Contacts of the helix formed by residues 119 - 142 (chain F) in PDB entry 5K58
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 ASP 119 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29E SER* 2.9 31.1 + - - -
30E GLN* 2.7 26.2 + - - +
114F LEU 5.7 1.6 - - - -
117F GLU 4.5 2.2 - - - +
118F GLN* 1.3 69.9 - - - +
120F ARG* 1.3 62.2 + - - +
121F LEU 2.9 7.8 + - - -
122F GLN* 3.2 18.4 + - + +
123F GLY* 3.4 8.5 + - - -
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Residues in contact with ARG 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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56F THR* 3.4 22.0 - - + +
57F ARG* 4.5 13.7 - - - +
60F ASP* 2.3 38.9 + - - -
118F GLN* 3.1 5.8 + - + -
119F ASP* 1.3 77.7 - - - +
121F LEU* 1.3 69.7 + - + +
123F GLY* 3.6 3.2 + - - +
124F ARG* 3.2 29.9 + - + +
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Residues in contact with LEU 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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56F THR* 3.6 26.2 - - + +
59F PHE* 3.6 13.2 - - + -
60F ASP* 3.2 24.7 - - - +
63F ILE* 3.7 14.3 - - + +
114F LEU* 3.6 12.8 - - + -
117F GLU* 3.0 39.9 - - + +
118F GLN* 3.2 26.7 - - + +
119F ASP 2.9 0.6 - - - -
120F ARG* 1.3 84.8 - - + +
122F GLN* 1.3 65.4 + - - +
123F GLY 3.2 0.2 - - - -
124F ARG* 3.2 8.6 + - - +
125F ILE* 3.0 25.6 + - - +
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Residues in contact with GLN 122 (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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112E HIS* 5.5 0.9 + - - -
175E ARG* 3.5 33.6 - - + +
177E GLU* 5.5 5.2 - - - +
109F LEU 5.2 0.2 - - - +
110F THR 4.8 1.0 - - - +
111F GLY* 3.6 25.6 - - - -
114F LEU* 3.5 19.9 + - + +
118F GLN 4.6 0.4 + - - -
119F ASP* 3.2 12.3 + - + +
121F LEU* 1.3 77.4 - - - +
123F GLY* 1.3 51.7 + - - +
125F ILE* 2.8 12.2 + - - +
126F ASN* 2.5 68.9 + - - +
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Residues in contact with GLY 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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119F ASP 3.4 9.3 + - - -
120F ARG* 3.9 4.5 - - - -
121F LEU 3.2 0.4 - - - -
122F GLN* 1.3 79.0 - - - +
124F ARG* 1.3 56.1 + - - +
126F ASN* 3.4 16.7 + - - +
127F GLN* 3.2 35.9 + - - +
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Residues in contact with ARG 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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60F ASP* 2.8 40.1 + - - +
63F ILE* 3.7 20.9 - - + +
64F GLU* 3.8 30.7 + - - +
67F GLU* 3.4 29.1 + - - +
120F ARG* 3.2 19.6 + - - +
121F LEU* 3.5 9.4 - - - +
122F GLN 3.1 0.6 - - - -
123F GLY* 1.3 76.3 - - - +
125F ILE* 1.3 62.4 + - - +
127F GLN* 3.7 24.8 - - - +
128F LEU* 3.6 16.5 + - - +
131F ARG* 4.7 0.3 + - - -
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Residues in contact with ILE 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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63F ILE* 3.8 26.0 - - + -
66F ILE* 5.0 2.0 - - + -
108F ILE* 4.2 17.0 - - + +
109F LEU* 3.8 30.7 - - + +
114F LEU* 3.7 16.8 - - + -
121F LEU 3.0 16.9 + - - +
122F GLN* 2.8 22.0 + - - +
124F ARG* 1.3 76.9 - - - +
126F ASN* 1.3 65.3 + - - +
127F GLN 3.2 1.6 - - - -
128F LEU* 3.2 23.7 + - + +
129F PHE* 3.2 30.6 + - + -
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Residues in contact with ASN 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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175E ARG* 2.7 48.2 + - - +
176E SER* 4.6 4.2 - - - +
177E GLU* 6.3 0.4 - - - +
122F GLN* 2.5 47.1 + - - +
123F GLY* 3.4 16.0 - - - +
125F ILE* 1.3 71.9 - - - +
127F GLN* 1.3 51.4 + - + +
129F PHE* 3.2 5.6 + - - +
130F GLU* 2.8 43.1 + - + +
