Contacts of the helix formed by residues 110 - 135 (chain F) in PDB entry 5TJG
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 110 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F LEU 5.3 1.8 - - - +
109F LEU* 1.3 76.1 - - - +
111F LEU* 1.3 54.9 + - - +
112F GLU* 3.5 16.1 + - - +
113F GLU* 2.9 40.5 + - - +
114F GLU* 2.6 34.8 + - - +
249F LYS* 5.8 0.2 - - - -
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Residues in contact with LEU 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349D PRO* 4.8 18.2 - - + -
350D HIS* 5.1 10.8 - - + +
109F LEU 4.0 0.4 + - - -
110F THR* 1.3 73.4 - - - +
112F GLU* 1.3 59.1 + - + +
114F GLU* 4.1 8.3 - - + +
115F ILE* 3.0 54.6 + - + +
249F LYS* 4.2 31.9 - - + +
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Residues in contact with GLU 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D PHE* 3.7 29.4 - - + +
209D ARG* 3.1 32.4 + - - -
349D PRO* 3.7 35.8 - - + +
391D ALA* 3.3 23.3 - - - +
110F THR* 3.1 12.3 + - - +
111F LEU* 1.3 75.7 - - + +
113F GLU* 1.3 58.6 + - - +
115F ILE* 3.3 4.5 + - - +
116F ASP* 2.9 28.9 + - - +
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Residues in contact with GLU 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D THR* 6.0 1.6 - - - +
206D ARG* 4.1 19.9 + - - +
207D PHE* 3.8 26.5 - - + -
108F LEU 4.5 2.1 - - - +
109F LEU* 3.5 26.9 - - + +
110F THR* 2.9 36.6 + - - +
112F GLU* 1.3 75.5 - - - +
114F GLU* 1.3 57.5 + - - +
116F ASP* 4.3 0.4 - - - -
117F LEU* 2.8 39.9 + - + +
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Residues in contact with GLU 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F LEU* 3.6 28.7 - - + +
110F THR 2.6 20.1 + - - +
111F LEU* 3.7 11.3 - - + +
113F GLU* 1.3 73.6 - - - +
115F ILE* 1.3 63.6 + - + +
117F LEU* 4.4 0.9 - - - +
118F ALA* 3.2 25.0 + - + +
202F LEU* 5.1 5.0 - - + +
206F ASN* 4.9 0.3 - - - +
242F PHE* 5.3 3.0 - - + -
248F PHE 4.8 0.3 - - - +
249F LYS* 3.2 32.5 - - - +
250F PHE* 2.6 47.5 + - + +
6G T 3.7 14.0 - - - +
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Residues in contact with ILE 115 (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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349D PRO 3.6 25.6 - - - +
350D HIS* 4.3 31.2 - - + +
111F LEU* 3.0 40.5 + - + +
112F GLU 3.8 3.4 - - - +
114F GLU* 1.3 79.7 - - + +
116F ASP* 1.3 60.4 + - - +
118F ALA* 3.5 0.6 + - - -
119F ARG* 2.9 29.2 + - + +
242F PHE* 6.2 1.1 - - + -
244F TYR* 3.5 43.3 - - + +
247F ARG* 6.1 1.8 - - - -
248F PHE 5.7 4.7 - - - +
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Residues in contact with ASP 116 (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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206D ARG* 5.6 2.3 + - - -
207D PHE* 3.5 29.1 - - + -
352D ASN* 5.2 1.9 - - - +
112F GLU 2.9 18.3 + - - +
113F GLU* 3.8 3.1 - - - +
115F ILE* 1.3 78.1 - - - +
117F LEU* 1.3 62.6 + - - +
119F ARG* 2.8 36.8 + - - +
120F LYS* 3.0 54.6 + - - +
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Residues in contact with LEU 117 (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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109F LEU* 3.7 26.9 - - + -
113F GLU* 2.8 23.9 + - + +
114F GLU* 4.4 1.3 - - - +
116F ASP* 1.3 80.5 - - - +
118F ALA* 1.3 62.5 + - - +
120F LYS* 3.3 6.6 + - + +
121F VAL* 3.0 27.9 + - - +
198F ALA* 3.5 29.9 - - + +
201F HIS* 3.9 17.9 - - + +
202F LEU* 3.9 34.1 - - + +
205F ALA* 5.8 0.2 - - + -
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Residues in contact with ALA 118 (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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114F GLU* 3.2 19.5 + - + +
115F ILE 3.9 0.9 - - - +
117F LEU* 1.3 78.4 - - - +
119F ARG* 1.3 61.8 + - - +
121F VAL* 3.6 4.7 + - - +
