Contacts of the helix formed by residues 126 - 155 (chain C) in PDB entry 2NS8
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 SER 126 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C THR* 4.1 0.4 - - - -
124C GLY 3.5 3.4 + - - -
125C PHE* 1.3 75.2 - - - +
127C LEU* 1.3 58.9 + - - +
128C GLU* 3.6 10.5 + - - +
129C ASN* 3.0 39.2 + - - +
130C ALA* 2.8 27.5 + - - +
206C GLN* 4.6 1.3 + - - -
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Residues in contact with LEU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C LEU* 3.9 29.2 - - + -
121C THR* 3.8 18.4 - - + +
125C PHE 3.8 1.0 + - - -
126C SER* 1.3 72.1 - - - +
128C GLU* 1.3 64.8 + - - +
130C ALA* 3.3 1.0 + - - +
131C LEU* 3.0 27.0 + - + +
169D LEU* 4.0 26.7 - - + +
172D GLN* 4.1 41.7 - - + +
173D ALA* 4.1 18.6 - - + +
176D LEU* 4.3 9.6 - - + -
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Residues in contact with GLU 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C SER* 3.7 8.4 - - - +
127C LEU* 1.3 79.2 - - - +
129C ASN* 1.3 58.3 + - - +
131C LEU* 3.1 8.8 - - - +
132C TYR* 3.0 60.7 + - + +
206C GLN* 3.1 39.8 + - - +
176D LEU* 4.0 26.7 - - + +
180D GLN* 5.1 3.3 - - - +
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Residues in contact with ASN 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C PHE* 4.0 22.6 - - + -
126C SER* 3.0 28.0 + - - +
128C GLU* 1.3 78.9 - - - +
130C ALA* 1.3 66.1 + - - +
132C TYR* 3.8 6.1 - - - +
133C ALA* 3.0 24.8 + - - +
200C GLN* 2.9 32.9 + - + +
206C GLN* 3.1 25.1 + - - +
188D HIS* 3.1 17.2 + - - +
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Residues in contact with ALA 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C LEU* 4.2 14.8 - - + +
120C LEU* 4.0 30.2 - - + +
121C THR* 4.4 7.0 - - + -
125C PHE* 4.1 9.5 - - + +
126C SER 2.8 17.3 + - - +
127C LEU* 3.5 12.3 - - - +
129C ASN* 1.3 72.7 - - - +
131C LEU* 1.3 58.4 + - - +
133C ALA* 3.2 2.5 + - - +
134C LEU* 3.0 36.2 + - - +
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Residues in contact with LEU 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C LEU* 4.3 7.8 - - + +
127C LEU* 3.0 11.6 + - + +
128C GLU 3.1 9.4 - - - +
130C ALA* 1.3 79.6 - - - +
132C TYR* 1.3 62.2 + - + +
134C LEU* 3.4 2.8 + - - +
135C SER* 2.8 33.9 + - - -
173D ALA* 3.8 40.4 - - + +
176D LEU* 4.1 27.8 - - + -
177D PHE* 3.5 28.3 - - + -
3F TRP* 3.5 33.9 - - + -
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Residues in contact with TYR 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C GLU* 3.0 48.9 + - + +
129C ASN* 3.8 11.9 - - - +
130C ALA 3.3 0.2 - - - -
131C LEU* 1.3 81.2 - - + +
133C ALA* 1.3 56.7 + - - +
135C SER* 3.6 3.2 + - - -
136C ALA* 2.9 30.7 + - - +
197C PHE* 5.1 0.2 - - - -
206C GLN* 4.6 1.1 - - - -
176D LEU* 4.7 4.7 - - + -
177D PHE* 5.3 3.1 - + - -
180D GLN* 2.3 39.9 + - - -
184D PRO* 3.4 9.5 - - + +
185D ALA* 3.6 35.4 - - + +
188D HIS* 3.2 52.3 - + + +
189D GLY* 5.1 3.0 - - - +
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Residues in contact with ALA 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C LEU* 5.0 7.6 - - + -
120C LEU* 5.1 4.3 - - + -
125C PHE* 5.5 6.5 - - + -
129C ASN 3.0 16.7 + - - +
130C ALA* 3.6 5.8 - - - +
132C TYR* 1.3 75.6 - - - +
134C LEU* 1.3 59.6 + - - +
136C ALA 3.4 0.2 + - - -
137C VAL* 3.0 35.1 + - - +
197C PHE* 3.4 44.1 - - + -
