Contacts of the helix formed by residues 166 - 191 (chain B) in PDB entry 1XR2
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 ARG 166 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589A LYS* 4.2 19.9 - - + +
592A TRP* 4.8 3.6 - - - -
625A ASN* 4.3 6.3 + - - +
626A GLU* 3.7 54.2 + - - +
165B ARG* 1.3 77.7 - - + +
167B PRO* 1.3 68.1 - - + +
168B ASN* 3.4 32.1 + - - +
169B GLN* 2.8 65.2 + - - +
170B MET* 3.0 11.4 + - - +
208B GLU* 5.6 4.3 - - - +
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Residues in contact with PRO 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ASP* 5.7 0.7 - - - +
589A LYS* 6.2 2.5 - - + -
590A SER* 4.3 13.7 - - - +
166B ARG* 1.3 85.6 - - + +
168B ASN* 1.3 58.3 + - - +
170B MET* 3.1 2.2 + - + +
171B GLU* 2.9 34.0 + - - +
208B GLU* 3.4 27.8 - - - +
210B ALA* 3.8 29.2 - - + +
211B HIS* 3.5 27.8 - - + +
214B LEU* 3.6 16.8 - - + +
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Residues in contact with ASN 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A LYS* 3.1 33.5 + - - +
590A SER* 4.7 1.5 - - - +
592A TRP* 4.0 14.8 - - + -
593A PRO* 3.7 31.0 - - + +
626A GLU 5.1 0.2 + - - -
630A TYR* 2.8 31.5 + - - +
166B ARG* 3.4 36.2 + - - +
167B PRO* 1.3 79.4 - - - +
169B GLN* 1.3 66.4 + - - +
171B GLU* 4.3 6.0 + - - +
172B LYS* 5.0 3.5 + - - +
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Residues in contact with GLN 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ARG* 5.0 5.8 + - - +
162B GLU* 4.7 8.7 + - - +
163B TRP 2.8 25.9 + - - +
164B ILE* 3.8 23.2 - - + +
165B ARG* 3.6 2.8 + - - +
166B ARG* 2.8 79.1 + - + +
168B ASN* 1.3 86.1 - - - +
170B MET* 1.3 58.2 + - - +
172B LYS* 5.0 1.2 + - - +
173B LEU* 3.8 15.6 + - - +
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Residues in contact with MET 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B PHE* 3.4 64.2 - - + +
154B LEU* 3.7 19.7 - - + -
155B TYR* 4.2 5.6 - - + +
164B ILE* 3.6 27.6 - - + +
165B ARG* 4.2 14.1 - - - +
166B ARG 3.0 10.4 + - - +
167B PRO 3.9 4.3 - - - +
169B GLN* 1.3 78.1 - - - +
171B GLU* 1.3 66.4 + - - +
172B LYS 3.5 1.1 - - - -
173B LEU* 3.2 6.7 + - - +
174B LEU* 2.8 36.5 + - + +
211B HIS* 4.3 6.3 - - - -
214B LEU* 4.1 4.5 - - + -
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Residues in contact with GLU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A SER 4.2 10.0 - - - +
593A PRO* 3.8 29.2 - - + +
167B PRO 2.9 20.2 + - - +
168B ASN* 4.5 6.6 - - - +
169B GLN 3.7 0.8 - - - -
170B MET* 1.3 73.5 - - - +
172B LYS* 1.3 67.2 + - - +
174B LEU* 3.2 14.9 + - - +
175B GLU* 3.5 6.1 + - - +
214B LEU* 3.7 30.0 - - + +
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Residues in contact with LYS 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A PRO* 6.1 2.0 - - + +
120B GLU* 5.4 1.2 - - + +
168B ASN 5.0 3.9 + - - +
169B GLN 5.0 1.3 + - - +
170B MET 3.5 0.6 - - - -
171B GLU* 1.3 78.7 - - + +
173B LEU* 1.3 68.4 + - + +
174B LEU 3.1 1.0 + - - -
175B GLU* 3.1 19.9 + - - +
176B SER* 3.8 4.7 + - - -
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE* 4.2 15.9 - - + -
120B GLU* 3.7 35.2 - - + +
122B PHE* 3.6 21.2 - - + -
154B LEU* 4.2 13.9 - - + -
159B ARG* 4.0 25.8 - - - +
164B ILE* 4.0 31.0 - - + -
169B GLN 3.8 17.4 + - - +
170B MET 3.2 7.7 + - - +
172B LYS* 1.3 79.7 - - + +
174B LEU* 1.3 61.9 + - - +
176B SER* 3.4 2.8 + - - -
177B LEU* 3.0 23.1 + - - +
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B PRO* 4.3 24.5 - - + +
151B PHE* 4.7 7.4 - - + +
