Contacts of the helix formed by residues 171 - 195 (chain B) in PDB entry 4P9U
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 LYS 171 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LYS 4.6 2.9 + - - +
168B ASP* 2.3 31.3 + - - +
170B LEU* 1.3 68.6 - - - +
172B ARG* 1.3 57.6 + - - -
173B GLN 3.2 0.7 - - - -
174B GLU* 3.1 52.1 + - + +
175B ILE* 2.9 36.6 + - + +
221B SER* 4.3 19.3 + - - +
223B PRO* 6.2 0.6 - - - +
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Residues in contact with ARG 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLN* 2.9 56.4 + - - +
159B GLN* 5.7 0.6 - - - +
160B HIS* 4.0 18.2 + - + +
168B ASP* 2.3 49.7 + - - +
169B GLU* 4.2 17.5 + - - +
171B LYS* 1.3 70.8 - - - +
173B GLN* 1.3 63.3 + - + +
176B LEU* 2.9 32.4 + - + +
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Residues in contact with GLN 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B PRO* 3.0 41.6 - - + +
143B SER* 3.3 26.0 + - - +
169B GLU* 3.0 38.3 + - + +
170B LEU* 3.9 15.0 - - - +
171B LYS 3.2 0.2 - - - -
172B ARG* 1.3 81.4 - - + +
174B GLU* 1.3 53.2 - - - +
176B LEU* 3.2 17.1 - - + +
177B ILE* 2.8 36.0 + - - +
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Residues in contact with GLU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B PRO* 4.4 15.8 - - - +
170B LEU 3.0 25.7 - - - +
171B LYS* 3.1 55.2 + - + +
173B GLN* 1.3 72.9 - - - +
175B ILE* 1.3 56.7 + - - +
176B LEU 3.0 1.1 - - - -
177B ILE* 3.0 27.9 + - - +
178B ALA* 2.9 27.0 + - - +
221B SER* 5.0 5.0 - - - -
226B ARG* 5.2 7.1 + - - -
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Residues in contact with ILE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLN* 3.1 35.2 - - - +
160B HIS* 4.9 8.5 - - + +
168B ASP* 4.5 8.1 - - - +
171B LYS* 2.9 32.8 + - + +
174B GLU* 1.3 75.1 - - - +
176B LEU* 1.3 58.4 + - - +
178B ALA* 3.4 7.1 + - - +
179B LYS* 2.9 47.1 + - + +
217B SER* 4.8 9.9 - - - +
221B SER* 5.7 4.3 - - - -
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Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B SER* 6.3 2.2 - - - -
156B LYS 3.8 21.5 - - - +
158B GLN* 3.5 27.8 - - + +
172B ARG* 2.9 46.7 + - - +
173B GLN* 3.2 24.2 - - + +
174B GLU 3.0 0.2 - - - -
175B ILE* 1.3 76.6 - - - +
177B ILE* 1.3 57.2 + - - +
179B LYS* 3.6 11.8 - - + +
180B THR* 2.9 31.5 + - - +
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Residues in contact with ILE 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ALA* 4.7 21.5 - - + +
138B LEU* 5.8 4.0 - - + -
142B PRO* 4.4 25.4 - - + +
144B TRP* 6.1 0.7 - - + -
173B GLN 2.8 22.0 + - - +
174B GLU* 3.0 34.7 + - - +
176B LEU* 1.3 69.9 - - - +
178B ALA* 1.3 59.7 + - - +
180B THR* 3.1 12.3 - - + +
181B PHE* 2.9 30.4 + - + +
226B ARG* 3.5 38.4 - - - +
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Residues in contact with ALA 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B GLU 2.9 11.0 + - - +
175B ILE* 3.4 10.1 - - - +
177B ILE* 1.3 77.4 - - - +
179B LYS* 1.3 56.7 + - - +
182B ASN* 2.9 31.6 + - - +
216B GLY 4.1 0.2 - - - +
217B SER* 3.2 26.7 - - - +
220B PHE* 3.2 35.2 + - - +
221B SER* 3.6 8.1 - - - +
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Residues in contact with LYS 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B GLU 5.2 8.7 - - - +
156B LYS* 5.6 2.5 - - - -
157B ILE 3.1 26.4 + - - +
158B GLN* 3.5 17.6 - - - +
175B ILE* 2.9 39.6 + - + +
176B LEU* 3.6 21.1 - - + +
178B ALA* 1.3 77.6 - - - +
180B THR* 1.3 56.9 + - - +
182B ASN* 3.7 8.7 + - - +
183B PHE* 2.9 26.9 + - - +
217B SER* 4.0 24.9 - - - +