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Residues in contact with GLN 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 GLY 3.2 18.3 + - - +
124F ARG* 3.7 26.5 - - - +
125F ILE 3.2 0.2 - - - -
126F ASN* 1.3 74.2 - - + +
128F LEU* 1.3 56.4 + - - +
130F GLU* 2.8 12.4 + - + +
131F ARG* 2.8 68.9 + - - +
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Residues in contact with LEU 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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63F ILE* 4.4 4.0 - - + +
66F ILE* 4.1 27.8 - - + +
67F GLU* 3.7 45.8 - - + +
70F LEU* 5.0 6.7 - - + -
71F ILE* 4.3 14.4 - - + -
109F LEU* 4.8 7.2 - - + -
124F ARG 3.6 5.4 + - - +
125F ILE* 3.2 34.9 + - + +
127F GLN* 1.3 78.8 - - - +
129F PHE* 1.3 60.2 + - + +
131F ARG* 3.2 12.9 + - - +
132F ILE* 3.1 36.9 + - + +
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Residues in contact with PHE 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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175E ARG* 3.5 38.6 - - - +
95F LEU* 5.6 2.2 - - + -
109F LEU* 3.9 36.6 - - + -
110F THR* 6.2 0.2 - - - -
125F ILE* 3.2 26.8 + - + -
126F ASN 3.2 7.9 + - - +
127F GLN 3.2 0.2 - - - -
128F LEU* 1.3 77.5 - - + +
130F GLU* 1.3 69.0 + - - +
132F ILE* 3.4 13.4 - - + +
133F GLU* 3.0 26.5 + - - +
163F LEU* 3.7 29.5 - - + +
167F GLU* 3.8 28.3 - - + -
170F LEU* 4.9 12.8 - - + -
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Residues in contact with GLU 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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172E ARG* 3.8 22.2 + - - -
175E ARG* 4.7 5.2 + - - -
126F ASN* 2.8 30.8 + - + +
127F GLN* 2.8 14.6 + - + +
129F PHE* 1.3 77.8 - - - +
131F ARG* 1.3 64.0 + - + +
133F GLU* 3.8 13.0 - - - +
134F ALA* 3.3 21.8 + - - +
137F ARG* 5.4 1.0 + - - -
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Residues in contact with ARG 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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67F GLU* 4.7 12.2 + - - +
71F ILE* 3.7 27.7 - - + +
124F ARG 4.7 1.8 + - - -
127F GLN* 2.8 42.4 + - - +
128F LEU* 3.2 40.4 - - - +
130F GLU* 1.3 77.9 - - + +
132F ILE* 1.3 59.8 + - - +
134F ALA* 3.2 6.3 + - - +
135F GLN* 2.8 37.1 + - - +
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Residues in contact with ILE 132 (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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70F LEU* 5.4 5.4 - - + -
71F ILE* 3.6 19.1 - - + +
74F ILE* 3.4 28.7 - - + -
91F ILE* 6.3 0.2 - - + -
95F LEU* 5.0 15.9 - - + -
128F LEU* 3.1 22.2 - - + +
129F PHE* 3.4 27.1 - - + +
131F ARG* 1.3 74.9 - - - +
133F GLU* 1.3 58.3 + - - +
135F GLN* 3.6 7.3 - - - +
136F LEU* 2.9 40.2 + - + +
163F LEU* 3.5 34.5 - - + -
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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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172E ARG* 2.8 38.7 + - - -
180E TYR* 4.9 0.7 + - - -
129F PHE 3.0 18.7 + - - +
130F GLU* 3.8 14.2 - - - +
131F ARG 3.1 0.2 - - - -
132F ILE* 1.3 78.8 - - - +
134F ALA* 1.3 58.8 + - - +
136F LEU* 3.2 9.9 + - - +
137F ARG* 3.0 50.7 + - + +
156F THR* 5.0 2.0 - - - -
159F ALA* 4.4 4.3 - - + -
160F SER* 3.2 32.0 - - - +
163F LEU* 4.3 11.7 - - + -
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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 GLU 3.3 13.2 + - - +
131F ARG* 3.2 5.9 + - - +
133F GLU* 1.3 75.1 - - - +
135F GLN* 1.3 56.1 + - - +
137F ARG* 3.0 33.5 + - - +
138F GLN* 2.7 32.4 + - - +
141F ARG* 4.9 0.3 + - - -
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Residues in contact with GLN 135 (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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71F ILE* 3.9 19.4 - - - +
74F ILE* 4.5 20.6 - - + +
75F ASN* 2.9 34.5 + - - +
78F LEU* 5.3 7.7 - - + +