154B LEU* 3.7 21.1 - - + -
170B MET* 2.8 25.8 + - + +
171B GLU 3.3 8.7 - - - +
172B LYS 3.1 0.2 - - - -
173B LEU* 1.3 74.0 - - - +
175B GLU* 1.3 67.1 + - - +
177B LEU* 4.3 3.1 - - + -
178B VAL* 2.9 31.5 + - + +
214B LEU* 3.7 38.4 - - + -
218B VAL* 3.9 29.2 - - + -
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Residues in contact with GLU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B GLU 3.5 5.8 + - - +
172B LYS* 3.1 12.7 + - - +
174B LEU* 1.3 75.2 - - - +
176B SER* 1.3 59.7 + - - +
178B VAL* 2.9 27.4 - - - +
179B SER* 3.1 11.1 + - - -
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Residues in contact with SER 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLU 3.8 16.4 - - - -
121B GLU* 3.7 4.8 - - - +
122B PHE* 2.9 32.2 + - - +
172B LYS 3.8 3.3 + - - -
173B LEU 3.4 7.3 + - - -
174B LEU 3.3 0.2 - - - -
175B GLU* 1.3 80.8 - - - +
177B LEU* 1.3 62.7 + - - +
179B SER* 3.2 21.6 + - - -
180B VAL* 3.5 10.0 + - - +
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL* 3.8 33.2 - - + -
122B PHE* 3.5 25.0 - - + -
150B PRO* 3.4 37.9 - - + +
153B PHE* 4.0 16.2 - - + -
154B LEU* 3.6 19.1 - - + -
173B LEU 3.0 17.5 + - - +
174B LEU* 3.2 5.1 + - + +
176B SER* 1.3 78.0 - - - +
178B VAL* 1.3 62.7 + - - +
180B VAL* 3.2 12.6 + - - +
181B TYR* 3.2 29.1 + - + -
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Residues in contact with VAL 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B PRO* 4.5 9.9 - - + -
174B LEU* 2.9 22.0 + - + +
175B GLU* 2.9 29.6 - - - +
177B LEU* 1.3 73.7 - - - +
179B SER* 1.3 56.4 + - - +
181B TYR* 2.9 11.0 + - - +
182B LYS* 2.7 41.5 + - - +
218B VAL* 3.7 40.8 - - + +
221B GLU* 5.0 12.6 - - + -
222B LEU* 4.2 12.0 - - + +
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Residues in contact with SER 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B GLU 3.1 13.7 + - - -
176B SER* 3.2 13.1 + - - -
177B LEU 3.2 0.2 - - - -
178B VAL* 1.3 80.8 - - - +
180B VAL* 1.3 59.1 + - - +
182B LYS* 3.3 17.8 + - - +
183B GLU* 3.0 26.0 + - - +
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Residues in contact with VAL 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B MET 4.5 1.1 - - - +
74B VAL* 3.9 24.2 - - + -
122B PHE* 3.7 12.8 - - + +
123B TYR* 3.6 33.0 - - - +
124B LEU* 3.7 31.9 - - + +
176B SER 3.8 9.4 - - - +
177B LEU 3.2 6.5 + - - +
178B VAL 3.1 0.4 - - - -
179B SER* 1.3 76.2 - - - +
181B TYR* 1.3 66.3 + - - +
183B GLU* 3.1 6.8 + - - +
184B VAL* 3.0 26.4 + - + +
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Residues in contact with TYR 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B THR* 3.5 17.4 - - + +
73B MET* 4.1 18.2 - - + -
74B VAL* 4.3 10.8 - - + -
147B VAL* 4.7 6.3 - - + -
148B ILE 2.6 28.8 + - - -
149B GLY* 3.5 8.4 + - - -
150B PRO* 3.6 40.5 - - + +
153B PHE* 4.0 2.1 - - - +
177B LEU* 3.2 41.6 + - + -
178B VAL* 2.9 11.1 + - - +
180B VAL* 1.3 76.7 - - - +
182B LYS* 1.3 58.9 + - - +
184B VAL* 3.2 6.5 + - - +
185B PHE* 2.9 61.2 + + + -
198B VAL* 5.9 0.2 - - + -
222B LEU* 4.4 10.8 - - + -
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Residues in contact with LYS 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B VAL* 2.7 17.6 + - - +
179B SER* 3.4 20.8 + - - +
180B VAL 3.2 0.2 - - - -
181B TYR* 1.3 73.9 - - - +
183B GLU* 1.3 57.3 + - - +
186B GLU* 2.9 31.6 + - + +
221B GLU* 3.9 33.8 + - - +
222B LEU* 4.1 6.4 - - + +
224B GLU* 4.4 8.7 + - - +
225B PHE* 3.6 28.1 - - + -