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Residues in contact with THR 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ALA* 4.5 11.2 - - + -
144B TRP* 3.7 36.9 - - - +
153B TYR* 5.6 2.4 - - - -
176B LEU 2.9 18.0 + - - +
177B ILE* 3.1 22.7 - - + +
179B LYS* 1.3 73.7 - - - +
181B PHE* 1.3 60.8 + - + +
183B PHE* 3.2 11.0 - - - +
184B TYR* 3.0 40.9 + - - -
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Residues in contact with PHE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B CYS* 3.7 29.6 - - + -
137B ALA* 6.3 3.1 - - + -
138B LEU* 4.5 5.4 - - + -
177B ILE* 2.9 19.1 + - + +
178B ALA 3.9 2.5 - - - +
180B THR* 1.3 79.0 - - + +
182B ASN* 1.3 57.8 + - - +
184B TYR* 3.3 6.0 + - - +
185B ASP* 2.9 23.7 + - - +
220B PHE* 3.4 27.8 - + + -
226B ARG* 3.3 50.5 - - + -
229B ALA* 3.5 23.6 - - + -
230B MET* 3.6 22.0 - - + -
233B TYR* 3.8 11.2 - + - -
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Residues in contact with ASN 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ALA 2.9 18.8 + - - +
179B LYS* 3.7 6.3 + - - +
181B PHE* 1.3 74.5 - - - +
183B PHE* 1.3 67.7 + - - +
185B ASP* 3.5 0.7 - - - +
186B TYR* 2.9 23.7 + - - +
212B TYR* 3.1 30.1 - - - +
213B ASP* 3.1 36.4 + - - +
216B GLY* 3.2 28.0 - - - -
217B SER* 4.1 4.7 + - - +
220B PHE* 3.5 12.7 - - + -
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Residues in contact with PHE 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B PRO 5.1 2.2 - - - -
153B TYR* 3.7 33.2 - + - -
155B GLU* 4.0 42.8 - - + -
179B LYS 2.9 16.7 + - - +
180B THR* 3.2 13.5 - - - +
182B ASN* 1.3 80.1 - - - +
184B TYR* 1.3 78.9 + + - +
186B TYR* 3.5 7.4 + + - +
187B MET* 2.9 58.3 + - + +
209B LYS* 5.9 3.4 - - - -
213B ASP* 5.5 1.1 - - - -
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Residues in contact with TYR 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASN* 4.5 7.6 - - - -
131B VAL* 3.8 20.7 - - + +
134B SER* 3.4 46.4 + - - -
135B CYS* 3.8 24.7 - - - -
144B TRP* 4.0 8.0 - + - -
148B ILE* 4.4 5.0 - - - +
153B TYR* 2.6 28.3 + + - -
180B THR* 3.0 42.6 + - - +
181B PHE* 3.9 0.9 - - - +
183B PHE* 1.3 85.3 - + - +
185B ASP* 1.3 61.3 + - - +
187B MET* 3.5 28.8 - - + +
188B LEU* 2.9 28.9 + - - +
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Residues in contact with ASP 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ARG* 3.7 3.5 + - - -
181B PHE 2.9 16.7 + - - +
182B ASN 3.3 5.6 + - - +
184B TYR* 1.3 75.6 - - - +
186B TYR* 1.3 62.0 + - - +
188B LEU* 3.1 6.1 + - - +
189B PHE* 3.0 37.0 + - - -
212B TYR* 2.4 39.4 + - + -
220B PHE* 3.4 29.1 - - + -
233B TYR* 2.6 34.1 + - - +
255B TYR* 4.2 6.8 + - - -
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Residues in contact with TYR 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ASN 2.9 15.9 + - - +
183B PHE* 3.8 7.0 - + - +
185B ASP* 1.3 74.0 + - - +
187B MET* 1.3 72.6 + - + +
189B PHE* 4.1 0.8 - - - +
190B GLN* 2.9 45.9 + - + +
205B PHE* 3.3 42.3 + + + -
206B ASN* 3.4 23.6 + - - -
209B LYS* 3.4 47.9 - - + +
212B TYR* 3.8 35.9 - + + -
213B ASP* 4.4 8.5 - - - +
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Residues in contact with MET 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ILE* 5.7 0.7 - - + +
130B ASN* 4.2 18.4 - - - +
131B VAL* 4.5 8.5 - - + -
183B PHE* 2.9 49.6 + - + +
184B TYR* 3.5 24.0 - - + +
185B ASP 3.3 0.2 - - - -
186B TYR* 1.3 81.6 - - + +
188B LEU* 1.3 65.0 + - - +
190B GLN* 4.9 1.6 - - - -
191B ARG* 2.9 77.1 + - - +
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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
----------------------------------------------------------
