Contacts of the helix formed by residues 193 - 230 (chain A) in PDB entry 3PIK
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 ASN 193 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A VAL* 4.6 0.5 - - - +
187A LEU* 3.6 12.9 - - - +
192A SER* 1.3 90.4 + - - +
194A VAL* 1.3 64.5 + - + +
195A LEU* 2.8 37.2 + - - +
196A ALA* 2.9 17.5 + - - +
197A LEU* 3.3 17.5 + - - +
395A TYR* 6.1 1.6 - - - -
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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
----------------------------------------------------------
187A LEU* 4.2 10.8 - - + +
193A ASN* 1.3 75.6 - - + +
195A LEU* 1.3 67.4 + - + +
197A LEU* 3.7 15.6 - - + +
198A GLU* 3.2 26.7 + - + +
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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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193A ASN* 2.8 17.5 + - - +
194A VAL* 1.3 81.5 - - + +
196A ALA* 1.3 63.3 + - - +
198A GLU* 3.1 7.6 + - + +
199A GLN* 2.9 55.4 + - + +
401A SER* 6.4 2.2 - - - -
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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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183A VAL* 4.1 5.8 - - + +
192A SER* 3.6 23.8 - - - +
193A ASN* 2.9 14.0 + - - +
195A LEU* 1.3 75.7 - - - +
197A LEU* 1.3 57.4 + - - +
199A GLN* 3.3 15.1 + - - +
200A ALA* 3.0 28.6 + - - +
395A TYR* 3.8 5.6 - - + +
402A TYR* 3.5 30.5 - - + -
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Residues in contact with LEU 197 (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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180A TYR* 3.6 33.6 - - + +
183A VAL* 3.7 11.8 - - + +
184A GLU* 3.8 44.2 - - - +
187A LEU* 4.0 20.4 - - + -
193A ASN 3.3 11.2 + - - +
194A VAL* 3.7 16.6 - - + +
195A LEU 3.1 0.4 - - - -
196A ALA* 1.3 80.1 - - - +
198A GLU* 1.3 68.0 + - - +
200A ALA* 3.2 2.3 + - - +
201A ARG* 3.0 21.9 + - + +
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Residues in contact with GLU 198 (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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194A VAL* 3.2 17.4 + - + +
195A LEU* 3.1 8.8 + - + +
197A LEU* 1.3 86.1 - - - +
199A GLN* 1.3 59.4 + - + +
201A ARG* 3.2 23.6 + - - +
202A GLY* 2.9 27.7 + - - -
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Residues in contact with GLN 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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195A LEU* 2.9 42.2 + - + +
196A ALA* 3.5 22.0 + - - +
197A LEU 3.2 0.2 - - - -
198A GLU* 1.3 78.4 - - - +
200A ALA* 1.3 63.0 + - - +
201A ARG 3.3 0.3 + - - -
202A GLY* 3.4 7.9 + - - -
203A VAL* 3.4 15.6 + - - +
402A TYR* 3.7 21.8 - - + +
403A LEU* 4.2 29.0 + - - +
406A LEU* 3.9 30.0 - - + +
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Residues in contact with ALA 200 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A TYR 4.5 1.6 - - - +
179A SER* 4.7 1.8 - - - -
180A TYR* 3.9 30.7 - - + +
183A VAL* 4.5 5.6 - - + -
196A ALA 3.0 16.6 + - - +
197A LEU* 3.7 5.2 - - - +
199A GLN* 1.3 76.5 - - - +
201A ARG* 1.3 62.3 + - - +
203A VAL* 3.3 19.8 - - - +
204A ILE* 3.6 14.0 - - - +
402A TYR* 4.0 23.5 - - + +
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Residues in contact with ARG 201 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A TYR* 3.6 38.3 + - + -
197A LEU 3.0 16.8 + - - +
198A GLU* 3.6 25.4 + - - +
200A ALA* 1.3 75.8 - - - +
202A GLY* 1.3 68.4 + - - +
204A ILE* 3.1 24.3 + - + +
205A GLU* 3.4 22.0 + - + +
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Residues in contact with GLY 202 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A GLU* 2.9 16.5 + - - -
