Contacts of the helix formed by residues 120 - 150 (chain F) in PDB entry 2BS3
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 HIS 120 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E ARG* 3.8 19.5 - - - +
211E LEU 3.4 24.0 - - - -
213E ALA* 3.5 20.1 - - + +
216E ASP* 2.6 41.7 + - + +
217E VAL* 5.8 0.9 - - + -
115F LYS 4.5 0.8 + - - -
118F MET* 3.0 21.9 - - + +
119F ARG* 1.3 76.2 - - - +
121F GLY* 1.3 69.6 + - - +
122F ASP* 3.7 13.8 + - + -
123F THR* 2.9 32.0 + - - +
124F THR* 2.9 26.0 + - - -
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Residues in contact with GLY 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E ARG* 5.2 0.2 - - - +
119F ARG 3.9 3.4 + - - -
120F HIS* 1.3 75.4 - - - +
122F ASP* 1.3 58.9 + - - +
124F THR* 3.2 5.9 + - - -
125F LEU* 2.9 37.6 + - - +
210F LYS* 6.0 2.7 - - - -
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Residues in contact with ASP 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211E LEU* 3.2 21.4 - - - +
212E LEU* 3.9 5.5 - - - +
120F HIS* 3.5 10.3 + - + -
121F GLY* 1.3 74.2 - - - +
123F THR* 1.3 58.8 + - - +
125F LEU* 3.8 15.5 - - - +
126F TRP* 3.4 2.6 + - - +
188F TYR* 2.6 42.3 + - - -
189F ARG* 2.9 35.3 + - - +
206F ARG* 2.7 23.0 + - - -
210F LYS* 4.1 12.9 - - - +
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Residues in contact with THR 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160E ALA 4.9 1.7 + - - -
162E GLY 5.8 0.2 - - - +
211E LEU* 4.1 19.5 - - + +
213E ALA* 3.9 11.6 - - - +
111F PHE* 3.8 27.7 - - + -
114F HIS* 5.0 10.5 - - + -
115F LYS* 4.5 18.4 - - + -
118F MET* 5.0 3.1 - - + +
120F HIS* 2.9 36.5 + - + +
122F ASP* 1.3 75.1 - - - +
124F THR* 1.3 67.3 + - - +
126F TRP* 3.1 14.0 + - - +
127F TRP* 3.3 10.7 + - - +
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Residues in contact with THR 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F LYS* 3.8 32.3 + - + +
119F ARG* 4.8 2.6 - - - -
120F HIS 2.9 22.6 + - - -
121F GLY* 3.6 7.0 - - - -
123F THR* 1.3 79.4 - - - +
125F LEU* 1.3 63.4 + - + +
127F TRP* 3.1 15.2 + - + +
128F ILE* 3.1 25.4 + - + +
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Residues in contact with LEU 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121F GLY* 2.9 22.8 + - - +
122F ASP* 3.8 20.0 - - - +
123F THR 3.2 0.2 - - - -
124F THR* 1.3 75.5 - - + +
126F TRP* 1.3 59.0 + - - +
128F ILE* 3.3 24.1 + - + +
129F GLN* 3.0 29.3 + - - +
185F VAL* 3.9 24.7 - - + +
188F TYR* 5.1 1.6 - - + -
189F ARG* 3.6 15.7 - - - +
210F LYS* 6.2 0.7 - - - -
213F LYS* 4.0 30.1 - - - +
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Residues in contact with TRP 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166E MET* 4.5 1.8 - - + -
209E MET* 3.5 28.4 - - + -
211E LEU* 3.5 24.5 - - + -
100F LYS* 3.2 34.3 - - + -
101F PHE* 4.5 0.2 - - - -
102F PRO* 4.0 23.6 - - + -
111F PHE* 3.6 32.3 - + - -
122F ASP 3.4 0.4 + - - +
123F THR 3.1 10.5 + - - +
125F LEU* 1.3 73.2 - - - +
127F TRP* 1.3 68.8 + + - +
129F GLN* 3.0 27.5 + - - +
130F ALA* 2.9 43.8 + - + -
189F ARG* 3.2 15.6 - - - +
1255F HEM 2.8 32.9 + - + +
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Residues in contact with TRP 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F PRO* 4.3 20.4 - - + -
108F TYR* 3.6 41.3 - + - -
111F PHE* 3.6 33.0 - + + -
112F LYS* 4.6 18.2 - - + -
115F LYS* 3.5 37.7 - - + +
123F THR 3.3 5.5 + - - +
124F THR* 3.1 11.8 + - + +
126F TRP* 1.3 89.7 - + - +
128F ILE* 1.3 59.8 + - + +
130F ALA* 3.2 7.7 + - + +
