Contacts of the helix formed by residues 135 - 165 (chain F) in PDB entry 5MG3
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 GLY 135 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F GLY* 4.3 0.2 - - - -
100F PRO* 4.7 0.2 - - - -
133F PHE* 4.4 15.7 - - - -
134F VAL* 1.4 76.6 - - - +
136F PRO* 1.3 70.7 - - - +
137F SER 3.5 1.8 - - - -
138F VAL* 3.3 14.7 + - - +
139F GLY* 2.8 27.5 + - - -
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Residues in contact with PRO 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F THR* 3.8 17.4 - - - +
100F PRO* 4.3 20.4 - - + -
133F PHE* 5.8 0.9 - - + -
135F GLY* 1.3 86.4 - - - +
137F SER* 1.4 60.2 + - - +
139F GLY 3.6 0.2 + - - -
140F ALA* 3.1 23.9 + - - +
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Residues in contact with SER 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F PRO* 1.4 80.7 - - - +
138F VAL* 1.4 68.7 + - - +
140F ALA* 3.2 16.4 + - - +
141F ASP* 3.3 19.1 + - - +
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Residues in contact with VAL 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F VAL* 4.5 10.3 - - + -
135F GLY* 3.5 15.5 - - - +
136F PRO 3.3 0.2 - - - -
137F SER* 1.4 81.2 - - - +
139F GLY* 1.4 64.5 + - - +
140F ALA 3.4 0.3 + - - -
141F ASP* 3.5 6.8 + - - +
142F LEU* 3.4 29.2 + - + +
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Residues in contact with GLY 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F ASP 3.2 10.0 - - - +
53F THR* 3.2 11.1 + - - -
54F GLY 3.5 22.2 - - - -
134F VAL* 3.6 13.3 - - - +
135F GLY 2.8 15.5 + - - -
138F VAL* 1.4 71.6 - - - +
140F ALA* 1.4 62.8 + - - +
142F LEU* 3.2 3.3 + - - -
143F ALA 3.1 19.1 + - - -
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Residues in contact with ALA 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F THR* 3.9 12.2 - - + +
136F PRO 3.1 15.1 + - - +
137F SER* 3.3 14.1 - - - +
138F VAL 3.2 0.4 - - - -
139F GLY* 1.4 72.6 - - - +
141F ASP* 1.3 68.9 + - - +
144F GLN* 2.8 44.0 + - + +
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Residues in contact with ASP 141 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572D THR* 4.8 3.8 - - + -
137F SER 3.3 11.5 + - - +
138F VAL* 3.5 7.0 + - - +
139F GLY 3.5 0.4 - - - -
140F ALA* 1.3 79.0 - - - +
142F LEU* 1.3 52.9 + - + +
144F GLN* 4.7 5.3 - - - +
145F THR* 2.7 45.3 + - + +
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Residues in contact with LEU 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572D THR* 3.6 27.5 + - + +
573D GLY* 4.6 7.4 - - - +
51F ASP* 3.1 39.9 - - + +
134F VAL* 4.4 10.1 - - + -
138F VAL* 3.4 25.1 - - + +
139F GLY* 3.2 7.0 + - - +
141F ASP* 1.3 75.0 - - + +
143F ALA* 1.4 50.9 + - - +
145F THR* 3.1 2.1 + - - -
146F GLY* 2.8 31.9 + - - -
197F LEU* 3.4 20.3 - - + +
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Residues in contact with ALA 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F ASP 3.6 2.4 + - - -
52F PHE* 3.7 29.9 - - + -
53F THR* 3.4 31.2 - - - +
139F GLY 3.1 13.4 + - - +
142F LEU* 1.4 72.2 - - - +
144F GLN* 1.4 69.0 + - - +
146F GLY* 3.2 0.3 + - - -
147F ALA* 2.8 31.6 + - - +
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Residues in contact with GLN 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F THR* 4.9 3.6 + - - +
140F ALA* 2.8 50.2 + - + +
141F ASP* 4.0 5.6 - - - +
143F ALA* 1.4 80.6 - - - +
145F THR* 1.3 59.8 + - + +
147F ALA* 3.3 7.3 + - - +
148F MET* 2.8 50.5 + - + +
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Residues in contact with THR 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570D VAL* 3.6 23.9 - - + +
571D GLY* 4.8 1.8 - - - -
572D THR* 2.6 41.4 + - + +
141F ASP* 2.7 23.9 + - + +
142F LEU 3.1 1.7 + - - -
144F GLN* 1.3 71.2 - - + +
146F GLY* 1.3 57.9 + - - +
148F MET* 3.2 14.3 + - - +
149F ALA* 2.8 34.9 + - - +
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Residues in contact with GLY 146 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572D THR* 4.8 0.2 + - - -