122F GLU* 3.3 21.8 + - - +
202F LEU* 3.9 14.0 - - + +
242F PHE* 3.8 38.0 - - + +
244F TYR* 3.9 16.9 + - + -
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Residues in contact with ARG 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352D ASN* 3.1 47.5 - - - +
115F ILE* 2.9 21.0 + - - +
116F ASP* 2.8 30.3 + - - +
117F LEU 3.1 0.4 - - - -
118F ALA* 1.3 73.7 - - - +
120F LYS* 1.3 79.7 + - - +
122F GLU* 3.2 4.0 + - - +
123F GLU* 2.8 71.9 + - + +
244F TYR* 3.2 35.6 - - + +
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Residues in contact with LYS 120 (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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116F ASP* 3.0 45.2 + - - +
117F LEU* 5.0 4.7 - - + +
119F ARG* 1.3 94.1 - - - +
121F VAL* 1.3 58.3 + - - +
123F GLU* 3.8 9.5 - - - +
124F GLY 2.8 24.4 + - - -
191F ILE 4.6 0.9 - - - +
194F GLU* 2.8 38.7 + - + +
195F GLY* 3.2 18.3 - - - +
198F ALA* 3.7 22.0 - - + -
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Residues in contact with VAL 121 (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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117F LEU 3.0 21.2 + - - +
118F ALA* 3.8 7.2 - - - +
119F ARG 3.2 0.2 - - - -
120F LYS* 1.3 77.2 - - - +
122F GLU* 1.3 60.2 + - - +
124F GLY* 3.2 1.6 + - - -
125F MET* 2.9 46.1 + - + +
143F ARG* 5.8 1.8 - - - +
195F GLY* 3.7 8.6 - - - +
198F ALA* 3.8 2.5 - - + +
199F ARG* 3.5 42.0 - - + +
202F LEU* 4.3 9.9 - - + -
239F VAL* 4.4 21.8 - - + +
240F GLU* 5.3 1.6 - - - +
242F PHE 5.7 3.4 - - - +
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Residues in contact with GLU 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F ALA 3.3 11.4 + - - +
119F ARG* 3.2 6.2 + - - +
121F VAL* 1.3 80.6 - - + +
123F GLU* 1.3 62.2 + - + +
125F MET* 3.5 8.4 + - + +
126F GLU* 3.0 49.1 + - + +
242F PHE 4.6 5.4 - - - +
243F GLU* 4.1 21.4 - - - +
244F TYR* 3.5 29.6 - - + -
245F LYS* 3.9 19.0 - - - +
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Residues in contact with GLU 123 (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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352D ASN* 4.2 3.6 + - - -
119F ARG* 2.8 62.0 + - + +
120F LYS* 3.8 9.1 - - - +
122F GLU* 1.3 77.7 - - + +
124F GLY* 1.3 57.6 + - - +
126F GLU* 3.3 9.7 + - - +
127F ALA* 2.8 29.3 + - - +
191F ILE* 3.7 21.1 - - + +
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Residues in contact with GLY 124 (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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120F LYS 2.8 21.5 + - - -
121F VAL 3.7 1.1 - - - -
123F GLU* 1.3 74.5 - - - +
125F MET* 1.3 55.8 + - - +
127F ALA* 3.1 4.3 + - - +
128F ILE* 3.0 36.2 + - - +
143F ARG* 5.6 1.8 - - - -
191F ILE* 3.6 19.7 - - - +
192F ALA* 3.9 8.7 - - - +
195F GLY* 4.3 5.6 - - - -
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Residues in contact with MET 125 (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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121F VAL* 2.9 32.7 + - + +
122F GLU* 3.9 8.7 - - + +
124F GLY* 1.3 75.5 - - - +
126F GLU* 1.3 63.5 + - + +
128F ILE* 3.4 11.2 + - + +
129F LYS* 3.4 18.9 + - - +
139F GLN* 4.8 3.1 + - - -
143F ARG* 4.6 22.4 - - - +
240F GLU* 3.4 29.8 - - + +
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Residues in contact with GLU 126 (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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122F GLU* 3.0 43.0 + - + +
123F GLU* 3.8 8.8 - - - +
125F MET* 1.3 74.8 - - + +
127F ALA* 1.3 64.9 + - - +
129F LYS* 3.4 8.2 + - - +
130F LYS* 3.2 43.9 + - - +
245F LYS* 6.0 0.3 - - - -
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Residues in contact with ALA 127 (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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123F GLU 2.8 17.4 + - - +
