Contacts of the helix formed by residues 171 - 193 (chain C) in PDB entry 4P3E
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 171 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50C LEU 3.4 9.9 + - - +
51C SER* 3.2 22.7 + - - -
169C ARG 4.3 0.2 - - - -
170C VAL* 1.3 78.8 - - - +
172C ALA* 1.3 62.1 + - - +
173C LYS* 3.4 12.3 + - - +
174C THR* 2.8 36.1 + - - -
175C LYS* 3.3 16.1 + - - +
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Residues in contact with ALA 172 (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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171C ASP* 1.3 70.8 - - - +
173C LYS* 1.3 60.1 + - - +
174C THR 3.2 1.6 - - - -
175C LYS* 3.2 28.4 + - + +
176C LEU* 3.0 32.9 + - + +
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Residues in contact with LYS 173 (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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51C SER* 5.9 2.2 + - - +
52C LEU 4.9 0.8 + - - -
53C GLU* 3.2 47.5 + - - +
171C ASP* 3.3 13.1 + - - +
172C ALA* 1.3 77.4 - - - +
174C THR* 1.3 63.7 + - - +
176C LEU* 3.3 13.8 + - - +
177C GLU* 3.2 34.4 + - + +
213C LEU* 4.2 11.3 - - + +
217C PHE* 3.7 34.3 - - + -
225C TYR* 4.0 12.7 + - - -
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Residues in contact with THR 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C SER* 4.0 1.7 + - - -
52C LEU* 3.1 56.9 + - + +
54C ILE* 5.0 2.9 - - + -
165C CYS* 3.6 24.7 - - - -
170C VAL* 3.6 15.0 - - + -
171C ASP* 2.8 23.4 + - - -
173C LYS* 1.3 77.3 + - - +
175C LYS* 1.3 63.7 + - - +
177C GLU* 3.4 3.2 + - - +
178C ALA* 3.1 23.2 + - - +
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Residues in contact with LYS 175 (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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165C CYS* 3.4 25.4 + - - +
166C GLU* 4.4 15.8 + - + +
167C SER 4.1 12.1 + - - -
168C ASN* 4.6 11.1 + - - +
170C VAL 3.5 20.9 + - - -
171C ASP 3.3 8.0 + - - +
172C ALA* 3.2 29.8 + - + +
174C THR* 1.3 79.3 - - - +
176C LEU* 1.3 63.1 + - + +
178C ALA* 3.4 1.7 + - - +
179C GLN* 3.2 42.5 + - - +
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Residues in contact with LEU 176 (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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172C ALA* 3.0 18.6 + - + +
173C LYS* 3.4 11.2 - - - +
174C THR 3.2 0.2 - - - -
175C LYS* 1.3 76.0 - - + +
177C GLU* 1.3 66.3 + - - +
179C GLN* 3.3 11.1 + - - +
180C ALA* 2.9 25.6 + - - +
209C ILE* 3.6 20.2 - - + +
212C LYS* 4.7 32.1 - - + +
213C LEU* 3.6 33.2 - - + -
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Residues in contact with GLU 177 (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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52C LEU 4.5 1.8 - - - +
53C GLU* 4.5 1.7 - - - +
54C ILE* 3.6 29.9 + - + +
55C LEU* 2.9 38.3 + - - +
56C GLN 5.1 0.7 + - - -
173C LYS* 3.2 29.0 + - - +
174C THR* 3.4 8.3 + - - +
176C LEU* 1.3 76.1 - - - +
178C ALA* 1.3 53.4 + - - +
180C ALA* 3.1 6.2 + - - +
181C TYR* 2.7 37.1 + - - +
210C TYR* 4.3 6.6 + - - -
213C LEU* 4.3 12.1 - - + -
225C TYR* 3.0 28.4 + - - -
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Residues in contact with ALA 178 (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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54C ILE* 3.4 17.4 - - + +
161C LEU* 4.8 5.3 - - + +
162C GLU* 4.1 26.0 - - + +
165C CYS* 4.3 15.5 - - + -
174C THR 3.1 14.2 + - - +
175C LYS 3.8 4.3 - - - +
177C GLU* 1.3 78.3 - - - +
179C GLN* 1.3 55.1 + - - +
181C TYR* 3.6 2.7 - - - +
182C THR* 2.7 38.3 + - - -
