Contacts of the helix formed by residues 133 - 160 (chain D) in PDB entry 5YWB
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 PRO 133 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D PHE* 1.3 92.5 - - + +
134D LYS* 1.3 92.8 + - + +
135D LEU 3.7 0.2 - - - -
136D LEU* 4.1 10.2 + - + +
137D ILE* 3.3 27.0 + - - +
194D ARG* 3.5 28.7 - - + +
195D TYR* 4.5 7.6 - - - +
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Residues in contact with LYS 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D PHE* 3.4 7.7 - - + +
133D PRO* 1.3 113.8 - - + +
135D LEU* 1.3 72.1 + - + +
136D LEU 3.1 1.8 - - - -
137D ILE* 3.1 18.7 + - + +
138D ALA* 2.9 20.5 + - - +
195D TYR 5.5 2.4 + - - -
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Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ILE* 3.7 41.1 - - + -
123D TYR* 4.1 15.1 - - + -
126D ASN* 4.8 10.3 - - + +
127D ILE* 3.5 35.8 - - + +
132D PHE* 3.6 38.7 - - + +
134D LYS* 1.3 78.9 - - + +
136D LEU* 1.3 57.1 + - + +
138D ALA* 3.0 12.1 + - + +
139D LEU* 2.9 28.1 + - - +
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Residues in contact with LEU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D PHE* 4.8 13.5 - - + -
74D ARG* 6.0 0.2 - - - +
124D TYR* 4.5 15.5 - - + -
127D ILE* 3.6 32.1 - - + -
132D PHE 3.3 24.2 - - - +
133D PRO* 4.2 9.2 - - + +
134D LYS 3.1 0.6 - - - -
135D LEU* 1.3 73.2 - - - +
137D ILE* 1.3 61.4 + - + +
139D LEU* 2.9 24.0 + - + +
140D LEU* 2.9 14.0 + - - +
186D GLU* 4.0 17.4 - - - +
189D VAL* 4.0 26.2 - - + -
193D ARG* 5.2 6.1 - - - -
194D ARG 6.5 0.2 - - - -
195D TYR* 6.1 8.5 - - + -
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Residues in contact with ILE 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D PRO 3.3 21.1 - - - +
134D LYS* 3.1 18.5 + - + +
136D LEU* 1.3 75.2 - - + +
138D ALA* 1.3 63.2 + - - +
140D LEU* 3.0 27.0 + - + -
141D ILE* 3.0 17.6 + - + +
195D TYR* 3.8 30.1 - - + +
196D ILE* 4.8 10.3 - - + -
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Residues in contact with ALA 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D PHE* 5.7 3.3 - - - -
39D LEU* 4.3 10.0 - - + +
42D ILE* 5.3 9.6 - - + -
46D ILE* 6.3 0.4 - - + -
123D TYR* 4.7 17.5 - - + +
134D LYS 2.9 12.0 + - - +
135D LEU* 3.0 19.3 + - + +
137D ILE* 1.3 77.4 - - - +
139D LEU* 1.3 61.0 + - - +
141D ILE* 3.9 6.0 + - - +
142D TYR* 3.9 13.9 + - - +
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Residues in contact with LEU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LEU* 4.3 21.8 - - + -
74D ARG* 4.8 2.5 - - - +
120D SER* 3.9 37.0 - - - +
123D TYR* 4.3 24.9 - - + -
124D TYR* 4.5 17.3 - - + -
127D ILE* 4.8 7.9 - - + -
135D LEU 2.9 9.9 + - - +
136D LEU* 2.9 12.0 + - + +
138D ALA* 1.3 76.1 - - - +
140D LEU* 1.3 67.3 + - - +
142D TYR* 3.1 8.8 + - + +
143D TRP* 3.0 31.8 + - - +
186D GLU* 3.6 22.4 - - - +
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Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D LEU 2.9 12.3 + - - +
137D ILE* 3.0 19.2 + - + +
139D LEU* 1.3 76.2 - - - +
141D ILE* 1.3 64.2 + - - +
143D TRP* 3.2 6.6 + - - +
144D THR* 3.0 29.9 + - + -
183D LEU* 3.7 26.2 - - + +
186D GLU* 4.1 24.2 - - + -
187D VAL* 4.8 10.5 - - + -
190D ILE* 5.5 16.6 - - + -
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Residues in contact with ILE 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D PHE* 5.2 12.3 - - + -
137D ILE* 3.0 16.3 + - + +
138D ALA* 4.2 6.7 - - - +
140D LEU* 1.3 77.1 - - - +
142D TYR* 1.3 62.1 + - - +
144D THR* 2.5 22.8 + - - -
145D LEU* 3.0 20.5 + - + +