131F MET* 2.9 65.9 + - + +
1257F LMT 4.2 15.7 - - + -
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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
----------------------------------------------------------
124F THR* 3.1 25.1 + - + +
125F LEU* 3.5 27.8 - - + +
126F TRP 3.2 0.2 - - - -
127F TRP* 1.3 81.4 - - + +
129F GLN* 1.3 59.6 + - - +
131F MET* 4.4 9.0 - - - -
132F THR* 2.8 45.4 + - + +
181F LEU* 4.2 29.8 - - + -
185F VAL* 5.4 5.2 - - + -
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Residues in contact with GLN 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 LEU 3.0 13.3 + - - +
126F TRP* 3.0 21.4 + - + +
128F ILE* 1.3 77.6 - - - +
130F ALA* 1.3 57.3 + - - +
132F THR* 3.7 5.2 - - - -
133F GLY* 2.9 13.3 + - - -
182F HIS* 2.9 38.7 + - + +
185F VAL* 3.5 22.7 - - + -
186F GLY* 3.7 22.0 - - - -
189F ARG* 2.6 42.8 + - - +
1255F HEM 3.8 33.1 + - + +
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Residues in contact with ALA 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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101F PHE* 3.4 35.0 - - + -
102F PRO* 5.2 2.2 - - + -
126F TRP* 2.9 33.7 + - + +
127F TRP* 3.2 12.8 + - + +
129F GLN* 1.3 77.4 - - - +
131F MET* 1.3 57.1 + - + +
133F GLY 3.3 0.5 + - - -
134F PHE* 3.0 26.9 + - - +
1255F HEM 4.2 4.9 - - + +
1257F LMT 4.4 7.4 - - + +
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Residues in contact with MET 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127F TRP* 2.9 52.5 + - + +
128F ILE* 3.8 8.7 - - - +
130F ALA* 1.3 75.8 - - - +
132F THR* 1.3 64.8 + - + +
134F PHE* 3.3 4.9 + - - +
135F ALA* 3.0 23.4 + - - +
1257F LMT 3.2 32.3 - - + +
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Residues in contact with THR 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128F ILE* 2.8 37.9 + - + +
129F GLN* 3.6 0.9 - - - -
131F MET* 1.3 74.2 - - + +
133F GLY* 1.3 64.3 + - - +
135F ALA* 3.4 7.5 + - - +
136F MET* 3.0 30.6 + - - +
178F ALA* 3.5 36.8 - - + +
181F LEU* 4.5 9.2 - - + -
182F HIS* 2.8 31.2 + - - +
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Residues in contact with GLY 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 GLN 2.9 18.7 + - - -
130F ALA 3.7 1.6 - - - -
131F MET 3.2 0.4 - - - -
132F THR* 1.3 77.2 + - - +
134F PHE* 1.3 62.1 + - - +
136F MET* 3.2 10.9 + - - -
137F PHE 3.6 4.9 + - - -
182F HIS* 3.7 4.5 - - - -
1255F HEM 3.1 48.2 - - - +
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Residues in contact with PHE 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ILE* 4.2 13.9 - - + -
95C PHE* 3.8 37.7 - + + -
98C MET* 3.5 34.8 - - + -
137C PHE* 4.2 15.0 - + - -
101F PHE* 4.1 9.9 - + + -
130F ALA 3.0 16.1 + - - +
131F MET 3.3 5.4 + - - +
133F GLY* 1.3 76.6 - - - +
135F ALA* 1.3 64.6 + - + +
137F PHE* 3.2 34.6 + + - +
138F PHE* 3.4 30.7 - + - -
1257F LMT 4.2 19.1 - - + -
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Residues in contact with ALA 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F MET 3.0 16.7 + - - +
132F THR* 3.8 9.0 - - - +
133F GLY 3.3 0.4 - - - -
134F PHE* 1.3 81.0 - - + +
136F MET* 1.3 61.4 + - + +
137F PHE 3.1 1.5 + - - -
138F PHE* 3.2 13.6 + - - +
139F LEU* 3.2 36.7 + - + +
174F VAL* 6.1 0.7 - - + -
178F ALA* 5.2 4.0 - - + -
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Residues in contact with MET 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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90F PHE* 3.4 15.9 - - + -
132F THR 3.0 20.6 + - - +