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Residues in contact with GLN 179 (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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162C GLU* 3.2 33.5 + - + +
166C GLU* 3.9 22.2 + - - +
175C LYS* 3.2 31.4 + - - +
176C LEU* 4.0 11.5 - - - +
178C ALA* 1.3 76.8 - - + +
180C ALA* 1.3 57.5 + - - +
182C THR* 4.0 1.9 - - - -
183C ALA* 3.2 24.1 + - - +
205C LYS* 4.3 9.4 + - - -
209C ILE* 3.9 18.4 - - + +
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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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176C LEU 2.9 17.4 + - - +
177C GLU* 3.4 5.8 - - - +
179C GLN* 1.3 77.6 - - - +
181C TYR* 1.3 58.1 + - - +
183C ALA* 3.5 5.7 + - - +
184C TYR* 3.0 24.9 + - - +
206C CYS* 3.7 9.6 - - - +
209C ILE* 3.8 24.0 - - + +
210C TYR* 3.8 32.2 + - + -
213C LEU* 4.9 0.4 - - + -
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Residues in contact with TYR 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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54C ILE* 3.9 19.7 - - + -
58C ILE* 3.7 22.9 - - + -
120C LEU* 3.5 24.6 - - + +
123C ALA* 3.9 13.1 + - + +
124C GLU* 2.3 46.4 + - - +
127C TRP* 4.9 0.5 - - - +
158C ALA* 4.2 11.2 - - + -
161C LEU* 4.5 8.7 - - + -
177C GLU 2.7 17.1 + - - +
178C ALA* 3.6 6.1 - - - +
180C ALA* 1.3 73.5 - - - +
182C THR* 1.3 61.2 + - - +
183C ALA 3.1 1.3 - - - -
184C TYR* 2.8 29.8 + + + +
185C LEU* 3.0 43.8 + - + +
210C TYR* 4.5 8.0 + - - +
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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
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155C VAL* 5.2 4.2 - - + +
158C ALA* 3.1 33.7 + - + +
159C GLU* 4.4 22.9 - - + +
162C GLU* 3.2 25.7 + - - +
178C ALA 2.7 24.4 + - - -
179C GLN 4.1 3.1 - - - -
181C TYR* 1.3 76.4 - - - +
183C ALA* 1.3 57.6 + - - +
185C LEU* 4.1 1.3 - - - +
186C SER* 3.0 34.8 + - - -
205C LYS* 5.9 3.8 - - - +
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Residues in contact with ALA 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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179C GLN 3.2 17.6 + - - +
180C ALA* 3.5 7.0 - - - +
181C TYR 3.1 0.6 - - - -
182C THR* 1.3 79.7 - - - +
184C TYR* 1.3 55.0 + - - +
186C SER* 3.6 5.6 - - - -
187C GLY* 2.7 32.1 + - - -
202C ALA* 3.7 24.9 - - - +
203C PHE* 5.1 0.2 - - - -
205C LYS* 4.1 19.5 - - + +
206C CYS* 3.8 14.4 - - + +
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Residues in contact with TYR 184 (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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127C TRP* 3.9 31.4 + + - -
180C ALA 3.0 14.1 + - - +
181C TYR* 2.8 22.0 + + + +
183C ALA* 1.3 75.8 - - - +
185C LEU* 1.3 69.7 + - + +
187C GLY* 3.1 4.0 + - - -
188C MET* 2.9 59.2 + - + +
203C PHE* 4.1 6.7 - + - -
206C CYS* 4.2 14.6 - - - +
210C TYR* 5.4 3.4 - + - +
228C ARG* 3.1 36.7 + - - -
231C GLU* 3.8 10.3 + - - -
232C ILE* 3.7 28.7 - - + -
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Residues in contact with LEU 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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123C ALA* 4.5 4.3 - - + +
127C TRP* 3.3 33.7 - - + -
151C LEU* 4.9 3.5 - - + +
154C ALA* 3.6 36.1 - - + +
155C VAL* 3.9 16.2 - - + +
158C ALA* 3.9 4.5 - - + -
181C TYR* 3.0 45.0 + - + +
182C THR 4.2 3.1 - - - +
184C TYR* 1.3 92.5 - - + +
186C SER* 1.3 58.5 + - - +
188C MET* 2.7 25.1 + - + +
189C LEU* 2.8 15.6 + - - +
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Residues in contact with SER 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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155C VAL* 3.9 17.6 - - - +