199A GLN* 3.4 3.5 + - - -
201A ARG* 1.3 77.5 - - - +
203A VAL* 1.3 55.5 + - - +
205A GLU* 2.8 28.0 + - - +
206A SER* 3.1 11.6 + - - -
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Residues in contact with VAL 203 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A TYR* 3.8 35.2 - - + -
199A GLN 3.4 9.7 + - - +
200A ALA* 3.3 22.4 - - - +
202A GLY* 1.3 69.9 - - - +
204A ILE* 1.3 61.8 + - - +
206A SER* 3.1 16.8 + - - +
207A THR* 2.6 28.8 + - - -
406A LEU* 3.4 29.6 - - + -
409A GLU* 4.7 2.7 - - - +
410A ARG* 4.5 17.9 - - + +
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Residues in contact with ILE 204 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A LEU* 3.8 19.2 - - + +
176A TYR* 3.8 26.7 - - + +
177A GLN* 4.0 15.3 - - + +
180A TYR* 3.7 36.6 - - + -
200A ALA 3.6 9.9 - - - +
201A ARG* 3.1 14.8 + - + +
203A VAL* 1.3 78.3 - - - +
205A GLU* 1.3 71.4 + - - +
207A THR* 3.2 5.7 + - - -
208A ARG* 3.0 40.6 + - - +
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Residues in contact with GLU 205 (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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201A ARG* 3.6 31.6 + - + +
202A GLY* 2.8 13.0 + - - +
204A ILE* 1.3 84.0 - - - +
206A SER* 1.3 65.0 + - - +
208A ARG* 3.1 21.6 + - - +
209A SER* 3.0 20.6 + - - -
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Residues in contact with SER 206 (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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176A TYR* 5.4 0.5 - - - -
202A GLY 3.1 8.2 + - - -
203A VAL* 3.1 23.0 + - - +
205A GLU* 1.3 76.8 - - - +
207A THR* 1.3 61.4 + - - +
209A SER* 3.2 11.6 + - - -
210A ASP* 3.0 24.4 + - - +
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Residues in contact with THR 207 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ALA* 3.4 28.3 - - - +
172A THR* 4.2 10.3 - - + +
173A LEU* 3.7 20.9 - - + +
176A TYR* 3.1 20.1 - - - -
203A VAL 2.6 23.5 + - - -
204A ILE* 3.5 4.7 - - - -
206A SER* 1.3 77.2 + - - +
208A ARG* 1.3 59.5 + - - +
210A ASP* 3.0 6.9 + - - +
211A ILE* 2.9 28.0 + - - +
413A PHE* 4.3 14.6 - - + -
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Residues in contact with ARG 208 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A LEU* 4.0 13.8 - - + +
177A GLN* 3.4 16.3 - - - +
204A ILE* 3.0 31.2 + - - +
205A GLU* 3.1 22.5 + - - +
207A THR* 1.3 74.4 - - - +
209A SER* 1.3 61.4 + - - +
211A ILE* 3.4 11.7 + - + +
212A ALA* 3.0 23.7 + - - +
449A SO4 2.8 43.8 + - - -
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Residues in contact with SER 209 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A GLU 3.0 11.6 + - - -
206A SER* 3.2 14.4 - - - -
207A THR 3.1 0.2 - - - -
208A ARG* 1.3 78.0 - - - +
210A ASP* 1.3 55.9 + - - +
212A ALA* 3.3 8.1 + - - +
213A LYS* 3.0 28.3 + - - +
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Residues in contact with ASP 210 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A GLN* 4.6 0.9 - - - +
169A ALA* 3.4 13.3 - - + +
206A SER 3.0 12.4 + - - +
207A THR* 3.0 11.8 + - - +
209A SER* 1.3 77.7 - - - +
211A ILE* 1.3 55.3 + - - +
213A LYS* 3.1 25.5 + - - +
214A ARG* 2.9 57.4 + - - +
413A PHE* 3.4 28.6 - - + -
417A GLN* 3.4 15.2 - - - +
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Residues in contact with ILE 211 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LEU* 3.9 12.0 - - + +
169A ALA* 3.7 28.0 - - + +
170A GLU* 4.1 17.0 - - + +
173A LEU* 3.6 41.5 - - + -
207A THR 2.9 17.7 + - - +
208A ARG* 3.5 13.7 - - + +
210A ASP* 1.3 75.6 - - - +
212A ALA* 1.3 57.3 + - - +
214A ARG* 3.1 4.4 + - - +
