Contacts of the helix formed by residues 128 - 153 (chain C) in PDB entry 5W97
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 GLU 128 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ASN* 3.3 40.4 + - - +
126C PRO 3.3 2.4 - - - -
127C LEU* 1.3 82.5 - - - +
129C VAL* 1.3 69.8 + - + +
130C PRO* 3.3 1.8 - - + -
131C LEU* 3.0 12.3 + - - +
132C LEU* 3.2 9.2 + - - +
31G CYS 5.4 0.3 - - - +
34G ASN* 5.1 2.2 - - - -
35G SER* 4.7 16.2 - - - +
38G HIS* 3.6 43.3 - - + +
101G CDL 4.2 3.9 + - - +
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Residues in contact with VAL 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C GLU* 1.3 79.9 - - + +
130C PRO* 1.3 64.9 - - + +
132C LEU* 3.0 8.2 + - + +
133C ASN* 2.7 38.7 + - - +
176C LEU* 4.0 30.1 - - + +
179C SER* 5.7 2.7 - - - +
180C GLU* 3.5 38.6 - - + +
35G SER* 3.9 16.2 - - - +
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Residues in contact with PRO 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C LEU* 4.8 2.9 - - + -
125C ASN 3.5 21.3 - - - +
126C PRO* 3.7 4.9 - - + +
128C GLU* 3.5 1.3 - - + -
129C VAL* 1.3 93.3 - - + +
131C LEU* 1.3 58.3 + - - +
133C ASN* 3.6 12.2 - - + +
134C THR* 2.8 29.3 + - - -
180C GLU* 3.6 13.2 - - - +
249C TRP* 3.9 2.8 - - + -
253C TYR* 3.6 23.7 - - + -
257C TYR* 3.5 37.2 - - + -
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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
----------------------------------------------------------
126C PRO 3.2 14.7 + - - +
127C LEU* 3.8 11.9 - - + +
128C GLU 3.0 10.9 + - - +
130C PRO* 1.3 74.8 - - - +
132C LEU* 1.3 66.7 + - - +
134C THR* 3.3 4.9 + - - -
135C SER* 3.0 22.2 + - - -
253C TYR* 3.8 18.6 - - + +
31G CYS* 4.1 12.3 - - + -
34G ASN* 4.7 4.9 - - - +
101G CDL 3.7 86.4 - - + +
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Residues in contact with LEU 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C GLU 3.2 6.4 + - - +
129C VAL* 3.0 13.8 + - - +
131C LEU* 1.3 79.5 - - - +
133C ASN* 1.3 61.4 + - - +
135C SER* 3.1 7.4 + - - +
136C VAL* 3.0 38.1 + - + +
172C TYR* 3.8 13.7 - - + +
176C LEU* 3.6 34.1 - - + -
28G VAL* 4.0 4.0 - - + +
31G CYS* 3.9 27.9 - - + +
32G THR* 3.6 24.9 - - + +
35G SER* 4.1 20.2 - - - +
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Residues in contact with ASN 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C VAL* 2.7 32.9 + - - +
130C PRO* 3.6 14.3 - - - +
131C LEU 3.4 0.2 - - - -
132C LEU* 1.3 70.4 - - - +
134C THR* 1.3 63.1 + - - +
136C VAL* 3.2 6.7 + - - +
137C LEU* 3.0 22.0 + - - +
173C PHE* 3.7 38.8 - - + +
176C LEU* 3.5 26.3 - - - +
177C GLN* 3.4 26.2 + - - +
180C GLU* 4.8 1.4 + - - +
249C TRP* 3.7 12.6 - - + -
257C TYR* 5.5 0.4 + - - -
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Residues in contact with THR 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C PRO 2.8 12.8 + - - -
131C LEU* 3.4 12.8 - - - -
132C LEU 3.2 0.2 - - - -
133C ASN* 1.3 79.8 - - - +
135C SER* 1.3 60.8 + - - +
137C LEU* 3.5 1.2 + - - +
138C LEU* 3.1 42.4 + - + +
249C TRP* 2.6 26.3 + - - +
250C LEU* 4.0 20.0 - - + -
253C TYR* 3.5 14.9 - - + -
101G CDL 4.0 22.7 - - + -
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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 3.0 13.7 + - - -
132C LEU* 3.1 10.8 + - - +
134C THR* 1.3 77.4 - - - +
136C VAL* 1.3 59.0 + - - +
138C LEU* 4.2 3.0 - - - +
139C ALA* 3.0 31.2 + - - +
27G SER* 4.5 7.4 - - - -
28G VAL* 3.5 22.0 - - - +
31G CYS* 3.8 23.8 - - - +
101G CDL 4.2 23.9 - - - +
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Residues in contact with VAL 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU* 3.0 30.1 + - + +
133C ASN* 3.5 9.0 - - - +
135C SER* 1.3 79.0 + - - +
137C LEU* 1.3 59.2 + - - +
139C ALA* 3.3 4.0 + - - +
140C SER* 3.0 26.2 + - - -
169C LEU* 3.0 43.1 - - + +