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Residues in contact with TYR 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D PRO* 3.5 34.5 - - + -
36D HIS* 2.8 41.0 + + - -
38D PHE* 5.4 8.4 - + + -
39D LEU* 3.5 41.3 - - + -
113D ALA* 4.7 0.7 + - - -
116D ALA* 3.2 18.7 - - + +
117D ALA* 4.9 0.5 + - - -
120D SER* 5.6 0.4 - - - -
138D ALA 3.9 2.6 + - - +
139D LEU* 3.1 11.0 + - + +
141D ILE* 1.3 78.7 - - - +
143D TRP* 1.3 101.5 + + - +
145D LEU* 3.3 7.0 + - - +
146D ALA* 2.9 26.5 + - + +
179D TYR* 3.5 10.0 + + - -
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Residues in contact with TRP 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D ARG* 4.1 4.2 - - - +
78D THR* 6.0 1.1 - - - -
81D LEU* 4.3 10.5 - - + -
117D ALA* 5.8 3.1 - - - -
120D SER* 3.8 27.1 - - - -
139D LEU* 3.0 31.0 + - + +
140D LEU* 3.7 3.6 - - - +
142D TYR* 1.3 95.4 - + - +
144D THR* 1.3 63.5 + - - +
146D ALA* 3.3 2.5 + - - +
147D PHE* 3.0 24.1 + - - +
179D TYR* 3.3 47.6 - + - -
182D LEU* 3.6 43.7 - - + -
183D LEU* 3.5 27.5 - - + +
186D GLU* 3.2 41.2 + - + +
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Residues in contact with THR 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D LEU* 3.0 25.1 + - + +
141D ILE* 2.5 26.0 + - - -
143D TRP* 1.3 73.6 - - - +
145D LEU* 1.3 67.2 + - - +
147D PHE* 3.3 7.5 + - - +
148D ILE* 3.0 31.7 + - - +
183D LEU* 3.6 19.7 - - + -
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Residues in contact with LEU 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D PRO* 4.2 22.0 - - + -
38D PHE* 5.3 15.0 - - + -
141D ILE* 3.0 23.1 + - + +
142D TYR* 3.3 6.0 + - - +
144D THR* 1.3 80.3 - - - +
146D ALA* 1.3 62.0 + - - +
148D ILE* 3.2 22.2 + - + +
149D THR* 3.0 28.3 + - + +
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Residues in contact with ALA 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D PRO* 4.6 5.5 - - + +
36D HIS* 5.0 5.6 - - + -
142D TYR* 2.9 29.1 + - + +
143D TRP 3.8 0.2 - - - +
145D LEU* 1.3 75.8 - - - +
147D PHE* 1.3 62.3 + - - +
149D THR* 2.7 23.1 + - - +
150D LYS* 3.0 18.5 + - + +
179D TYR* 3.3 37.5 - - + +
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Residues in contact with PHE 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D TRP 3.0 14.3 + - - +
144D THR* 3.5 9.9 - - - +
146D ALA* 1.3 77.2 - - - +
148D ILE* 1.3 68.8 + - + +
150D LYS* 3.3 5.3 + - - +
151D THR* 2.9 42.6 + - + -
176D VAL* 3.7 37.2 - - + -
179D TYR* 4.7 8.6 - - + -
180D GLY* 4.5 9.9 - - - -
183D LEU* 3.8 22.2 - - + -
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Residues in contact with ILE 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D THR* 3.0 19.1 + - - +
145D LEU* 3.2 26.0 + - + +
147D PHE* 1.3 84.2 - - + +
149D THR* 1.3 67.0 + - + +
151D THR* 3.2 6.8 + - - -
152D ILE* 3.0 36.6 + - + +
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Residues in contact with THR 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LEU* 3.4 39.5 - - + +
32D ASN* 3.4 34.8 + - - +
35D PRO* 4.1 12.5 - - + +
145D LEU 3.0 11.7 + - - +
146D ALA* 2.7 26.7 + - - -
148D ILE* 1.3 77.6 - - + +
150D LYS* 1.3 61.3 + - - +
152D ILE* 3.2 9.1 + - - +
153D LYS* 3.0 18.2 + - - +
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Residues in contact with LYS 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D ASN* 3.4 24.6 - - - +
36D HIS* 5.6 5.5 + - - -
88D GLU* 3.6 9.3 + - - -
109D PRO* 5.4 6.5 - - - +
146D ALA* 3.0 23.4 + - - +
147D PHE* 3.8 5.2 - - - +
149D THR* 1.3 77.7 + - - +
151D THR* 1.3 57.8 + - - +
153D LYS* 3.2 17.7 + - + +
154D PHE* 2.9 28.6 + - - +
172D THR* 5.3 7.4 - - - +
175D LEU* 2.7 41.5 - - + +
176D VAL* 3.3 26.5 - - + +