215A GLN* 2.9 47.5 + - - +
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Residues in contact with ALA 212 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A ARG 3.0 13.9 + - - +
209A SER* 3.6 10.1 - - - +
211A ILE* 1.3 75.8 - - - +
213A LYS* 1.3 62.9 + - - +
215A GLN* 3.5 18.0 + - - +
216A GLY* 3.2 17.2 + - - -
452A SO4 3.8 6.4 + - - +
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Residues in contact with LYS 213 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A SER 3.0 13.5 + - - +
210A ASP* 3.1 31.4 + - - +
212A ALA* 1.3 77.5 - - - +
214A ARG* 1.3 73.0 + - - +
216A GLY* 3.1 4.2 + - - -
217A GLU* 3.0 45.8 + - + +
417A GLN* 5.1 0.6 + - - -
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Residues in contact with ARG 214 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LEU* 6.2 0.8 - - - +
162A ALA* 4.6 5.7 - - - +
165A GLN* 3.6 57.9 + - - +
166A LEU* 3.8 25.1 - - + +
169A ALA* 4.7 1.6 - - + -
210A ASP* 2.9 39.4 + - - +
211A ILE 3.1 3.8 + - - +
213A LYS* 1.3 83.3 - - - +
215A GLN* 1.3 61.0 + - - +
217A GLU* 2.9 32.4 + - - +
218A LEU* 2.9 31.0 + - - +
417A GLN* 2.9 28.3 + - - +
421A ASP* 5.0 7.3 + - - -
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Residues in contact with GLN 215 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LEU* 3.9 22.0 - - + +
170A GLU* 5.0 4.2 + - - -
211A ILE* 2.9 29.6 + - - +
212A ALA* 3.5 21.2 + - - +
214A ARG* 1.3 76.9 - - - +
216A GLY* 1.3 62.5 + - - +
218A LEU* 3.3 7.4 + - + +
219A ALA* 3.0 18.9 + - - +
452A SO4 3.3 36.5 + - - +
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Residues in contact with GLY 216 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A ALA 3.2 9.7 + - - -
213A LYS 3.1 8.4 + - - -
215A GLN* 1.3 74.8 - - - +
217A GLU* 1.3 56.1 + - - +
219A ALA* 3.1 9.2 + - - +
220A GLN* 2.9 36.3 + - - +
452A SO4 3.5 10.8 + - - -
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Residues in contact with GLU 217 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ASN* 5.2 0.9 + - - -
162A ALA* 4.1 12.1 - - + +
165A GLN* 5.3 0.9 - - - +
213A LYS* 3.0 37.4 + - + +
214A ARG* 2.9 42.7 + - - +
216A GLY* 1.3 74.1 - - - +
218A LEU* 1.3 58.5 + - - +
220A GLN* 3.3 18.6 + - - +
221A ALA* 2.8 30.7 + - - +
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Residues in contact with LEU 218 (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 GLN* 4.0 26.5 - - + +
162A ALA* 3.6 20.7 - - + +
163A TYR* 3.8 34.5 - - + -
166A LEU* 4.1 20.0 - - + -
214A ARG 2.9 16.8 + - - +
215A GLN* 3.5 6.7 - - - +
217A GLU* 1.3 76.7 - - - +
219A ALA* 1.3 63.7 + - - +
221A ALA* 3.0 4.6 + - - +
222A ASN* 2.9 34.9 + - - +
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Residues in contact with ALA 219 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A GLN 3.0 13.6 + - - +
216A GLY* 3.5 9.4 - - - +
218A LEU* 1.3 76.6 - - - +
220A GLN* 1.3 63.2 + - + +
222A ASN* 3.3 10.4 + - - +
223A ASN* 3.0 35.1 + - - +
452A SO4 4.6 11.9 - - - +
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Residues in contact with GLN 220 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A GLY* 2.9 13.0 + - - +
217A GLU* 3.6 29.3 + - - +
219A ALA* 1.3 75.8 - - + +
221A ALA* 1.3 58.0 + - - +
223A ASN* 3.4 9.4 + - - +
224A ALA* 3.0 29.5 + - - +
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Residues in contact with ALA 221 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A SER* 4.3 3.6 + - - +
158A ASN* 3.7 22.4 - - - +
159A GLN* 3.7 32.9 - - + +
162A ALA* 4.7 0.9 - - + -
217A GLU 2.8 17.7 + - - +
218A LEU* 3.0 7.8 + - - +
220A GLN* 1.3 75.8 - - - +
222A ASN* 1.3 58.7 + - - +
224A ALA* 3.4 6.4 + - - +
225A LEU* 3.0 30.0 + - - +