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Residues in contact with GLU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 4.2 20.5 - - + +
179B SER 3.0 14.0 + - - +
180B VAL* 3.1 11.4 + - - +
182B LYS* 1.3 77.3 - - - +
184B VAL* 1.3 62.5 + - - +
186B GLU* 3.3 6.5 + - - +
187B LYS* 3.1 23.9 + - - +
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Residues in contact with VAL 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B MET* 4.0 26.9 - - + -
124B LEU* 4.1 20.0 - - + -
127B ASN* 3.6 31.9 + - - +
129B PRO* 4.2 19.3 - - + -
147B VAL* 6.1 0.4 - - + -
180B VAL* 3.0 19.4 + - + +
181B TYR* 3.6 8.1 - - - +
183B GLU* 1.3 75.9 - - - +
185B PHE* 1.3 76.6 + - + +
187B LYS* 3.3 4.2 + - - +
188B LEU* 3.1 26.4 + - + +
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Residues in contact with PHE 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B VAL* 4.4 11.7 - - + -
150B PRO* 6.1 0.2 - - + -
181B TYR* 2.9 43.5 + + - +
182B LYS 3.8 2.5 - - - +
184B VAL* 1.3 88.9 - - + +
186B GLU* 1.3 64.3 + - - +
188B LEU* 3.3 5.4 + - + +
189B VAL* 3.1 28.1 + - - +
196B ILE* 3.8 30.4 - - + +
198B VAL* 4.1 20.4 - - + -
222B LEU* 4.2 15.5 - - + -
225B PHE* 3.7 36.8 - + + -
227B LEU* 3.7 28.0 - - + -
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Residues in contact with GLU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LYS* 2.9 19.7 + - + +
183B GLU* 3.6 7.2 - - - +
184B VAL 3.3 0.2 - - - -
185B PHE* 1.3 76.6 - - - +
187B LYS* 1.3 58.7 + - - +
189B VAL* 3.4 4.6 + - - +
190B GLU* 2.9 43.4 + - - +
225B PHE* 3.8 15.0 - - + -
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Residues in contact with LYS 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 6.2 0.9 - - + -
127B ASN* 4.0 17.3 - - - +
130B LEU* 4.2 12.6 - - + -
183B GLU 3.1 16.4 + - - +
184B VAL 3.3 4.0 + - - +
186B GLU* 1.3 73.7 - - - +
188B LEU* 1.3 64.8 + - - +
190B GLU* 3.4 13.6 + - - +
191B ASN* 2.6 34.7 + - - +
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Residues in contact with LEU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PRO* 3.8 6.3 - - + +
130B LEU* 3.7 32.3 - - + -
133B TYR* 3.7 24.9 - - + -
145B PRO* 3.7 27.4 - - + -
147B VAL* 6.2 0.2 - - + -
184B VAL* 3.1 31.9 + - + +
185B PHE* 3.6 10.1 - - + +
187B LYS* 1.3 77.9 - - - +
189B VAL* 1.3 63.0 + - - +
191B ASN* 3.0 15.0 + - - +
192B GLY 3.4 0.3 + - - -
193B CYS* 3.0 27.7 + - + +
196B ILE* 4.0 23.3 - - + -
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Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B PHE 3.1 16.7 + - - +
186B GLU* 3.8 5.8 - - - +
188B LEU* 1.3 74.2 - - + +
190B GLU* 1.3 66.5 + - + +
192B GLY* 2.9 14.9 + - - -
193B CYS 3.9 16.8 - - - +
196B ILE* 5.1 3.8 - - + -
224B GLU 5.7 0.2 - - - +
225B PHE* 4.5 9.4 - - + -
226B PRO* 3.8 29.8 - - + -
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Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLU* 2.9 33.2 + - - +
187B LYS* 3.6 13.6 + - - +
189B VAL* 1.3 78.4 - - + +
191B ASN* 1.3 62.9 + - - +
192B GLY 3.3 1.3 + - - -
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Residues in contact with ASN 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU* 3.6 26.7 - - + +
133B TYR* 3.4 9.1 - - + -
134B LEU* 3.7 24.6 - - + +
137B LYS* 3.4 23.4 + - - -
187B LYS* 2.6 24.6 + - - +
188B LEU 3.0 8.9 + - - +
189B VAL 3.0 1.2 - - - -
190B GLU* 1.3 83.8 + - - +
192B GLY* 1.3 56.2 + - - +
193B CYS 3.5 1.6 - - - -
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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