Contacts of the helix formed by residues 178 - 205 (chain A) in PDB entry 5L04
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 THR 178 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A PRO* 3.4 8.5 - - - +
177A LYS* 1.3 87.2 - - + +
179A GLU* 1.3 58.3 + - - +
180A GLN* 2.9 14.9 + - - +
181A ASP* 2.8 23.4 + - + +
182A GLY 2.9 23.9 + - - -
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Residues in contact with GLU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A PRO* 5.6 0.4 - - - -
178A THR* 1.3 72.7 - - - +
180A GLN* 1.3 62.1 + - - +
182A GLY* 3.5 3.3 + - - +
183A HIS* 3.1 51.6 + - + +
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Residues in contact with GLN 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A THR* 2.9 14.3 + - - +
179A GLU* 1.3 75.3 - - - +
181A ASP* 1.3 61.6 + - - +
183A HIS* 3.7 6.3 + - - +
184A ASP* 3.1 23.1 + - - +
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Residues in contact with ASP 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ARG* 3.3 27.9 + - - -
175A ASP 4.4 1.4 - - - +
176A PRO* 3.9 3.1 - - - +
177A LYS* 3.1 37.8 + - + +
178A THR* 2.8 29.9 + - + +
180A GLN* 1.3 71.8 - - - +
182A GLY* 1.3 54.9 + - - +
184A ASP* 2.8 30.5 + - - +
185A ILE* 2.8 23.8 + - - +
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Residues in contact with GLY 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A PRO* 3.5 23.3 - - - +
178A THR 2.9 11.0 + - - -
179A GLU* 3.7 5.6 - - - -
181A ASP* 1.3 74.3 - - - +
183A HIS* 1.3 63.9 + - - +
185A ILE* 3.5 6.1 + - - +
186A GLU* 3.2 28.9 + - - +
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Residues in contact with HIS 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLU* 3.1 47.5 + - + +
180A GLN* 4.1 6.3 - - - +
182A GLY* 1.3 74.7 - - - +
184A ASP* 1.3 57.7 + - - +
186A GLU* 3.2 23.1 + - - +
187A ASN* 3.0 32.7 + - - +
232A ARG* 5.2 5.5 + - - -
239A ARG* 6.3 0.7 - - - -
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Residues in contact with ASP 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ARG* 5.6 3.1 + - - +
180A GLN* 3.1 17.9 + - - +
181A ASP* 2.8 29.9 + - - +
183A HIS* 1.3 70.2 - - - +
185A ILE* 1.3 62.3 + - - +
187A ASN* 3.2 9.1 + - - +
188A GLU* 3.0 34.8 + - - +
265B ARG* 5.4 12.2 + - - -
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Residues in contact with ILE 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ILE* 4.2 31.6 - - + -
174A ARG* 3.5 55.6 - - + +
175A ASP 4.1 0.4 - - - -
176A PRO* 3.9 25.6 - - + -
181A ASP* 2.8 23.8 + - - +
182A GLY* 3.7 7.2 - - - +
184A ASP* 1.3 71.8 - - - +
186A GLU* 1.3 60.5 + - + +
188A GLU* 3.0 10.0 + - - +
189A CYS* 2.9 27.1 + - - -
277A LEU* 4.1 14.7 - - + +
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Residues in contact with GLU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ILE* 6.0 1.6 - - + -
182A GLY 3.2 14.9 + - - +
183A HIS* 3.4 24.3 - - - +
184A ASP 3.2 0.2 - - - -
185A ILE* 1.3 85.2 - - + +
187A ASN* 1.3 63.3 + - - +
189A CYS* 3.2 11.2 + - - +
190A LEU* 3.2 24.3 + - - +
225A LEU* 3.5 28.1 - - + +
229A ILE* 4.3 4.6 - - + +
232A ARG* 2.9 42.5 + - - -
240A ILE* 5.0 4.2 - - - +
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Residues in contact with ASN 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A HIS* 3.0 17.1 + - - +
184A ASP* 3.2 11.4 + - - +
186A GLU* 1.3 75.3 - - - +
188A GLU* 1.3 67.5 + - + +
190A LEU* 3.0 24.7 + - - +
191A GLY 3.0 10.4 + - - -
239A ARG* 4.8 12.6 + - - +
243A VAL* 4.2 7.6 - - - +
247A PHE* 3.2 33.5 - - + -
261B ALA* 4.5 7.5 - - - +
262B LYS 4.1 6.5 + - - +
264B PRO* 3.8 13.9 - - + +
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Residues in contact with GLU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ARG* 5.7 3.4 - - - +