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Residues in contact with ASN 222 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A GLN* 2.8 35.0 + - - +
163A TYR* 5.1 3.2 + - - -
218A LEU* 2.9 32.0 + - - +
219A ALA* 3.5 11.7 - - - +
220A GLN 3.2 0.2 - - - -
221A ALA* 1.3 76.9 - - - +
223A ASN* 1.3 60.6 + - - +
225A LEU* 3.3 6.3 + - - +
226A GLN* 3.0 33.8 + - - +
235A LEU* 3.3 30.8 - - + +
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Residues in contact with ASN 223 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ALA* 3.0 25.1 + - - +
220A GLN* 3.8 7.9 - - - +
221A ALA 3.3 0.2 - - - -
222A ASN* 1.3 80.9 - - - +
224A ALA* 1.3 61.3 + - - +
226A GLN* 4.0 14.7 - - - +
227A LEU* 3.1 22.2 + - - +
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Residues in contact with ALA 224 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A SER* 4.1 8.3 - - - +
158A ASN* 6.2 0.9 - - - +
220A GLN 3.0 17.8 + - - +
221A ALA* 3.8 6.7 - - - +
223A ASN* 1.3 73.2 - - - +
225A LEU* 1.3 65.3 + - - +
227A LEU* 3.3 10.6 + - - +
228A LEU* 3.0 28.3 + - + +
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Residues in contact with LEU 225 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 4.3 24.2 - - + -
152A VAL* 4.2 15.7 - - + +
155A SER* 3.3 27.3 + - - +
156A TYR* 4.1 12.6 - - - +
159A GLN* 4.3 25.1 - - + +
221A ALA 3.0 15.0 + - - +
222A ASN* 3.3 5.4 + - - +
224A ALA* 1.3 77.9 - - - +
226A GLN* 1.3 56.0 + - - +
228A LEU* 3.2 5.7 + - + +
229A LEU* 2.9 43.8 + - + +
235A LEU* 4.0 20.9 - - + -
236A PRO* 4.3 7.4 - - + -
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Residues in contact with GLN 226 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ASN* 3.0 19.4 + - - +
223A ASN* 4.0 15.3 - - - +
225A LEU* 1.3 73.9 - - - +
227A LEU* 1.3 64.9 + - - +
229A LEU* 4.4 4.0 - - + -
230A GLY* 3.0 19.6 + - - -
231A SER 3.5 20.8 + - - +
232A TYR* 3.5 44.1 + - + +
233A GLY 3.2 25.4 + - - +
235A LEU* 3.8 29.5 - - + +
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Residues in contact with LEU 227 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ASN* 4.3 3.6 + - - -
58A ARG 5.7 0.9 + - - -
223A ASN 3.1 14.2 + - - +
224A ALA* 3.6 12.3 - - - +
226A GLN* 1.3 74.9 - - - +
228A LEU* 1.3 66.8 + - + +
230A GLY* 3.2 12.0 + - - -
232A TYR* 4.8 13.4 - - - +
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Residues in contact with LEU 228 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ALA* 4.0 5.4 - - - +
57A ASN* 2.6 32.5 + - - +
148A LEU* 3.9 23.7 - - + +
151A ASN* 3.8 28.5 - - + +
152A VAL* 4.3 10.5 - - + +
155A SER* 3.6 34.5 - - - +
224A ALA* 3.0 15.3 + - + +
225A LEU* 3.6 7.0 - - + +
227A LEU* 1.3 80.2 - - + +
229A LEU* 1.3 60.9 + - + +
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Residues in contact with LEU 229 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 3.1 58.1 - - + +
52A GLU* 3.9 12.6 - - + +
53A ALA* 3.9 18.8 - - + +
56A ASN* 3.2 19.1 - - - +
57A ASN 3.6 6.1 + - - -
152A VAL* 4.4 7.6 - - + -
225A LEU* 2.9 32.2 + - + +
226A GLN* 3.9 3.8 - - + +
228A LEU* 1.3 76.2 - - - +
230A GLY* 1.3 63.2 + - - +
231A SER* 3.4 25.6 + - - +
235A LEU* 5.3 7.0 - - + -
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Residues in contact with GLY 230 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASN* 3.6 23.2 - - - +
57A ASN* 4.7 2.0 - - - -
58A ARG* 5.3 7.2 - - - -
226A GLN 3.0 9.4 + - - -
227A LEU* 3.2 6.8 + - - -
228A LEU 3.2 4.2 + - - -
229A LEU* 1.3 78.9 - - - +
231A SER* 1.3 60.4 + - - +
232A TYR* 4.2 12.8 - - - -
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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