124F GLY 3.1 6.9 + - - +
126F GLU* 1.3 77.4 - - - +
128F ILE* 1.3 60.1 + - - +
130F LYS* 3.6 1.0 + - - -
131F LEU* 3.2 26.6 + - - +
188F TYR* 3.3 47.3 - - + +
191F ILE* 3.8 15.9 - - + -
192F ALA* 4.1 2.0 - - + +
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Residues in contact with ILE 128 (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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124F GLY 3.0 20.6 + - - +
125F MET* 3.6 12.6 - - + +
126F GLU 3.2 0.4 - - - -
127F ALA* 1.3 75.9 - - - +
129F LYS* 1.3 64.9 + - - +
131F LEU* 3.0 18.6 + - - +
132F SER* 3.0 10.2 + - - -
139F GLN* 3.4 36.3 - - + +
142F ILE* 4.0 20.3 - - + +
143F ARG* 3.6 46.0 - - + +
146F VAL* 5.5 4.3 - - + -
192F ALA* 3.9 18.2 - - + +
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Residues in contact with LYS 129 (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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125F MET 3.4 9.3 + - - +
126F GLU* 3.4 9.8 + - - +
127F ALA 3.4 0.2 - - - -
128F ILE* 1.3 78.1 - - - +
130F LYS* 1.3 62.2 + - + +
132F SER* 3.2 12.9 + - - -
133F GLU* 3.3 30.8 + - + +
139F GLN* 3.1 29.6 + - - +
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Residues in contact with LYS 130 (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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126F GLU* 3.2 34.0 + - - +
128F ILE 3.3 0.2 - - - -
129F LYS* 1.3 78.3 - - + +
131F LEU* 1.3 58.3 + - - +
133F GLU* 3.7 21.5 + - - +
134F ALA* 3.2 24.8 + - - +
185F LEU* 5.6 2.3 - - - +
188F TYR* 3.4 45.2 - - + +
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Residues in contact with LEU 131 (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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127F ALA 3.2 19.2 + - - +
128F ILE* 3.0 11.9 + - - +
130F LYS* 1.3 76.4 - - - +
132F SER* 1.3 56.4 + - - +
133F GLU 3.2 1.6 - - - -
134F ALA* 4.3 4.5 - - + +
135F THR* 2.3 42.3 + - + +
142F ILE* 4.1 28.9 - - + -
146F VAL* 6.0 0.7 - - + -
178F LEU* 4.4 16.6 - - + -
181F LEU* 4.2 18.6 - - + -
185F LEU* 4.0 21.3 - - + +
188F TYR* 4.0 23.8 - - + +
189F LEU* 4.2 13.7 - - + +
192F ALA* 4.9 3.6 - - + -
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Residues in contact with SER 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128F ILE 3.0 6.8 + - - -
129F LYS* 3.2 6.2 + - - -
131F LEU* 1.3 76.0 - - - +
133F GLU* 1.3 58.3 + - - +
135F THR* 4.3 1.1 - - - -
136F GLY* 3.2 22.2 - - - -
137F LEU 2.6 27.3 + - - -
138F ASP* 4.4 3.6 - - - -
139F GLN* 3.1 29.6 + - - +
142F ILE* 3.9 5.1 - - - +
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Residues in contact with GLU 133 (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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129F LYS* 3.3 36.3 + - + +
130F LYS* 3.9 22.4 - - - +
131F LEU 3.2 0.4 - - - -
132F SER* 1.3 79.9 - - - +
134F ALA* 1.3 65.6 + - - +
136F GLY* 4.3 3.3 + - - -
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Residues in contact with ALA 134 (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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130F LYS 3.2 16.6 + - - +
131F LEU* 3.4 6.9 + - + +
133F GLU* 1.3 82.4 - - - +
135F THR* 1.3 65.3 + - + +
181F LEU* 4.9 5.2 - - + -
185F LEU* 3.8 34.8 - - + -
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Residues in contact with THR 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F LEU* 2.3 33.7 + - + +
134F ALA* 1.3 75.7 - - + +
136F GLY* 1.3 59.4 + - - +
137F LEU* 3.2 27.7 + - - +
177F LYS* 4.7 17.3 + - + +
178F LEU* 3.9 24.7 - - + +
181F LEU* 4.2 28.5 - - + -
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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