188D HIS* 5.3 0.4 - - - -
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Residues in contact with LEU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C PHE* 4.5 2.9 - - + -
79C LEU* 4.0 23.3 - - + -
82C ASN* 5.6 5.4 - - - +
116C GLN* 3.7 31.4 - - + +
117C LEU* 3.9 18.4 - - + -
120C LEU* 3.8 18.2 - - + -
130C ALA 3.0 19.4 + - - +
131C LEU 3.9 2.7 - - - +
133C ALA* 1.3 77.8 - - - +
135C SER* 1.3 61.7 + - - +
137C VAL* 3.5 4.7 + - + +
138C GLY* 3.0 21.3 + - - -
1F TRP 5.0 0.2 - - - +
3F TRP* 3.6 44.0 - - + +
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Residues in contact with SER 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C LEU 2.8 19.2 + - - -
132C TYR* 3.9 4.7 + - - -
134C LEU* 1.3 76.3 - - - +
136C ALA* 1.3 57.8 + - - +
139C HIS* 2.7 55.0 + - - +
140D PHE* 5.9 1.2 - - - -
177D PHE* 4.9 2.4 - - - -
185D ALA* 4.3 19.7 + - - +
2F THR 3.2 16.3 - - - +
3F TRP* 3.7 17.0 + - - +
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Residues in contact with ALA 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C TYR 2.9 20.0 + - - +
133C ALA 3.6 4.7 - - - +
134C LEU 3.2 0.2 - - - -
135C SER* 1.3 75.5 + - - +
137C VAL* 1.3 65.5 + - - +
139C HIS* 4.2 0.2 - - - -
140C PHE* 3.1 27.9 + - - +
193C LEU* 3.8 12.1 - - + +
197C PHE* 4.1 15.7 - - + -
140D PHE* 4.3 15.1 - - + -
185D ALA 5.8 0.4 - - - +
189D GLY* 4.2 22.2 - - - -
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Residues in contact with VAL 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C LEU* 4.2 24.0 - - + +
82C ASN* 5.1 5.4 - - - +
83C ALA* 3.6 33.9 - - + +
133C ALA 3.0 16.4 + - - +
134C LEU* 4.0 4.5 - - + +
136C ALA* 1.3 76.4 - - - +
138C GLY* 1.3 55.0 + - - +
140C PHE* 3.8 1.2 - - - +
141C THR* 2.7 38.5 + - - +
190C LEU* 4.0 11.4 - - + -
193C LEU* 3.9 13.2 - - + -
194C ILE* 5.6 0.7 - - + -
197C PHE* 3.6 24.0 - - + -
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Residues in contact with GLY 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C PHE* 4.1 10.3 - - - -
134C LEU 3.0 16.8 + - - -
135C SER 3.7 0.9 - - - -
137C VAL* 1.3 79.0 - - - +
139C HIS* 1.3 57.0 + - - +
141C THR* 3.9 1.9 - - - -
142C LEU* 3.0 30.0 + - - +
1F TRP 4.3 6.1 - - - -
2F THR* 3.8 23.1 - - - +
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Residues in contact with HIS 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C SER* 2.7 43.9 + - - +
136C ALA 4.4 1.8 - - - +
138C GLY* 1.3 71.4 - - - +
140C PHE* 1.3 59.0 + - - +
142C LEU* 4.6 3.8 - - - -
143C GLY* 2.9 26.5 + - - -
139D HIS 4.1 0.5 - - - +
140D PHE* 4.4 8.0 - + + -
143D GLY* 3.6 9.5 - - - -
144D SER* 3.7 33.4 - - - +
147D GLU* 3.6 27.3 - - + +
148D ASP* 4.7 0.4 + - - -
2F THR* 3.1 23.4 + - - -
4F ASN* 3.1 38.9 + - - +
5F ALA 5.2 0.2 - - - -
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Residues in contact with PHE 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C ALA 3.1 20.3 + - - +
137C VAL 3.8 1.3 - - - +
139C HIS* 1.3 75.8 - - - +
141C THR* 1.3 60.5 + - - +
143C GLY 3.8 0.3 - - - -
144C SER* 2.4 47.1 + - - -
185C ALA 4.6 1.1 - - - -
186C PHE* 3.4 55.0 - + - -
189C GLY* 3.7 13.2 - - - -
190C LEU* 3.7 14.6 - - + -
193C LEU* 4.0 20.2 - - + -
135D SER 5.5 0.2 - - - -
136D ALA* 4.0 39.0 - - + -
139D HIS* 4.5 4.5 - + + +
140D PHE* 4.2 21.7 - - + +
193D LEU* 5.5 2.0 - - + -