575D ILE* 5.7 0.4 - - - -
52F PHE* 4.9 1.3 - - - -
142F LEU 2.8 20.5 + - - -
143F ALA* 3.2 2.9 + - - -
145F THR* 1.3 76.5 + - - +
147F ALA* 1.4 54.3 + - - +
149F ALA* 4.3 4.0 - - - -
150F LEU* 3.0 31.0 + - - +
197F LEU* 3.5 21.5 - - - +
200F VAL* 3.4 16.0 - - - +
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Residues in contact with ALA 147 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F PHE* 4.6 12.4 - - + -
143F ALA 2.8 19.5 + - - +
144F GLN* 3.6 9.2 - - - +
146F GLY* 1.4 68.9 - - - +
148F MET* 1.4 63.9 + - + +
150F LEU* 3.6 8.9 - - - +
151F MET* 3.2 33.2 + - + +
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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
----------------------------------------------------------
570D VAL* 3.7 21.3 - - + -
144F GLN* 2.8 44.9 + - + +
145F THR* 3.8 9.2 - - - +
147F ALA* 1.4 74.3 - - + +
149F ALA* 1.4 54.9 + - - +
151F MET* 3.2 4.5 + - - +
152F ALA* 2.9 34.2 + - + +
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Residues in contact with ALA 149 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566D ILE* 4.6 1.9 - - - +
567D LEU* 3.5 31.3 - - + +
570D VAL* 4.1 9.8 - - - +
571D GLY* 3.9 25.6 - - - +
575D ILE* 4.9 2.9 - - + -
145F THR 2.8 21.2 + - - +
146F GLY* 3.6 7.0 - - - +
148F MET* 1.4 70.8 - - - +
150F LEU* 1.3 65.1 + - - +
152F ALA* 4.4 1.8 - - - +
153F ALA* 3.4 16.5 + - - +
200F VAL* 4.6 4.0 - - + -
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Residues in contact with LEU 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146F GLY 3.0 16.1 + - - +
147F ALA* 3.6 7.9 - - - +
149F ALA* 1.3 83.9 - - - +
151F MET* 1.4 84.7 + - + +
154F LEU* 3.6 3.8 + - - +
200F VAL* 4.0 20.5 - - + +
203F LEU* 3.8 45.8 - - + -
204F MET* 3.5 41.5 - - + +
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Residues in contact with MET 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F ALA* 3.2 20.8 + - + +
148F MET* 3.2 4.9 + - - +
150F LEU* 1.4 103.0 - - + +
152F ALA* 1.4 63.6 + - - +
154F LEU* 3.3 13.0 + - - +
155F LEU* 3.1 24.3 + - - +
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Residues in contact with ALA 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566D ILE* 3.5 26.5 - - + +
570D VAL* 5.1 9.0 - - + -
148F MET 2.9 18.2 + - - +
149F ALA* 4.4 1.3 - - - +
151F MET* 1.4 71.2 - - - +
153F ALA* 1.4 55.4 + - - +
155F LEU* 3.4 13.3 + - + +
156F SER* 2.7 35.3 + - - -
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Residues in contact with ALA 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563D LYS* 3.8 26.2 - - + +
566D ILE* 3.6 8.5 - - + +
567D LEU* 4.0 8.5 - - + -
149F ALA 3.4 15.8 + - - +
151F MET 3.4 0.4 - - - -
152F ALA* 1.4 77.5 - - - +
154F LEU* 1.4 51.8 + - - +
156F SER* 3.2 6.7 + - - -
157F ILE* 3.0 32.6 + - - +
204F MET* 3.4 28.7 - - + -
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Residues in contact with LEU 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150F LEU* 3.6 6.4 + - + +
151F MET* 3.3 15.8 + - - +
153F ALA* 1.4 70.1 - - - +
155F LEU* 1.3 66.9 + - - +
157F ILE* 3.4 5.7 + - + +
158F LEU* 2.9 22.9 + - - +
174F VAL* 4.1 32.4 - - + +
178F ALA* 5.2 10.8 - - + -
204F MET* 3.7 22.2 - - + +
207F ILE* 4.2 25.6 - - + -
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Residues in contact with LEU 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F MET 3.1 11.9 + - - +
152F ALA* 3.5 14.8 - - + +
154F LEU* 1.3 76.4 - - - +
156F SER* 1.4 62.9 + - - +
158F LEU* 3.2 20.1 + - + +
159F VAL* 3.2 43.5 + - + +
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Residues in contact with SER 156 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562D ILE* 3.8 28.5 - - - +
566D ILE* 3.9 22.0 - - - +
152F ALA 2.7 18.1 + - - -
153F ALA* 3.2 13.9 + - - -
155F LEU* 1.4 72.4 - - - +
157F ILE* 1.4 64.8 + - - +
159F VAL* 3.6 7.5 - - - +
160F TYR* 3.2 16.5 + - - +