113B MET* 4.4 6.7 - - + -
127B ILE* 6.0 2.5 - - - -
128B MET* 4.5 20.6 - - + -
131B VAL* 3.7 30.7 - - + +
184B TYR 2.9 14.2 + - - +
185B ASP* 3.3 9.9 - - - +
187B MET* 1.3 75.2 - - - +
189B PHE* 1.3 85.2 + - + +
191B ARG* 4.2 1.5 - - - +
192B LEU* 2.9 51.5 + - + +
233B TYR* 3.7 36.3 - - + -
236B LEU* 4.4 6.5 - - + -
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Residues in contact with PHE 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ARG* 3.6 32.5 - - + -
109B SER* 3.6 22.4 - - - -
112B PHE* 3.8 10.2 - + - -
113B MET* 3.6 19.5 - - + -
185B ASP* 3.0 33.9 + - - +
186B TYR 4.1 2.2 - - - +
188B LEU* 1.3 88.7 - - + +
190B GLN* 1.3 57.8 + - - +
192B LEU* 4.6 2.5 - - - -
193B ALA* 2.9 28.8 + - - +
205B PHE* 3.6 23.3 - + + -
212B TYR* 3.2 23.8 - - + +
232B PHE* 3.9 25.4 - + - -
233B TYR* 4.9 2.2 - + - -
252B ILE* 6.3 0.2 - - + -
255B TYR* 4.6 5.2 - + - -
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Residues in contact with GLN 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU* 3.1 26.4 + - - +
186B TYR* 2.9 47.5 + - + +
187B MET* 4.3 1.6 - - - +
189B PHE* 1.3 75.3 - - - +
191B ARG* 1.3 84.1 + - - +
193B ALA* 2.9 21.7 + - - +
194B PHE* 3.0 26.7 + - + -
202B GLY 4.2 7.0 - - - +
205B PHE* 3.8 18.8 - - + -
206B ASN* 2.9 31.1 + - - +
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Residues in contact with ARG 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU* 5.5 5.6 + - - +
127B ILE* 3.6 35.5 - - + +
131B VAL* 6.0 0.7 - - - -
187B MET* 2.9 64.9 + - - +
188B LEU* 4.2 0.9 - - - +
190B GLN* 1.3 89.7 + - - +
192B LEU* 1.3 61.3 + - - +
194B PHE* 3.3 5.3 + - - +
195B HIS* 2.8 38.2 + - + +
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Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 3.6 14.4 - - + -
113B MET* 4.1 20.2 - - + -
116B ALA* 3.5 27.6 - - + +
117B PHE* 4.2 10.8 - - + -
124B ALA* 3.8 25.8 - - + -
127B ILE* 3.8 19.7 - - + -
128B MET* 4.0 26.9 - - + -
188B LEU* 2.9 42.3 + - + +
189B PHE* 3.9 3.6 - - - +
191B ARG* 1.3 77.1 - - - +
193B ALA* 1.3 61.2 + - - +
194B PHE 3.4 0.3 + - - -
195B HIS* 3.5 5.9 + - + +
196B SER* 3.8 1.2 + - - -
236B LEU* 4.9 0.9 - - + -
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Residues in contact with ALA 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 3.5 18.6 - - + -
189B PHE 2.9 18.5 + - - +
190B GLN 2.9 7.9 + - - +
192B LEU* 1.3 77.5 - - - +
194B PHE* 1.3 55.1 + - - +
196B SER* 2.7 20.8 + - - -
198B ASN 3.5 4.5 - - - +
201B TYR* 3.4 37.1 - - + +
202B GLY* 3.6 3.7 + - - +
205B PHE* 3.8 11.7 - - + -
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Residues in contact with PHE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A MET* 3.1 32.8 - - + -
76A GLU* 4.2 8.3 - - - -
190B GLN* 3.0 34.3 + - - -
191B ARG* 3.3 8.7 + - - +
192B LEU 3.2 0.4 - - - -
193B ALA* 1.3 77.1 - - - +
195B HIS* 1.3 62.8 + - + +
196B SER* 3.0 10.3 + - - -
197B GLY* 3.6 9.7 + - - -
198B ASN 4.7 3.8 + - - +
199B GLN* 3.7 34.1 - - + -
202B GLY* 3.5 17.0 - - - -
203B LEU* 3.9 9.4 - - + -
206B ASN* 3.1 27.4 - - - -
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Residues in contact with HIS 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B TYR 4.6 0.2 - - - +
116B ALA* 3.2 23.4 - - + -
119B LEU* 4.6 0.7 - - - +
120B ASN* 3.5 38.3 + - + +
123B SER* 3.4 35.6 + - - -
124B ALA* 5.3 2.7 - - + +
127B ILE* 4.2 22.6 - - + +
191B ARG* 2.8 31.7 + - + +
192B LEU* 3.5 6.6 + - - +
194B PHE* 1.3 80.6 - - + +
196B SER* 1.3 59.0 + - - +
197B GLY 3.4 1.3 - - - -
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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