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Residues in contact with THR 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ALA* 3.6 34.8 - - - +
86C PHE* 4.3 14.5 - - + -
87C ARG* 3.7 25.8 - - + +
90C LEU* 4.5 1.3 - - + -
137C VAL* 2.7 24.5 + - - +
138C GLY 3.9 2.9 - - - -
140C PHE* 1.3 75.0 - - - +
142C LEU* 1.3 66.3 + - - +
144C SER* 3.2 2.4 + - - -
145C VAL* 3.1 24.5 + - - +
186C PHE* 3.6 24.6 - - + -
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Residues in contact with LEU 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C PHE* 4.4 7.4 - - + -
90C LEU* 3.7 36.2 - - + +
97C ALA* 3.8 17.0 - - + +
100C HIS* 4.1 8.1 - - + -
101C LEU* 3.6 34.3 - - + -
138C GLY 3.0 18.0 + - - +
139C HIS* 4.1 2.9 - - - +
141C THR* 1.3 75.2 - - - +
143C GLY* 1.3 59.5 + - - +
144C SER 3.2 0.2 + - - -
145C VAL* 3.3 1.4 + - - +
146C LEU* 2.9 40.4 + - + +
143D GLY 5.3 1.8 - - - +
147D GLU* 3.6 25.1 - - + +
2F THR* 4.1 9.4 - - + -
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Residues in contact with GLY 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C HIS 2.9 19.4 + - - -
140C PHE 3.8 0.2 - - - -
142C LEU* 1.3 76.6 - - - +
144C SER* 1.3 59.9 + - - +
146C LEU* 4.0 7.5 - - - +
147C GLU* 3.3 19.9 + - - +
139D HIS* 3.6 20.8 - - - -
142D LEU* 5.0 2.6 - - - +
143D GLY* 3.6 20.6 - - - -
146D LEU* 5.4 0.9 - - - -
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Residues in contact with SER 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ARG* 5.3 3.1 - - - -
140C PHE* 2.4 44.3 + - - -
141C THR 3.5 5.8 - - - -
142C LEU 3.1 0.2 - - - -
143C GLY* 1.3 79.0 - - - +
145C VAL* 1.3 62.9 + - - +
147C GLU* 3.7 1.6 + - - +
148C ASP* 3.2 33.3 + - - +
186C PHE* 4.1 18.8 - - - -
139D HIS* 3.7 16.9 - - - +
4G ASN* 4.3 0.2 + - - -
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Residues in contact with VAL 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ARG* 3.8 35.4 - - + +
90C LEU* 4.0 21.3 - - + -
91C LEU* 3.8 20.4 - - + -
97C ALA* 4.0 9.6 - - + -
141C THR 3.1 16.7 + - - +
142C LEU 4.1 2.0 - - - +
144C SER* 1.3 75.3 - - - +
146C LEU* 1.3 67.8 + - - +
148C ASP* 3.6 5.7 - - - +
149C GLN* 2.8 49.6 + - - +
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Residues in contact with LEU 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ALA* 3.3 25.7 - - + +
98C LYS* 3.3 38.0 - - + +
101C LEU* 4.0 20.6 - - + -
142C LEU* 2.9 30.8 + - + +
143C GLY* 4.0 4.9 - - - +
145C VAL* 1.3 77.7 - - - +
147C GLU* 1.3 61.3 + - - +
149C GLN* 3.9 3.6 - - - +
150C GLU* 3.1 26.2 + - - +
101D LEU* 3.9 14.6 - - + +
143D GLY* 5.5 0.4 - - - -
146D LEU* 3.7 33.7 - - + -
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Residues in contact with GLU 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C GLY 3.3 4.6 + - - +
145C VAL 3.2 0.4 - - - -
146C LEU* 1.3 77.7 - - - +
148C ASP* 1.3 65.6 - - - +
150C GLU* 3.2 0.6 + - - -
151C HIS* 2.5 56.8 + - - -
100D HIS 4.9 1.3 - - - +
101D LEU* 3.2 10.4 - - + +
102D GLY 2.6 29.4 + - - -
103D THR* 4.7 1.0 + - - -
139D HIS* 3.6 22.4 - - + +
142D LEU* 3.4 28.9 - - + -
1G TRP* 5.0 0.9 + - - -
2G THR* 2.6 22.0 + - + +
4G ASN* 3.3 14.8 - - - +
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Residues in contact with ASP 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ARG* 3.3 17.3 + - - -
91C LEU* 5.3 7.6 - - + +
144C SER* 3.2 20.5 + - - +