172C TYR* 3.7 28.7 - - + -
173C PHE* 4.0 16.4 - - + +
176C LEU* 4.5 4.3 - - + -
28G VAL* 4.1 12.6 - - + -
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Residues in contact with LEU 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C ASN 3.0 9.9 + - - +
134C THR 4.3 1.8 - - - +
136C VAL* 1.3 74.7 - - + +
138C LEU* 1.3 67.2 + - - +
140C SER* 2.6 21.7 + - - +
141C GLY 3.1 5.4 + - - -
170C GLY* 4.9 2.5 - - - -
173C PHE* 3.4 53.8 - - + -
204C HIS* 4.1 8.1 - - + +
208C VAL* 4.9 2.5 - - + -
242C TRP* 3.9 31.0 - - + -
245C VAL* 4.5 5.6 - - + +
246C ASP* 3.2 26.4 - - + +
249C TRP* 3.7 27.8 - - + -
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Residues in contact with LEU 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C THR* 3.1 30.4 + - + +
135C SER* 4.2 2.7 - - - +
137C LEU* 1.3 76.8 - - - +
139C ALA* 1.3 61.6 + - - +
141C GLY* 3.1 10.4 + - - -
142C VAL* 3.3 16.1 + - - +
246C ASP* 3.7 20.6 - - - +
250C LEU* 4.0 26.7 - - + -
101G CDL 3.8 61.5 - - + +
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Residues in contact with ALA 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C SER 3.0 21.4 + - - +
136C VAL 3.6 4.5 - - - +
138C LEU* 1.3 77.1 - - - +
140C SER* 1.3 57.4 + - - +
142C VAL* 3.0 19.3 + - - +
143C SER* 3.0 14.7 + - - -
169C LEU* 4.0 10.7 - - + +
24G ALA* 3.8 30.3 - - + +
25G LEU* 4.8 2.5 - - + +
28G VAL* 3.6 19.3 - - + -
101G CDL 4.6 2.2 - - + +
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Residues in contact with SER 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C VAL 3.0 13.2 + - - -
137C LEU* 2.6 25.6 + - - +
139C ALA* 1.3 77.1 - - - +
141C GLY* 1.3 55.8 + - - +
143C SER* 3.1 10.4 + - - -
144C ILE* 2.9 31.2 + - - +
166C THR* 3.8 10.2 - - - +
169C LEU* 3.6 19.6 - - - +
242C TRP* 2.7 35.5 + - - -
246C ASP* 4.7 0.2 + - - -
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Residues in contact with GLY 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C LEU 3.1 11.1 + - - -
138C LEU 3.1 6.1 + - - -
140C SER* 1.3 77.8 + - - +
142C VAL* 1.3 59.5 + - - +
144C ILE* 3.2 15.0 - - - +
145C THR* 2.8 23.4 + - - -
242C TRP* 4.9 1.3 - - - -
243C HIS* 3.8 12.4 + - - -
246C ASP* 4.1 12.3 - - - -
16G TRP* 5.3 0.3 - - - -
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Residues in contact with VAL 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C LEU 3.3 12.3 + - - +
139C ALA 3.0 8.8 + - - +
141C GLY* 1.3 75.5 - - - +
143C SER* 1.3 63.7 + - - +
145C THR* 3.3 4.3 + - - -
146C TRP* 3.1 19.1 + - - +
16G TRP* 3.8 30.0 - - + +
19G LEU* 4.0 10.8 - - + +
20G THR* 3.5 33.1 + - - +
23G LEU* 6.4 0.4 - - + -
24G ALA* 4.1 10.1 - - + -
101G CDL 4.0 30.5 - - + -
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Residues in contact with SER 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C ALA 3.0 8.2 + - - -
140C SER* 3.1 20.3 + - - -
142C VAL* 1.3 75.4 - - - +
144C ILE* 1.3 57.4 + - - +
146C TRP* 3.3 6.7 + - - +
147C ALA* 2.9 28.1 + - - +
162C ALA* 3.6 11.3 - - - +
165C ILE* 4.2 11.4 - - - -
166C THR* 3.0 26.6 + - - -
169C LEU* 4.0 2.5 - - - +
20G THR* 3.7 26.2 + - - -
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Residues in contact with ILE 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C SER 2.9 18.6 + - - +
141C GLY* 3.2 19.7 - - - +
143C SER* 1.3 76.1 + - - +
145C THR* 1.3 56.5 + - - +
147C ALA* 3.4 4.3 + - - +
148C HIS* 3.0 26.0 + - - +
163C LEU* 4.3 5.4 - - + -
166C THR* 3.4 17.0 + - + -
215C LEU* 3.5 32.1 - - + -
235C PHE* 3.8 23.0 - - + -
239C ALA* 3.9 25.1 - - + +
242C TRP* 4.4 9.6 - - + -
243C HIS* 3.7 23.1 - - + +
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Residues in contact with THR 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C GLY 2.8 14.1 + - - -
142C VAL 3.3 8.4 + - - -
143C SER 3.2 0.2 - - - -
144C ILE* 1.3 76.6 - - - +