179D TYR* 4.4 25.4 - - + -
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Residues in contact with THR 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D PHE* 2.9 39.0 + - + -
148D ILE* 3.2 11.2 + - - -
150D LYS* 1.3 77.9 - - - +
152D ILE* 1.3 70.2 + - + +
154D PHE* 3.2 7.6 + - + +
155D VAL* 3.0 34.9 + - + +
176D VAL* 4.5 6.5 - - - +
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Residues in contact with ILE 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D VAL* 3.6 25.4 - - + -
31D LEU* 4.9 14.8 - - + -
148D ILE* 3.0 33.5 + - + +
149D THR* 3.2 9.2 + - - +
151D THR* 1.3 83.4 - - + +
153D LYS* 1.3 65.2 + - - +
155D VAL* 3.3 6.4 + - + +
156D LYS* 3.0 37.8 + - + +
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Residues in contact with LYS 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D GLY 4.6 2.2 + - - -
28D VAL* 3.5 21.3 - - + +
29D ASP* 3.5 30.8 - - - +
32D ASN* 3.4 38.8 - - - +
109D PRO* 5.0 7.4 - - - +
149D THR 3.0 7.9 + - - +
150D LYS* 3.4 21.1 - - + +
152D ILE* 1.3 77.4 - - - +
154D PHE* 1.3 62.5 + - - +
156D LYS* 3.4 4.1 + - - +
157D PHE* 2.9 24.7 + - - +
168D ARG* 5.7 8.5 - - - +
172D THR* 5.1 17.9 - - + -
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Residues in contact with PHE 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D LYS 2.9 14.5 + - - +
151D THR* 3.6 11.7 - - + +
153D LYS* 1.3 75.6 - - - +
155D VAL* 1.3 65.9 + - + +
157D PHE* 3.3 6.1 + - + +
158D TYR* 2.9 40.9 + + + +
169D PHE* 3.4 41.8 - + - -
172D THR* 5.1 12.7 - - - -
173D GLY* 5.1 17.9 - - - -
176D VAL* 5.1 8.1 - - + -
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Residues in contact with VAL 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D THR* 3.0 31.3 + - + +
152D ILE* 3.8 7.2 - - + +
154D PHE* 1.3 84.0 - - + +
156D LYS* 1.3 78.2 + - + +
158D TYR* 3.0 16.8 + - + +
159D ASP* 3.0 24.0 + - - +
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Residues in contact with LYS 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D VAL* 5.0 12.8 - - + -
152D ILE* 3.0 31.9 + - + +
153D LYS* 4.0 4.7 - - - +
155D VAL* 1.3 87.4 - - + +
157D PHE* 1.3 60.2 + - - +
159D ASP* 3.7 15.6 + - + +
160D HIS* 2.9 34.7 + - + +
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Residues in contact with PHE 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D LYS 2.9 18.9 + - - +
154D PHE* 3.6 6.7 - - - +
155D VAL 3.1 0.2 - - - -
156D LYS* 1.3 76.6 - - - +
158D TYR* 1.3 66.0 + - - +
160D HIS* 3.0 35.4 + - + +
167D LEU 5.8 2.0 - - - -
168D ARG* 3.8 29.4 - - + -
169D PHE* 3.7 47.3 - + + -
172D THR* 5.8 3.8 - - + +
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Residues in contact with TYR 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D PHE* 2.9 36.9 + + + +
155D VAL* 3.0 7.8 + - + +
157D PHE* 1.3 78.7 - - - +
159D ASP* 1.3 72.4 + - - +
160D HIS 3.1 5.7 + - - -
169D PHE* 5.2 11.8 - + + -
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Residues in contact with ASP 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D VAL* 3.0 26.7 + - - +
156D LYS* 4.0 18.1 + - + +
157D PHE 3.2 0.4 - - - -
158D TYR* 1.3 85.8 - - - +
160D HIS* 1.3 67.5 + - + +
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Residues in contact with HIS 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D LYS* 2.9 29.0 + - + +
157D PHE* 3.0 30.0 + - + +
158D TYR 3.9 4.9 - - - -
159D ASP* 1.3 89.0 - - + +
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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
------------------------------------------------------------
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