184A ASP* 3.0 28.8 + - - +
185A ILE* 3.0 8.7 + - - +
187A ASN* 1.3 75.6 - - - +
189A CYS* 1.3 62.7 + - - +
191A GLY* 3.1 3.1 + - - -
192A MET* 2.9 26.7 + - - +
273A THR* 4.7 6.9 - - + +
277A LEU* 3.8 21.5 - - + -
264B PRO* 3.4 9.9 - - - +
265B ARG* 2.7 40.0 + - - +
266B ALA* 2.8 36.1 + - + +
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Residues in contact with CYS 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU* 5.3 1.9 - - - +
173A ILE* 3.9 32.1 - - - -
185A ILE* 2.9 17.8 + - - -
186A GLU 3.4 9.2 - - - +
187A ASN 3.1 0.2 - - - -
188A GLU* 1.3 77.9 - - - +
190A LEU* 1.3 57.1 + - + +
192A MET* 3.4 11.4 + - - +
193A ALA 3.1 19.6 + - - -
221A ILE* 3.5 20.0 - - + +
222A PRO* 4.0 15.5 - - + -
225A LEU* 4.0 22.2 - - + -
277A LEU* 4.2 8.5 - - - -
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Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A GLU 3.2 16.6 + - - +
187A ASN* 3.0 20.0 + - - +
189A CYS* 1.3 74.1 - - + +
191A GLY* 1.4 54.1 + - - +
193A ALA* 2.8 24.4 + - - +
194A VAL* 2.9 21.0 + - - +
217A TYR* 4.1 34.8 - - + -
221A ILE* 4.7 5.2 - - + -
225A LEU* 6.3 1.6 - - + -
239A ARG* 6.2 0.7 - - - +
240A ILE* 4.1 34.5 - - + +
243A VAL* 4.2 15.0 - - + -
244A PHE* 4.0 20.9 - - + +
247A PHE* 4.2 9.4 - - + -
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Residues in contact with GLY 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ASN 3.0 10.5 + - - -
188A GLU 3.5 4.3 - - - -
190A LEU* 1.4 71.2 - - - +
192A MET* 1.3 57.6 - - - +
194A VAL* 2.7 19.7 + - - +
195A LEU* 2.8 13.0 + - - +
247A PHE* 4.7 0.4 - - - -
264B PRO* 3.8 23.2 - - - +
266B ALA* 4.3 5.6 - - - -
267B LEU* 3.5 21.8 - - - +
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Residues in contact with MET 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU* 3.8 22.0 - - + -
188A GLU 2.9 20.0 + - - +
189A CYS* 3.4 9.2 - - - +
191A GLY* 1.3 74.1 - - - +
193A ALA* 1.3 61.8 + - - +
195A LEU* 3.4 11.7 + - - +
196A ALA* 3.0 23.7 + - - +
220A TYR 4.8 2.7 - - - +
270A TYR* 3.4 60.2 - - + +
273A THR* 3.6 28.3 - - + -
274A LEU* 4.0 13.5 - - + +
277A LEU* 4.1 17.7 - - + -
266B ALA* 4.3 2.2 - - + +
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Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A CYS 3.1 11.1 + - - +
190A LEU 2.8 13.2 + - - +
192A MET* 1.3 76.2 - - - +
194A VAL* 1.3 57.2 + - - +
196A ALA* 3.3 1.2 + - - +
197A ILE* 3.0 36.3 + - - +
217A TYR* 4.1 8.1 - - + -
220A TYR* 3.6 29.2 - - + -
221A ILE* 4.0 12.1 - - + -
244A PHE* 4.0 14.6 - - + -
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Residues in contact with VAL 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A LEU 2.9 14.5 + - - +
191A GLY 2.7 10.1 + - - +
193A ALA* 1.3 78.3 - - - +
195A LEU* 1.3 49.5 + - - -
197A ILE* 3.8 0.6 - - - +
198A SER* 2.7 41.4 + - - +
244A PHE* 3.9 17.0 - - + -
247A PHE* 4.0 12.6 - - + -
248A LEU* 3.8 34.3 - - + +
251A PHE* 3.6 26.2 - - + -
267B LEU* 3.4 29.2 - - + -
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Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A PHE* 5.3 2.0 - - + -
191A GLY 2.8 18.7 + - - +
192A MET* 3.7 17.3 - - - +
194A VAL* 1.3 72.5 - - - +
196A ALA* 1.3 64.8 + - - +
198A SER* 3.9 2.9 - - - -
199A HIS* 2.9 28.0 + - - +
251A PHE* 4.0 7.6 - - + -
266A LEU* 4.0 16.5 - - + +
269A LYS* 4.0 4.5 - - + -
270A TYR* 3.8 42.4 - - + +
266B ALA* 3.6 22.2 - - + +
267B LEU* 3.5 21.1 - - + -
269B PHE* 3.9 22.7 - - + -
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Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A PHE* 4.6 8.1 - - - -
163A GLN* 3.7 27.4 + - + +
192A MET 3.0 18.6 + - - +
193A ALA 3.8 3.6 - - - +
195A LEU* 1.3 77.3 - - - +
