Contacts of the helix formed by residues 179 - 201 (chain C) in PDB entry 5M73
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 ASP 179 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58C HIS* 2.6 41.3 + - + +
59C HIS* 3.1 25.0 + - - +
177C ARG 4.4 0.4 + - - -
178C VAL* 1.3 75.6 - - - +
180C ALA* 1.3 63.8 + - - +
181C LYS* 3.7 12.5 - - - +
182C THR* 3.0 16.1 + - - -
183C LYS* 3.2 18.1 + - - +
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Residues in contact with ALA 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ASP* 1.3 74.4 - - - +
181C LYS* 1.3 64.7 + - - +
183C LYS* 3.1 16.7 + - + +
184C LEU* 2.9 30.4 + - + +
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Residues in contact with LYS 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C HIS* 3.2 22.1 - - + -
60C LEU 4.6 1.0 + - - +
61C GLU* 3.2 39.6 + - - +
179C ASP* 3.3 12.5 + - - +
180C ALA* 1.3 76.9 - - - +
182C THR* 1.3 59.6 + - - +
184C LEU* 3.2 8.2 + - - +
185C GLU* 2.9 34.5 + - + +
221C LEU* 4.5 10.7 - - + +
225C PHE* 3.5 42.0 - - + -
229C GLN* 5.9 2.0 - - - +
233C TYR* 3.6 20.1 + - - -
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Residues in contact with THR 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C HIS 5.1 0.2 - - - +
59C HIS* 3.3 1.7 + - - -
60C LEU* 2.8 57.2 + - + +
62C ILE* 4.9 4.9 - - + -
121C ASN* 6.0 0.2 - - - +
124C LEU* 4.5 5.4 - - + -
173C CYS* 4.0 15.0 - - - -
178C VAL* 3.7 17.3 - - + -
179C ASP* 3.0 21.4 + - - -
181C LYS* 1.3 74.3 - - - +
183C LYS* 1.3 68.2 + - - +
185C GLU* 3.2 2.0 + - - +
186C ALA* 2.9 22.3 + - - +
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Residues in contact with LYS 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C CYS* 2.9 45.6 + - + +
174C GLU* 3.2 23.4 + - - +
175C SER 3.3 7.4 + - - -
176C ASN* 5.1 2.1 + - - +
178C VAL* 3.3 24.0 - - + +
179C ASP 3.2 12.0 + - - +
180C ALA* 3.1 15.7 + - + +
182C THR* 1.3 77.1 - - - +
184C LEU* 1.3 59.7 + - + +
186C ALA* 3.4 1.2 + - - +
187C GLN* 2.9 39.8 + - + +
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Residues in contact with LEU 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ALA* 2.9 19.8 + - + +
181C LYS* 3.2 3.3 + - - +
183C LYS* 1.3 79.1 - - + +
185C GLU* 1.3 63.3 + - - +
187C GLN* 3.3 8.6 + - + +
188C ALA* 2.9 19.9 + - - +
217C ILE* 3.5 34.2 - - + +
220C LYS* 5.1 21.8 - - + +
221C LEU* 3.6 35.7 - - + -
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Residues in contact with GLU 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LEU 4.1 7.0 - - - +
61C GLU* 3.8 4.7 - - - +
62C ILE* 2.9 34.2 + - + +
63C LEU* 2.7 32.9 + - - +
64C GLN 5.0 0.3 + - - -
181C LYS* 2.9 28.7 + - - +
182C THR 3.2 4.9 + - - +
184C LEU* 1.3 75.3 - - - +
186C ALA* 1.3 58.5 + - - +
188C ALA* 3.3 5.0 + - - +
189C TYR* 2.9 27.0 + - - +
218C TYR* 4.3 8.4 + - - -
221C LEU* 3.7 15.2 - - + +
233C TYR* 2.2 35.7 + - - +
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Residues in contact with ALA 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C ILE* 3.6 11.6 - - + +
169C LEU* 3.5 26.6 - - + +
170C GLU* 4.4 8.5 - - + -
173C CYS* 4.3 18.4 - - + -
182C THR 2.9 15.8 + - - +
183C LYS 4.0 2.7 - - - +
185C GLU* 1.3 72.9 - - - +
187C GLN* 1.3 68.0 + - - +
189C TYR* 3.0 5.8 + - - +
190C THR* 2.9 27.0 + - - -