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Residues in contact with ILE 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559D THR* 3.6 27.1 - - + +
562D ILE* 4.5 10.3 - - + -
563D LYS* 4.3 20.6 - - + -
153F ALA 3.0 20.4 + - - +
154F LEU* 4.1 6.7 - - + +
156F SER* 1.4 74.3 - - - +
158F LEU* 1.3 64.3 + - - +
160F TYR* 3.1 5.0 + - + -
161F VAL* 3.1 31.0 + - + +
174F VAL* 5.5 0.4 - - - -
204F MET* 4.5 0.7 - - - -
207F ILE* 3.9 38.8 - - + +
211F LEU* 3.6 27.4 - - + -
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Residues in contact with LEU 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F LEU 2.9 15.1 + - - +
155F LEU* 3.2 26.0 + - + +
157F ILE* 1.3 75.9 - - - +
159F VAL* 1.4 56.3 + - + +
161F VAL* 3.6 2.8 + - - -
162F GLY 3.0 22.3 + - - -
167F TRP* 3.6 16.4 - - + -
170F ALA* 3.6 27.0 - - + +
171F ALA* 4.2 8.3 - - + +
174F VAL* 3.5 38.7 - - + +
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Residues in contact with VAL 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155F LEU* 3.2 32.5 - - + +
156F SER* 3.6 8.5 - - - +
158F LEU* 1.4 75.5 - - + +
160F TYR* 1.3 62.1 + - - +
162F GLY* 3.6 0.6 + - - -
163F PHE* 3.2 43.9 + - + +
167F TRP* 3.7 18.6 - - + -
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Residues in contact with TYR 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555D ASP* 2.9 30.1 + - + -
558D ILE* 3.5 38.3 - - + +
559D THR* 3.7 24.9 - - - -
562D ILE* 3.8 28.9 - - + -
156F SER 3.2 2.6 + - - +
157F ILE* 3.1 8.7 + - + +
159F VAL* 1.3 75.9 - - - +
161F VAL* 1.4 68.2 + - + +
163F PHE* 3.5 4.3 + - + +
164F ARG* 2.9 63.8 + - + +
165F PHE* 5.7 1.6 - + - -
215F ILE* 6.0 1.6 - - + -
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Residues in contact with VAL 161 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559D THR* 5.6 0.9 - - - +
157F ILE* 3.1 26.1 + - + +
158F LEU* 4.1 4.7 - - - +
160F TYR* 1.4 81.0 - - + +
162F GLY* 1.4 62.7 + - - +
164F ARG* 4.5 4.0 - - - -
165F PHE* 3.2 31.0 + - + +
166F GLU 3.3 7.6 + - - +
169F LEU* 3.8 21.5 - - + -
170F ALA* 3.8 23.3 - - + +
173F VAL* 5.2 5.6 - - + -
211F LEU* 4.2 24.2 - - + -
215F ILE* 5.4 7.4 - - + -
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Residues in contact with GLY 162 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158F LEU 3.0 13.3 + - - -
159F VAL 3.6 0.9 + - - -
160F TYR 3.3 0.2 - - - -
161F VAL* 1.4 75.8 - - - +
163F PHE* 1.4 59.2 + - - +
165F PHE 3.8 1.4 - - - +
166F GLU* 3.5 19.0 + - - -
167F TRP* 3.6 43.7 + - - -
170F ALA* 3.4 10.4 - - - +
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Residues in contact with PHE 163 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F VAL* 3.2 38.1 + - + +
160F TYR* 4.1 4.3 - - + +
162F GLY* 1.4 71.9 - - - +
164F ARG* 1.3 62.7 + - - +
165F PHE 3.6 1.4 + - - +
167F TRP* 4.0 22.4 - + - +
----------------------------------------------------------
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Residues in contact with ARG 164 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551D SER* 4.1 20.2 + - - -
555D ASP* 2.6 41.8 + - - -
160F TYR* 2.9 49.3 + - + +
161F VAL 4.2 0.2 - - - +
163F PHE* 1.3 74.2 - - - +
165F PHE* 1.3 102.0 + - + +
219F ASP* 4.2 6.5 + - - -
222F ARG* 5.1 1.4 - - - +
226F ARG* 5.4 10.3 + - - +
----------------------------------------------------------
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Residues in contact with PHE 165 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555D ASP* 3.7 20.6 - - - -
160F TYR* 5.7 2.0 - + - -
161F VAL* 3.2 22.3 + - + +
162F GLY 3.8 3.8 - - - +
163F PHE 4.9 0.9 - - - +
164F ARG* 1.3 119.1 - - + +
166F GLU* 1.3 66.3 + - + +
169F LEU* 5.3 1.3 - - + -
215F ILE* 3.8 37.5 - - + -
218F SER* 3.2 29.8 - - - +
219F ASP* 3.7 22.2 - - + -
222F ARG* 3.8 39.6 + - + +
226F ARG* 5.6 1.1 + - - -
----------------------------------------------------------
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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