197A ILE* 1.3 58.6 + - - +
199A HIS* 3.6 3.1 + - - +
200A TYR* 3.0 26.7 + - - +
220A TYR* 3.8 24.4 - - + +
270A TYR* 4.5 8.9 - - + +
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Residues in contact with ILE 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ALA 3.0 25.2 + - - +
194A VAL* 3.8 3.6 - - - +
196A ALA* 1.3 73.5 - - - +
198A SER* 1.4 70.7 + - - +
200A TYR* 3.0 9.5 + - + +
201A ALA* 2.9 26.2 + - + +
209A PRO* 6.2 4.7 - - + -
216A SER 4.6 3.8 - - - +
220A TYR* 3.0 53.4 - - + +
244A PHE* 4.5 15.3 - - + -
248A LEU* 4.2 22.4 - - + -
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Residues in contact with SER 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A VAL* 2.7 24.9 + - - +
195A LEU 3.9 2.2 - - - -
197A ILE* 1.4 75.6 - - - +
199A HIS* 1.3 58.2 + - - +
201A ALA* 3.1 5.0 + - - +
202A MET* 2.8 30.9 + - - +
248A LEU* 4.3 1.2 - - - +
251A PHE* 3.2 35.5 - - - -
252A ASN* 3.2 25.0 + - - +
256A ILE* 4.6 5.2 - - - -
266A LEU* 4.0 9.2 - - - -
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Residues in contact with HIS 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A GLU* 3.8 9.2 - - - -
159A PHE* 3.4 30.4 - + + -
195A LEU 2.9 19.6 + - - +
196A ALA 3.7 3.8 - - - +
198A SER* 1.3 77.4 - - - +
200A TYR* 1.3 64.3 + - - +
202A MET* 3.9 3.1 - - - +
203A MET* 3.1 40.3 + - + +
263A THR* 3.3 32.5 - - - -
266A LEU* 3.4 19.4 - - + +
267A LYS* 3.1 41.3 + - + +
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Residues in contact with TYR 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ALA 3.0 13.9 + - - +
197A ILE* 3.0 15.2 + - + +
199A HIS* 1.3 78.3 + - - +
201A ALA* 1.3 68.4 + - + +
203A MET* 3.2 8.3 + - + +
204A LYS* 3.2 60.7 + - + +
206A MET* 6.6 0.2 - - - -
209A PRO* 6.3 3.8 - - + -
220A TYR* 5.3 12.3 - + + +
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Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE* 2.9 16.0 + - + +
198A SER* 3.5 9.6 - - - +
200A TYR* 1.3 84.6 - - + +
202A MET* 1.3 62.2 + - + +
203A MET 3.0 0.4 + - - -
204A LYS* 3.1 3.2 + - - -
205A LYS 3.0 6.1 + - - -
206A MET* 3.0 48.1 + - + +
207A GLN* 5.3 1.6 - - - -
208A LEU 5.9 0.2 - - - +
209A PRO* 5.0 12.8 - - + -
252A ASN* 5.5 4.3 - - - +
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Residues in contact with MET 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A SER 2.8 19.4 + - - +
199A HIS 4.1 1.3 - - - +
200A TYR 3.4 0.2 - - - -
201A ALA* 1.3 73.2 - - + +
203A MET* 1.3 60.1 + - - +
205A LYS* 3.7 25.0 + - - +
206A MET 5.1 2.9 - - - +
252A ASN* 6.0 1.1 - - - +
256A ILE* 4.2 26.7 - - + -
261A VAL 3.2 26.5 - - - +
262A SER* 3.8 1.6 - - - -
263A THR* 3.5 37.1 - - + +
266A LEU* 3.8 22.4 - - - -
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Residues in contact with MET 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A GLU* 4.7 10.3 - - - +
199A HIS* 3.1 41.2 + - + +
200A TYR* 3.6 7.4 - - + +
201A ALA 3.0 1.2 - - - -
202A MET* 1.3 76.5 - - - +
204A LYS* 1.3 70.3 + - + +
205A LYS* 3.2 17.6 + - - +
263A THR* 3.3 40.8 - - + +
267A LYS* 4.0 7.6 - - - +
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Residues in contact with LYS 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASP* 6.3 1.2 - - - +
200A TYR* 3.2 53.3 + - + +
201A ALA* 3.1 5.3 + - - +
203A MET* 1.3 83.1 - - + +
205A LYS* 1.3 72.0 + - - +
206A MET* 3.4 22.7 - - + +
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Residues in contact with LYS 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ALA 3.0 4.2 + - - -
202A MET* 3.7 18.9 + - - +
203A MET* 3.2 15.5 + - - +
204A LYS* 1.3 81.9 - - - +
206A MET* 1.3 62.4 + - - +
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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