162 ILE* 3.0 21.4 - - + +
163 TRP* 4.8 9.6 - - + -
166 ALA* 3.5 18.4 - - + -
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Residues in contact with SER 127
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82 LEU* 3.8 18.0 - - - +
123 SER 3.3 9.4 + - - -
124 ILE* 3.0 19.4 + - - -
126 VAL* 1.3 78.5 - - - +
128 ILE* 1.4 63.9 + - - +
130 SER* 3.2 1.9 + - - -
131 LEU* 2.9 33.3 + - - +
268 ILE* 5.5 0.2 - - - +
272 PHE* 3.9 14.0 - - - +
312 SER* 4.5 7.8 + - - -
316 ASN* 4.1 18.5 + - - -
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Residues in contact with ILE 128
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124 ILE* 2.9 19.7 + - + +
125 THR* 3.0 22.9 - - - +
127 SER* 1.4 70.4 - - - +
129 PHE* 1.3 91.8 + - + +
131 LEU* 3.3 14.5 - - - +
132 VAL* 3.2 24.6 + - - +
219 GLN* 2.8 36.8 - - + +
220 TYR* 5.6 3.8 - - + -
223 PRO* 4.4 10.3 - - + -
224 LEU* 5.9 4.0 - - + -
227 ILE* 4.0 1.6 - - - +
272 PHE* 3.1 37.9 - - + -
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Residues in contact with PHE 129
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125 THR* 3.0 42.5 + - - +
128 ILE* 1.3 93.1 - - + +
130 SER* 1.3 64.3 + - - +
132 VAL* 3.1 15.2 + - + +
133 LEU 3.1 18.2 + - - -
162 ILE* 3.1 31.7 - - + +
165 LEU* 3.3 57.0 - - + -
166 ALA 3.7 6.5 - - - -
218 LEU* 4.3 9.9 - - + -
219 GLN* 4.3 17.3 - - + -
223 PRO* 3.9 19.7 - - + -
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Residues in contact with SER 130
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78 LEU* 3.6 15.9 - - - +
81 ASN* 3.6 13.0 + - - -
82 LEU* 3.6 23.9 - - - +
126 VAL 2.8 24.0 + - - -
127 SER 3.5 4.3 - - - -
129 PHE* 1.3 75.7 - - - +
131 LEU* 1.3 55.2 + - - +
133 LEU* 3.3 3.3 + - - +
134 ILE* 3.0 36.8 + - - +
162 ILE* 3.5 21.3 - - - +
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Residues in contact with LEU 131
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127 SER* 2.9 20.9 + - - +
128 ILE* 3.3 12.1 - - - +
129 PHE 3.3 0.2 - - - -
130 SER* 1.3 74.9 - - - +
132 VAL* 1.3 55.8 + - - +
134 ILE* 3.5 6.9 + - + +
135 ALA* 2.9 28.6 + - - +
224 LEU* 6.0 0.9 - - + -
227 ILE* 3.6 18.6 - - + +
265 LEU* 4.1 5.4 - - + +
268 ILE* 3.4 48.2 - - + -
269 VAL* 4.0 20.0 - - + -
272 PHE* 3.6 44.0 - - + -
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Residues in contact with VAL 132
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128 ILE 3.4 14.1 - - - +
129 PHE* 3.1 19.5 + - + +
131 LEU* 1.3 72.9 - - - +
133 LEU* 1.3 64.0 + - - +
135 ALA* 3.2 4.1 + - - +
136 VAL* 3.0 27.6 + - + +
165 LEU* 6.5 0.7 - - + -
223 PRO* 3.7 39.3 - - + +
226 PHE* 3.7 23.1 - - + -
227 ILE* 3.8 8.1 - - + -
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Residues in contact with LEU 133
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74 VAL* 4.5 9.0 - - + -
78 LEU* 3.4 37.0 - - + -
129 PHE 3.1 11.9 + - - +
130 SER 3.3 7.4 + - - +
132 VAL* 1.3 75.6 - - - +
134 ILE* 1.3 57.4 + - - +
136 VAL* 3.4 13.4 + - + +
137 GLU* 3.0 27.5 + - + +
154 HIS 5.0 3.8 - - - +
155 ALA* 4.5 4.7 - - - +
158 GLY* 3.2 39.5 - - - +
159 ILE 4.0 1.1 - - - +
161 VAL* 6.2 0.7 - - + -
162 ILE* 4.0 9.2 - - + +
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Residues in contact with ILE 134
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74 VAL* 5.8 0.9 - - + -
75 THR* 5.6 11.9 - - - +
78 LEU* 3.7 29.4 - - + -
82 LEU* 5.5 1.6 - - + -
130 SER* 3.0 25.3 + - - +
131 LEU* 3.9 7.9 - - + +
133 LEU* 1.3 72.1 - - - +
135 ALA* 1.3 56.0 + - - +
137 GLU* 3.2 8.7 + - + +
138 ARG* 2.7 47.4 + - + +
261 ILE* 5.7 5.2 - - + +
265 LEU* 3.4 44.0 - - + -
268 ILE* 4.7 12.1 - - + -
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Residues in contact with ALA 135
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131 LEU 2.9 15.7 + - - +
132 VAL 3.2 10.3 + - - +
134 ILE* 1.3 73.9 - - - +