145C VAL* 3.2 8.6 + - + +
147C GLU* 1.3 80.7 - - - +
149C GLN* 1.3 65.2 + - + +
152C GLN* 3.3 29.7 + - - +
182C ALA* 3.2 31.6 - - - +
139D HIS* 4.7 0.9 + - - -
4G ASN* 2.5 33.3 + - - +
6G TYR* 3.7 17.3 + - + -
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Residues in contact with GLN 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LEU 3.1 25.1 + - - -
91C LEU* 3.9 17.4 + - + +
93C HIS 3.2 17.2 + - - -
94C ARG* 5.0 0.6 - - - +
95C ASP* 3.6 16.3 - - - +
96C GLY 3.3 7.1 + - - +
97C ALA* 3.0 28.4 + - - +
98C LYS* 4.3 1.8 + - + +
145C VAL* 2.8 32.6 + - + +
146C LEU* 4.0 3.4 - - - +
148C ASP* 1.3 74.4 - - - +
150C GLU* 1.3 61.5 + - - +
152C GLN* 3.7 9.1 + - - +
153C VAL* 3.3 23.9 + - - +
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Residues in contact with GLU 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ASP* 5.2 2.9 - - - +
98C LYS* 2.5 36.1 + - - +
146C LEU 3.1 17.9 + - - +
147C GLU 3.9 2.2 - - - +
148C ASP 3.2 0.2 - - - -
149C GLN* 1.3 76.9 - - - +
151C HIS* 1.3 66.0 + - - +
152C GLN 3.0 1.8 - - - -
153C VAL* 3.0 26.9 + - - +
154C ALA* 3.0 20.7 + - + +
49D ARG* 3.8 16.0 + - - +
101D LEU* 3.8 27.6 - - + +
102D GLY* 3.9 15.3 - - - +
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Residues in contact with HIS 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C GLU* 2.5 60.4 + - - +
148C ASP 4.1 0.4 - - - +
150C GLU* 1.3 76.2 - - - +
152C GLN* 1.3 56.8 + - - +
154C ALA* 3.7 2.6 - - - +
155C LYS* 2.9 33.5 + - - +
158C ARG* 4.3 5.7 + - - -
102D GLY* 3.2 31.3 + - - -
103D THR 3.3 18.3 + - - -
1G TRP* 4.5 0.4 - - - -
2G THR* 4.2 1.4 + - - -
4G ASN* 3.5 20.7 - - - +
6G TYR* 3.7 24.5 - - + +
7G ALA* 3.5 25.2 - - + -
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Residues in contact with GLN 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C ASP* 3.3 22.0 + - - +
149C GLN* 3.9 9.1 - - - +
150C GLU 3.0 1.0 - - - -
151C HIS* 1.3 76.9 - - - +
153C VAL* 1.3 62.4 + - - +
155C LYS* 3.6 44.0 - - + +
156C GLU* 4.6 5.5 - - - +
6G TYR* 3.6 39.3 + - + -
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Residues in contact with VAL 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ARG* 6.1 6.3 - - + +
95C ASP* 5.0 10.3 - - - +
149C GLN 3.3 17.3 - - - +
150C GLU* 3.0 29.0 + - - +
152C GLN* 1.3 77.6 - - - +
154C ALA* 1.3 71.1 + - - +
155C LYS 3.2 0.2 - - - -
156C GLU* 3.1 20.9 + - - +
157C GLU* 3.7 20.0 - - - +
49D ARG* 4.5 7.2 - - - +
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Residues in contact with ALA 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C GLU* 3.0 15.9 + - - +
151C HIS* 3.3 3.3 + - - +
153C VAL* 1.3 77.7 - - - +
155C LYS* 1.3 59.4 + - - +
156C GLU 3.1 0.9 - - - -
157C GLU* 3.2 11.5 + - - +
158C ARG* 3.2 45.1 + - - +
49D ARG* 3.1 31.8 + - - +
102D GLY* 4.0 8.7 - - - +
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Residues in contact with LYS 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C HIS 2.9 14.8 + - - +
152C GLN* 3.6 48.0 - - + +
154C ALA* 1.3 76.0 - - - +
156C GLU* 1.3 79.6 + - - +
158C ARG* 3.7 9.5 - - - +
159C GLU 5.2 0.7 - - - +
104D ARG* 4.5 12.0 + - - +
6G TYR* 5.0 4.2 - - + +
9G ALA* 3.5 34.6 - - + +
10G ALA 3.7 19.3 + - - +
11G PRO* 3.3 26.9 + - - +
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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