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Residues in contact with GLN 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C GLU* 4.1 32.7 + - + +
174C GLU* 6.2 2.4 - - - +
183C LYS* 2.9 28.0 + - + +
184C LEU* 3.8 9.8 - - - +
186C ALA* 1.3 76.2 - - - +
188C ALA* 1.3 58.5 + - - +
190C THR* 3.8 1.4 - - - -
191C ALA* 2.9 29.6 + - - +
213C LYS* 4.4 15.2 + - - +
217C ILE* 3.5 24.2 - - + +
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Residues in contact with ALA 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C LEU 2.9 11.1 + - - +
185C GLU 3.7 0.9 - - - +
187C GLN* 1.3 78.3 - - - +
189C TYR* 1.3 57.1 + - - +
191C ALA* 3.5 4.9 + - - +
192C TYR* 2.9 28.4 + - - +
214C CYS* 4.0 6.5 - - - +
217C ILE* 3.5 29.5 - - + +
218C TYR* 3.4 40.3 + - + +
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Residues in contact with TYR 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C ILE* 4.8 13.2 - - + -
66C ILE* 4.5 19.3 - - + -
128C LEU* 3.6 28.9 - - + -
131C ALA* 3.9 16.1 - - + +
132C GLU* 2.3 50.3 + - - +
135C TRP* 5.1 0.5 - - - +
166C ALA* 4.0 15.9 - - + -
169C LEU* 4.9 6.3 - - + -
185C GLU 2.9 14.7 + - - +
186C ALA* 3.0 10.3 + - - +
188C ALA* 1.3 76.4 - - - +
190C THR* 1.3 63.4 + - - +
192C TYR* 2.9 24.7 + + - +
193C LEU* 3.0 36.8 + - + +
218C TYR* 4.1 9.6 + - - +
236C ARG* 5.4 2.0 - - - -
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Residues in contact with THR 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C VAL* 5.0 2.2 - - + +
166C ALA* 3.1 35.9 + - + +
167C GLU* 3.5 33.2 - - + +
169C LEU* 4.9 1.2 - - - +
170C GLU* 3.2 27.9 + - - +
186C ALA 2.9 12.8 + - - -
187C GLN 3.8 1.1 - - - -
189C TYR* 1.3 76.8 - - - +
191C ALA* 1.3 65.2 + - - +
193C LEU* 3.2 2.0 + - - +
194C SER* 2.9 27.3 + - - +
213C LYS* 6.1 2.2 - - - +
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Residues in contact with ALA 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C GLN 2.9 18.8 + - - +
188C ALA* 3.8 4.7 - - - +
190C THR* 1.3 77.4 - - - +
192C TYR* 1.3 65.0 + - - +
194C SER* 3.4 4.8 + - - -
195C GLY* 2.9 18.0 + - - -
210C ALA* 3.3 25.6 - - - +
213C LYS* 3.6 37.8 - - + +
214C CYS* 3.8 8.1 - - + +
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Residues in contact with TYR 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C TRP* 4.3 21.6 + + - -
188C ALA 2.9 15.6 + - - +
189C TYR* 2.9 17.7 + + + +
191C ALA* 1.3 77.4 - - - +
193C LEU* 1.3 82.9 + - + +
195C GLY* 3.1 4.1 + - - -
196C MET* 3.0 44.6 + - + +
211C PHE* 3.9 5.9 - + - -
214C CYS* 4.1 20.2 - - - +
218C TYR* 5.3 3.1 - - + +
236C ARG* 3.4 41.0 + - - -
239C GLU* 5.0 1.7 + - - -
240C ILE* 3.5 33.9 - - + +
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Residues in contact with LEU 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C ALA* 4.8 1.6 - - + -
135C TRP* 3.1 39.0 - - + +
159C LEU* 5.4 3.7 - - + +
162C ALA* 3.8 36.6 - - + +
163C VAL* 3.3 17.4 - - + +
166C ALA* 4.3 5.4 - - + -
189C TYR* 3.0 46.8 + - + +
190C THR* 4.1 2.9 - - - +
192C TYR* 1.3 84.6 - - + +
194C SER* 1.3 69.1 + - - +
195C GLY 2.9 1.6 - - - -
196C MET* 2.8 16.7 + - + +
197C LEU 2.9 12.0 + - - -
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Residues in contact with SER 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C VAL* 3.3 25.9 - - - +
167C GLU* 3.9 10.9 + - - -