133F GLY 3.2 5.5 + - - +
135F ALA* 1.3 72.2 - - - +
137F PHE* 1.3 66.1 + - - +
138F PHE 3.1 2.0 - - - -
139F LEU* 3.8 2.2 - - + +
140F GLY 2.9 22.8 + - - +
175F LEU* 3.9 18.8 - - + -
178F ALA* 4.3 9.2 - - + +
179F VAL* 3.8 33.0 - - - -
182F HIS* 3.4 45.1 - - + +
1255F HEM 3.6 33.7 - - + -
1256F HEM 4.2 2.9 - - - -
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Residues in contact with PHE 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C MET* 4.9 0.9 - - - -
134C PHE* 4.2 3.1 - + - -
137C PHE* 3.3 69.9 - + + +
138C PHE* 3.7 27.8 - + - -
90F PHE* 5.0 1.6 - - - -
94F ALA* 3.7 14.6 - - + -
98F MET* 4.2 16.2 - - - -
101F PHE* 4.2 13.2 - + - -
133F GLY 3.6 4.0 + - - -
134F PHE* 3.2 29.7 + + - +
135F ALA 3.1 0.6 - - - -
136F MET* 1.3 78.3 - - - +
138F PHE* 1.3 61.5 + - + +
141F SER* 2.6 27.6 + - - -
1255F HEM 3.5 31.2 - - + +
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Residues in contact with PHE 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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87C PHE* 4.1 18.6 - + + -
90C PHE* 4.0 14.6 - + - -
91C ILE* 3.7 42.6 - - + -
94C ALA* 4.5 2.9 - - + -
137C PHE* 3.7 30.5 - + - -
141C SER* 3.3 30.6 - - - +
134F PHE* 3.4 48.0 - + - -
135F ALA* 3.6 9.4 - - - +
137F PHE* 1.3 82.0 - - + +
139F LEU* 1.3 64.7 + - + +
141F SER 4.3 0.2 - - - -
142F VAL* 3.1 28.4 + - - +
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Residues in contact with LEU 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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145C TYR* 6.1 2.5 - - + -
135F ALA* 3.2 29.8 + - + +
136F MET* 4.3 1.6 - - - +
138F PHE* 1.3 77.7 - - + +
140F GLY* 1.3 67.2 + - - +
141F SER 3.5 0.3 + - - -
142F VAL* 3.5 16.3 + - - +
143F HIS 3.7 3.6 + - - -
171F LEU* 3.9 37.1 - - + +
174F VAL* 3.6 32.5 - - + -
175F LEU* 4.1 32.2 - - + +
178F ALA* 4.7 4.9 - - + -
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Residues in contact with GLY 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F PHE* 4.1 13.5 - - - -
136F MET* 2.9 18.6 + - - +
139F LEU* 1.3 75.0 - - - +
141F SER* 1.3 62.4 + - - +
142F VAL 3.3 0.2 + - - -
143F HIS* 3.3 3.5 + - - +
144F LEU* 3.0 29.2 + - - +
175F LEU* 4.3 6.8 - - - +
1256F HEM 4.3 19.1 - - - -
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Residues in contact with SER 141 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C PHE 4.4 1.3 - - - -
138C PHE* 3.3 48.5 - - - -
141C SER* 4.4 1.8 - - - -
142C VAL* 3.6 3.6 - - - +
87F PHE* 4.1 13.6 - - - -
90F PHE* 4.1 4.2 - - - -
136F MET 3.8 2.8 + - - -
137F PHE 2.6 26.3 + - - -
138F PHE 4.3 3.4 - - - -
139F LEU 3.4 1.0 - - - -
140F GLY* 1.3 75.8 - - - +
142F VAL* 1.3 63.1 + - - +
144F LEU* 4.0 0.3 - - - +
145F TYR* 3.1 26.5 + - - +
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Residues in contact with VAL 142 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C PHE* 5.6 1.3 - - + -
141C SER 3.6 24.2 - - - +
142C VAL* 4.1 16.0 - - + +
145C TYR* 3.8 25.8 - - + -
146C ILE* 5.2 1.8 - - + -
138F PHE 3.1 20.9 - - - +
139F LEU 3.7 1.1 - - - +
140F GLY 3.3 0.6 - - - -
141F SER* 1.3 78.0 - - - +
143F HIS* 1.3 63.1 + - - +
145F TYR* 3.9 1.9 - - - +
146F ILE* 3.3 40.9 + - + +
168F MET* 4.4 2.7 - - - -
171F LEU* 3.6 29.4 - - + -
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Residues in contact with HIS 143 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F LEU 3.7 6.8 + - - +
140F GLY 3.3 6.8 + - - +
142F VAL* 1.3 78.9 - - - +
144F LEU* 1.3 63.6 + - - +