136 VAL* 1.3 56.2 + - - +
138 ARG* 3.3 1.6 + - - +
139 HIS 2.9 24.9 + - - -
226 PHE* 3.9 12.6 - - + -
227 ILE* 4.0 25.8 - - + +
230 CYS* 2.9 19.8 - - + -
265 LEU* 3.5 15.3 - - + +
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Residues in contact with VAL 136
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132 VAL* 3.0 20.9 + - + +
133 LEU* 3.6 14.4 - - + +
135 ALA* 1.3 74.3 - - - +
137 GLU* 1.3 51.5 + - - +
139 HIS* 3.1 10.8 + - + +
140 GLN* 2.8 52.5 + - + +
226 PHE* 3.3 34.5 - - + -
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Residues in contact with GLU 137
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73 ASN* 5.9 0.3 - - - +
74 VAL* 3.3 48.0 + - + +
75 THR 4.6 3.3 + - - -
133 LEU* 3.0 19.6 + - + +
134 ILE* 3.7 8.1 - - - +
136 VAL* 1.3 75.8 - - - +
138 ARG* 1.3 78.3 + - - +
140 GLN* 3.2 10.6 + - - +
141 LEU* 2.8 33.5 + - - +
150 PRO* 4.0 19.4 - - + +
261 ILE* 4.7 8.7 - - - +
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Residues in contact with ARG 138
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134 ILE* 2.7 34.8 + - + +
135 ALA 3.5 4.5 - - - +
137 GLU* 1.3 90.4 + - - +
139 HIS* 1.3 55.6 + - - +
141 LEU* 3.3 22.4 + - - +
142 ILE* 2.9 63.5 + - - +
230 CYS* 5.3 1.3 - - - -
234 ILE* 4.3 11.2 - - + -
254 ARG* 6.1 0.2 - - - +
258 THR* 3.2 29.3 + - - -
261 ILE* 3.3 32.8 - - - +
262 ASN* 3.7 28.8 - - - +
265 LEU* 3.4 27.1 - - + -
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Residues in contact with HIS 139
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135 ALA 2.9 5.9 + - - -
136 VAL* 3.3 13.5 - - + +
138 ARG* 1.3 73.9 - - - +
140 GLN* 1.3 64.5 + - + +
142 ILE* 3.9 8.1 - - - -
143 ILE* 2.7 57.8 + - + +
145 PRO* 3.5 24.8 - - + +
226 PHE* 5.8 2.0 - + + -
230 CYS* 3.4 24.6 - - - +
233 LYS* 3.2 48.6 + - + +
234 ILE* 5.2 0.4 - - - +
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Residues in contact with GLN 140
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136 VAL* 2.8 35.5 + - + +
137 GLU* 3.2 11.8 + - - +
139 HIS* 1.3 77.4 - - + +
141 LEU* 1.3 56.9 + - - +
144 ASN* 3.0 26.2 - - - +
145 PRO* 3.9 12.2 - - + +
148 TRP* 5.1 10.5 + - - +
150 PRO* 3.9 35.3 - - + +
154 HIS* 6.2 0.6 - - - -
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Residues in contact with LEU 141
.
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137 GLU* 2.8 20.7 + - - +
138 ARG* 3.3 26.0 - - - +
140 GLN* 1.3 76.0 - - - +
142 ILE* 1.3 67.8 + - + +
144 ASN* 3.5 15.1 - - - +
150 PRO* 6.2 5.3 - - + +
254 ARG* 4.1 20.0 - - - +
258 THR* 2.9 37.9 - - + +
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Residues in contact with ILE 142
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138 ARG* 2.9 56.4 + - - +
139 HIS* 3.8 3.6 - - - +
141 LEU* 1.3 75.7 - - + +
143 ILE* 1.3 98.5 + - + +
144 ASN* 3.0 13.5 - - - +
234 ILE* 3.6 46.2 - - + +
237 ARG* 3.8 25.2 + - + +
238 LEU* 3.9 27.1 - - + -
258 THR* 5.0 0.2 - - + -
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Residues in contact with ILE 143
.
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139 HIS* 2.7 49.8 + - + +
142 ILE* 1.3 88.3 - - + +
144 ASN* 1.3 75.7 + - - +
145 PRO* 3.7 21.9 - - + +
233 LYS* 3.6 27.8 - - + +
236 ILE* 5.4 2.0 - - + -
237 ARG* 4.0 14.3 - - + +
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Residues in contact with ASN 144
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140 GLN 3.0 21.0 + - - +
141 LEU 3.5 12.1 - - - +
142 ILE 3.0 23.6 - - - +
143 ILE* 1.3 78.1 + - - +
145 PRO* 1.4 65.8 - - - +
146 ARG 3.3 4.1 + - - -
147 GLY* 4.4 11.9 + - - +
237 ARG* 5.7 0.9 - - - -
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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) + - + + + + + -
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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