190C THR* 2.9 18.5 + - - +
191C ALA* 3.6 7.0 - - - -
193C LEU* 1.3 75.4 - - - +
195C GLY* 1.3 62.4 + - - +
197C LEU* 3.8 1.9 - - - +
198C ARG* 3.0 52.5 + - - +
210C ALA* 4.1 11.4 - - - -
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Residues in contact with GLY 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C ALA 2.9 9.9 + - - -
192C TYR 3.4 0.7 - - - -
193C LEU 2.9 1.8 - - - -
194C SER* 1.3 79.5 - - - +
196C MET* 1.3 55.4 + - - -
198C ARG 3.7 1.0 - - - -
199C PHE* 3.0 28.1 + - - +
207C ALA* 4.2 7.9 - - - +
210C ALA* 3.5 14.1 - - - +
211C PHE* 3.2 29.8 - - - -
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Residues in contact with MET 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C TRP* 4.9 6.5 - - - +
139C MET* 6.2 7.6 - - + +
159C LEU* 3.9 17.9 - - + +
192C TYR* 3.0 51.8 + - + +
193C LEU* 2.8 16.6 + - + +
195C GLY* 1.3 70.5 - - - +
197C LEU* 1.3 70.4 + - - +
199C PHE* 3.2 11.0 + - - +
200C GLU* 3.0 17.8 + - - +
211C PHE* 4.1 9.4 - - + -
240C ILE* 4.6 5.6 - - + -
243C ASN* 3.5 28.9 - - - +
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Residues in contact with LEU 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C LEU* 4.2 10.3 - - + +
159C LEU* 3.6 36.5 - - + +
160C ARG* 4.1 29.6 - - + +
163C VAL* 4.3 13.2 - - + -
193C LEU 2.9 14.3 + - - +
194C SER 3.8 2.0 - - - +
196C MET* 1.3 71.5 - - - +
198C ARG* 1.3 77.4 + - + +
199C PHE 2.6 17.1 + - - -
200C GLU* 2.6 18.4 + - - +
201C HIS* 3.2 32.1 + - + +
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Residues in contact with ARG 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C VAL* 5.0 4.9 - - - +
167C GLU* 4.7 9.9 + - - -
194C SER* 3.0 41.3 + - - +
195C GLY 3.7 1.8 - - - -
197C LEU* 1.3 98.3 - - + +
199C PHE* 1.3 55.3 + - - +
201C HIS* 4.2 10.3 - - - +
203C GLU* 3.3 43.2 + - + +
206C ALA* 3.9 32.8 - - + +
207C ALA* 3.5 11.1 - - - +
209C GLU* 5.7 2.6 + - - -
210C ALA* 6.0 1.0 - - - +
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Residues in contact with PHE 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C GLY 3.0 18.2 + - - +
196C MET* 3.3 14.1 - - - +
197C LEU 2.6 5.7 + - - -
198C ARG* 1.3 73.6 - - - +
200C GLU* 1.3 74.6 + - - +
201C HIS 3.2 1.6 - - - -
202C GLN* 3.0 22.9 + - - +
203C GLU 5.0 0.2 - - - +
204C TRP* 3.9 21.5 - + - -
207C ALA* 4.2 4.3 - - + -
211C PHE* 4.8 4.3 - + + -
243C ASN* 4.3 39.0 - - + -
246C TYR* 4.2 20.4 - + - -
247C CYS* 4.1 25.6 - - - -
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Residues in contact with GLU 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C LYS* 3.5 33.0 - - + +
152C ARG* 3.7 36.4 + - - +
155C LEU* 4.3 13.9 - - + +
156C LEU* 3.7 22.8 - - + +
159C LEU* 4.2 12.6 - - + -
196C MET 3.0 12.7 + - - +
197C LEU 2.6 13.1 + - - +
199C PHE* 1.3 85.3 - - + +
201C HIS* 1.3 58.9 + - - +
202C GLN* 3.1 8.4 + - - +
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Residues in contact with HIS 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A G 3.8 29.8 + - - -
156C LEU* 3.4 41.1 - - + +
160C ARG* 4.3 14.2 + - - -
197C LEU* 3.2 26.2 + - + +
198C ARG* 4.6 3.2 - - - +
199C PHE 3.2 1.2 - - - -
200C GLU* 1.3 74.7 - - - +
202C GLN* 1.3 64.3 - - - +
203C GLU* 3.0 42.3 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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