91F ILE* 5.3 2.0 - - - +
131F ARG* 2.8 32.2 + - - +
132F ILE* 3.6 9.6 - - - +
134F ALA* 1.3 75.3 - - - +
136F LEU* 1.3 64.0 + - + +
138F GLN* 3.0 25.8 + - + +
139F VAL* 3.2 13.7 + - - +
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Residues in contact with LEU 136 (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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74F ILE* 5.9 0.9 - - + -
88F LEU* 4.5 13.8 - - + +
91F ILE* 3.4 37.9 - - + -
92F VAL* 6.2 1.6 - - + -
95F LEU* 6.1 2.7 - - + -
132F ILE* 2.9 31.0 + - + +
133F GLU* 3.3 12.1 - - - +
135F GLN* 1.3 76.8 - - + +
137F ARG* 1.3 60.4 + - - +
139F VAL* 3.3 8.9 + - - +
140F MET* 3.1 29.2 + - - +
159F ALA* 3.4 35.7 - - + +
162F ILE* 4.2 16.2 - - + -
163F LEU* 4.6 11.9 - - + +
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Residues in contact with ARG 137 (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 GLU 5.4 1.2 + - - -
133F GLU* 3.0 36.4 + - - +
134F ALA* 3.0 32.7 + - - +
136F LEU* 1.3 75.8 - - - +
138F GLN* 1.3 57.2 + - - +
139F VAL 3.4 0.2 - - - -
140F MET* 3.9 8.4 - - - +
141F ARG* 2.5 63.0 + - - +
155F GLU* 3.9 6.1 - - + +
156F THR* 3.7 46.8 + - - +
159F ALA* 3.8 13.5 - - + -
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Residues in contact with GLN 138 (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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78F LEU* 4.0 25.7 - - + +
134F ALA 2.7 11.6 + - - +
135F GLN* 3.0 19.5 + - + +
137F ARG* 1.3 78.6 - - - +
139F VAL* 1.3 59.8 + - - +
141F ARG* 3.9 9.7 + - - +
142F GLU* 3.3 50.0 + - - +
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Residues in contact with VAL 139 (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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78F LEU* 3.7 33.0 - - + -
84F THR* 4.1 23.9 + - + +
87F ARG* 3.9 32.5 + - + +
88F LEU* 3.8 22.0 - - + -
91F ILE* 4.1 14.6 - - + -
135F GLN 3.2 12.4 + - - +
136F LEU 3.3 7.1 + - - +
138F GLN* 1.3 75.8 - - - +
140F MET* 1.3 64.8 + - - +
142F GLU* 3.6 15.8 + - - +
143F LYS 4.1 0.2 + - - -
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Residues in contact with MET 140 (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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88F LEU* 4.4 24.5 - - + -
136F LEU* 3.1 13.9 + - + +
137F ARG* 4.0 6.1 - - - +
138F GLN 3.4 0.2 - - - -
139F VAL* 1.3 77.1 - - - +
141F ARG* 1.3 64.9 + - - +
142F GLU 3.4 0.2 + - - -
143F LYS* 3.5 16.5 + - - +
150F GLY* 5.8 1.2 - - - -
151F TYR* 3.9 24.8 + - + -
155F GLU* 3.5 22.2 - - + +
158F LEU* 2.9 56.1 - - + +
159F ALA* 3.1 27.6 - - + +
162F ILE* 4.5 8.5 - - + -
197F LEU* 5.1 0.7 - - + -
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Residues in contact with ARG 141 (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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134F ALA 5.5 0.4 - - - -
137F ARG* 2.5 69.3 + - - +
138F GLN* 4.1 12.3 - - - +
140F MET* 1.3 79.2 - - - +
142F GLU* 1.3 61.0 + - + +
143F LYS 2.8 7.5 + - - -
144F ARG* 3.5 26.2 + - - +
145F MET* 3.7 19.8 - - + +
155F GLU* 3.7 28.7 + - + +
156F THR* 5.5 1.2 + - - -
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Residues in contact with GLU 142 (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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84F THR* 4.3 2.5 + - - -
87F ARG* 3.0 27.2 + - - +
138F GLN* 3.3 38.4 + - - +
139F VAL 3.6 9.7 + - - +
140F MET 3.2 1.4 - - - -
141F ARG* 1.3 76.4 - - + +
143F LYS* 1.3 58.1 + - - +
144F ARG 3.6 0.4 - - - -
145F MET* 4.5 21.5 - - + -
146F ARG* 3.0 53.0 + - + +
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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
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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