146C TRP* 1.3 65.0 + - - +
148C HIS* 3.2 6.4 + - + +
149C HIS* 3.0 43.7 + - + +
243C HIS* 4.0 14.6 + - - -
16G TRP* 3.5 41.8 - - + -
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Residues in contact with TRP 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C VAL 3.1 11.7 + - - +
143C SER* 3.6 6.5 - - - +
145C THR* 1.3 76.3 - - - +
147C ALA* 1.3 56.0 + - - +
149C HIS* 3.2 3.2 + - - +
150C SER* 2.8 45.2 + - - -
158C HIS* 3.9 21.8 - + - +
161C GLN* 3.5 28.7 - - - -
162C ALA* 3.4 22.0 - - + -
165C ILE* 3.8 22.7 - - + -
13G ALA* 3.4 21.5 + - + +
16G TRP* 3.6 23.6 - - + +
17G ARG* 3.3 34.3 - - + +
20G THR* 3.6 22.4 - - + -
21G PHE* 3.6 17.3 - + - -
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Residues in contact with ALA 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C SER 2.9 10.5 + - - +
144C ILE* 3.5 13.2 - - + +
146C TRP* 1.3 75.0 - - - +
148C HIS* 1.3 63.2 + - - +
150C SER* 3.4 0.5 + - - -
151C LEU* 3.1 18.4 + - - +
159C MET* 3.4 21.1 - - + +
162C ALA* 3.4 23.6 - - + +
163C LEU* 3.8 17.5 - - + +
235C PHE* 3.9 15.7 - - + -
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Residues in contact with HIS 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C ILE 3.0 14.9 + - - +
145C THR* 3.6 11.0 - - + +
146C TRP 3.2 0.2 - - - -
147C ALA* 1.3 77.4 - - - +
149C HIS* 1.3 62.8 + - - +
151C LEU* 3.3 4.9 + - + +
152C MET* 2.5 69.5 + - + +
232C HIS* 3.5 5.3 + + - -
235C PHE* 3.6 29.4 - + + -
236C GLU* 4.0 15.3 - - + +
239C ALA* 5.9 4.9 - - + +
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Residues in contact with HIS 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C THR* 3.0 38.1 + - + +
146C TRP* 3.8 1.6 - - - +
148C HIS* 1.3 78.9 - - - +
150C SER* 1.3 65.7 + - - +
152C MET* 3.9 9.8 - - + +
153C GLU* 3.0 30.6 + - + +
11G TPO 5.6 2.6 + - - -
12G GLY* 3.8 23.2 - - - -
13G ALA* 3.6 22.4 - - - +
16G TRP* 3.7 26.2 + + - -
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Residues in contact with SER 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C TRP* 2.8 41.3 + - - -
147C ALA 3.6 3.4 - - - -
149C HIS* 1.3 77.0 - - - +
151C LEU* 1.3 57.2 + - - +
153C GLU* 3.2 4.0 + - - -
154C GLY 2.9 8.7 + - - -
155C ASP* 2.8 36.1 + - - +
158C HIS* 3.4 10.7 - - - +
159C MET* 3.6 24.7 - - - -
13G ALA* 3.7 10.7 - - - +
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Residues in contact with LEU 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C ALA 3.1 10.6 + - - +
148C HIS* 3.5 8.5 - - + +
149C HIS 3.3 0.2 - - - -
150C SER* 1.3 76.4 - - - +
152C MET* 1.4 60.5 + - - +
154C GLY* 2.9 20.1 + - - +
155C ASP 4.8 2.2 - - - +
159C MET* 3.8 25.9 - - + +
222C GLN* 3.8 21.5 - - - +
227C PHE* 4.1 8.5 - - + -
228C THR 4.3 1.6 - - - +
229C SER* 3.7 9.7 - - - -
232C HIS* 3.3 49.4 - - + +
235C PHE* 4.4 10.8 - - + -
6F VAL* 3.9 24.0 - - + -
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Residues in contact with MET 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C HIS* 2.5 56.3 + - + +
149C HIS* 4.1 10.8 - - + +
151C LEU* 1.4 74.5 - - - +
153C GLU* 1.3 60.1 + - + +
154C GLY 3.5 0.5 + - - -
229C SER* 3.7 28.3 - - - +
230C ASN* 5.3 3.4 - - - +
232C HIS* 2.3 44.0 - - + +
236C GLU* 4.1 13.5 - - - +
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Residues in contact with GLU 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C HIS* 3.0 17.0 + - + +
150C SER* 3.6 4.4 - - - +
151C LEU 3.1 0.2 - - - -
152C MET* 1.3 77.3 - - + +
154C GLY* 1.3 59.0 + - - +
155C ASP* 3.3 7.5 + - + +
229C SER* 5.3 0.2 - - - -
3F GLY 4.9 2.8 - - - +
11G TPO 4.2 2.7 - - - +
12G GLY* 3.4 10.4 - - - -
13G ALA* 2.9 44.0 + - - +
14G ARG 4.9 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) + - + + + + + -
------------------------------------------------------------
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