182C THR* 3.0 24.2 + - - -
183C ALA* 3.6 7.4 - - - -
185C LEU* 1.3 74.7 - - - +
187C GLY* 1.3 64.4 + - - +
189C LEU* 3.4 2.7 + - - +
190C ARG* 3.2 58.9 + - - +
202C ALA* 3.8 3.6 - - - +
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Residues in contact with GLY 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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183C ALA 2.7 19.2 + - - -
184C TYR 3.4 5.4 - - - -
185C LEU 3.1 0.2 - - - -
186C SER* 1.3 72.6 - - - +
188C MET* 1.3 55.4 + - - +
190C ARG 3.9 0.3 - - - -
191C PHE* 3.0 30.7 + - - +
199C ALA* 3.9 7.3 - - - +
202C ALA* 3.5 16.3 - - - +
203C PHE* 3.7 20.7 - - - -
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Residues in contact with MET 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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127C TRP* 4.8 8.3 - - - +
131C MET* 5.4 7.4 - - + +
151C LEU* 3.6 20.3 - - + +
184C TYR* 2.9 59.7 + - + +
185C LEU* 2.7 18.5 + - + +
187C GLY* 1.3 69.2 - - - +
189C LEU* 1.3 64.8 + - - +
191C PHE* 3.2 8.7 + - - +
192C GLU* 3.0 24.3 + - - +
203C PHE* 3.9 15.7 - - + -
232C ILE* 5.6 0.4 - - + -
235C ASN* 3.8 26.0 - - - +
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Residues in contact with LEU 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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148C LEU* 3.9 18.8 - - + +
151C LEU* 3.6 33.1 - - + +
152C ARG* 3.9 32.1 - - + +
155C VAL* 4.4 15.0 - - + -
185C LEU 2.8 16.2 + - - +
186C SER* 4.0 4.5 - - - +
187C GLY 3.4 0.2 - - - -
188C MET* 1.3 71.3 - - - +
190C ARG* 1.3 62.7 + - + +
192C GLU* 2.9 19.6 + - - +
193C HIS* 2.9 38.9 + - + +
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Residues in contact with ARG 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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186C SER* 3.2 36.8 + - - +
189C LEU* 1.3 81.8 - - + +
191C PHE* 1.3 55.3 + - - +
193C HIS* 3.4 5.1 + - - -
194C GLN 3.0 6.4 + - - -
195C GLU* 2.8 41.7 + - + +
198C ALA* 3.4 41.7 + - + +
199C ALA* 3.6 18.4 - - + +
201C GLU* 4.5 7.7 + - - +
202C ALA* 3.9 8.9 - - - +
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Residues in contact with PHE 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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134C LYS* 5.4 4.9 - - - -
187C GLY 3.0 20.0 + - - +
188C MET* 3.5 11.0 - - - +
189C LEU 3.1 0.2 - - - -
190C ARG* 1.3 77.4 - - - +
192C GLU* 1.3 73.2 + - - +
194C GLN* 3.4 15.7 + - - +
196C TRP* 4.1 13.2 - + - -
199C ALA* 3.6 5.1 - - + +
203C PHE* 3.6 14.4 - + + -
235C ASN* 3.5 29.4 - - - -
238C TYR* 3.9 34.1 - + + -
239C CYS* 3.4 33.4 - - - -
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Residues in contact with GLU 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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134C LYS* 2.7 45.2 + - - +
144C ARG* 3.2 50.0 + - - +
147C LEU* 3.6 25.6 - - + +
148C LEU* 3.6 17.9 - - + +
151C LEU* 4.3 7.0 - - + +
188C MET 3.0 11.0 + - - +
189C LEU 2.9 8.1 + - - +
191C PHE* 1.3 85.4 - - - +
193C HIS* 1.3 58.7 + - - +
194C GLN* 2.9 11.2 + - - +
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Residues in contact with HIS 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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168A G 5.8 5.6 - - - -
148C LEU* 4.0 30.0 + - + +
152C ARG* 6.1 0.6 - - - +
189C LEU* 2.9 49.2 + - + +
190C ARG* 3.8 7.4 - - - +
192C GLU* 1.3 73.8 - - - +
194C GLN* 1.3 69.8 + - - +
195C GLU* 3.3 20.3 + - + +
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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