146F ILE* 3.4 4.6 + - - +
147F MET* 3.0 48.8 + - + +
168F MET* 4.6 9.4 - - + +
171F LEU* 4.7 0.7 - - + -
172F TYR* 3.1 34.2 + + + -
175F LEU* 4.5 9.0 - - + -
1256F HEM 2.0 89.4 + + + -
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Residues in contact with LEU 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F ALA* 4.3 15.0 - - - +
86F VAL* 4.2 9.9 - - + +
87F PHE* 3.7 34.0 - - + +
90F PHE* 3.7 41.1 - - + -
140F GLY 3.0 19.9 + - - +
141F SER 4.0 0.7 - - - +
143F HIS* 1.3 78.8 - - - +
145F TYR* 1.3 62.9 + - - +
147F MET* 3.5 3.8 + - - +
148F MET* 3.1 24.1 + - - +
1256F HEM 3.9 50.0 - - + -
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Residues in contact with TYR 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C LEU* 6.1 2.5 - - + -
142C VAL* 3.8 24.9 - - + -
167C TRP 2.8 21.0 + - - -
168C MET* 3.5 23.6 - - - -
170C PRO* 3.1 20.9 - - + +
171C LEU* 3.4 32.7 - - + +
87F PHE* 3.9 13.2 - + + -
141F SER 3.1 18.1 + - - +
142F VAL 3.9 2.7 - - - +
144F LEU* 1.3 76.6 - - - +
146F ILE* 1.3 61.5 + - + +
148F MET* 3.3 30.9 + - + +
149F THR* 2.8 49.5 + - + +
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Residues in contact with ILE 146 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C VAL* 5.3 0.9 - - + -
146C ILE* 4.9 19.7 - - + -
150C GLN* 6.2 2.0 - - - +
142F VAL* 3.3 31.8 + - + +
143F HIS* 3.8 6.7 - - - +
144F LEU 3.3 0.2 - - - -
145F TYR* 1.3 79.5 - - + +
147F MET* 1.3 73.9 + - + +
149F THR* 3.7 5.8 - - - -
150F GLN* 2.7 54.1 + - + +
162F ARG* 4.0 25.4 - - - +
166F GLU* 6.0 0.4 - - - +
168F MET* 4.3 19.7 - - + -
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Residues in contact with MET 147 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F VAL* 4.3 7.4 - - - +
83F ALA* 4.1 6.3 - - + -
143F HIS* 3.0 44.1 + - + +
144F LEU* 3.9 4.7 - - - +
146F ILE* 1.3 85.0 - - + +
148F MET* 1.3 60.4 + - - +
150F GLN 5.0 3.1 - - - +
151F PRO* 3.6 24.1 - - - +
154F ILE* 4.0 17.9 - - + +
162F ARG* 3.5 38.1 - - - +
172F TYR* 4.0 0.4 - - - +
1256F HEM 3.5 57.4 - - + +
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Residues in contact with MET 148 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F SER* 2.9 39.8 + - - +
83F ALA* 3.6 14.8 - - + +
84F ALA* 3.8 27.8 - - + +
87F PHE* 4.4 15.5 - - + -
144F LEU 3.1 17.7 + - - +
145F TYR* 3.5 36.8 - - + +
146F ILE 3.1 0.2 - - - -
147F MET* 1.3 80.4 - - - +
149F THR* 1.3 63.0 + - + +
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Residues in contact with THR 149 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C SER 5.3 0.5 - - - +
166C GLU 3.8 8.3 + - - -
167C TRP* 3.7 42.3 - - + +
170C PRO* 5.2 2.9 - - + -
145F TYR* 2.8 57.2 + - + +
146F ILE* 3.6 6.9 + - - +
148F MET* 1.3 84.7 - - + +
150F GLN* 1.3 68.8 + - - +
151F PRO* 3.3 8.9 - - - +
152F GLN* 4.2 3.8 + - - +
----------------------------------------------------------
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Residues in contact with GLN 150 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C ILE* 6.2 1.4 - - - +
165C SER 5.6 0.7 - - - +
166C GLU* 3.8 44.9 + - - +
168C MET* 6.1 0.8 - - - +
146F ILE* 2.7 43.3 + - + +
147F MET* 4.2 1.9 - - - +
149F THR* 1.3 85.7 + - - +
151F PRO* 1.3 59.7 - - - +
152F GLN* 3.1 14.1 - - - +
153F THR* 2.5 46.5 + - + +
154F ILE* 4.4 2.9 - - - +
162F ARG* 4.6 2.3 + - - -
166F GLU* 5.3 0.2 - - - +
246F LYS* 3.6 23.4 + - - +
247F TYR* 4.8 3.9 + - - +
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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