Contacts of the helix formed by residues 198 - 227 (chain A) in PDB entry 4DUB
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 TYR 198 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ARG* 3.5 55.9 + - + +
191A ALA 5.2 1.7 + - - -
192A ASN* 3.4 23.3 + - + -
193A PRO 3.6 24.0 - - - +
195A ASP* 3.3 18.5 + - + +
196A PRO 3.1 1.0 - - - -
197A ALA* 1.3 86.4 - - + +
199A ASP* 1.3 63.6 + - - +
200A GLU 3.0 2.5 - - - -
201A ASN* 3.1 15.5 + - - +
202A LYS* 2.9 30.8 + - - +
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Residues in contact with ASP 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ASP 4.8 1.7 - - - +
195A ASP 4.1 2.8 - - - +
196A PRO* 2.9 39.9 + - - +
198A TYR* 1.3 77.1 - - - +
200A GLU* 1.3 56.5 + - - +
202A LYS* 3.5 19.7 + - - +
203A ARG* 3.1 27.5 + - - +
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Residues in contact with GLU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A PRO 4.6 0.8 + - - -
197A ALA 4.6 4.7 + - - +
198A TYR 3.0 1.0 - - - -
199A ASP* 1.3 75.4 - - - +
201A ASN* 1.3 68.6 + - - +
203A ARG* 2.8 45.2 + - - +
204A GLN* 2.9 34.9 + - + +
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Residues in contact with ASN 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLU* 3.1 34.2 - - - +
186A ASN* 5.7 0.9 + - - -
190A ARG* 3.6 11.5 + - - +
197A ALA 3.7 7.9 + - - -
198A TYR* 3.4 33.2 - - - +
200A GLU* 1.3 81.8 - - - +
202A LYS* 1.4 51.8 + - + +
204A GLN* 3.3 6.3 + - - +
205A PHE* 2.8 37.2 + - - +
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Residues in contact with LYS 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLU* 5.3 3.6 - - - +
187A LYS* 5.7 7.9 - - - +
190A ARG* 6.0 2.2 - - - +
193A PRO* 3.2 26.9 + - - -
194A ASP* 3.4 27.7 + - - +
195A ASP 4.6 1.6 + - - -
198A TYR* 2.9 21.8 + - + +
199A ASP* 3.7 18.6 + - - +
200A GLU 3.2 0.2 - - - -
201A ASN* 1.4 75.8 - - + +
203A ARG* 1.3 65.0 + - - +
205A PHE* 3.3 8.2 + - + +
206A GLN* 3.0 31.1 + - + +
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Residues in contact with ARG 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASP 3.1 18.6 + - - +
200A GLU* 2.8 44.6 + - - +
202A LYS* 1.3 71.3 - - - +
204A GLN* 1.3 86.4 + - - +
206A GLN* 3.2 8.9 + - - +
207A GLU* 2.9 52.9 + - + +
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Residues in contact with GLN 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ARG* 3.4 32.8 + - + +
200A GLU* 2.9 23.2 + - - +
201A ASN* 3.7 6.3 - - - +
203A ARG* 1.3 98.4 + - - +
205A PHE* 1.3 58.6 + - - +
207A GLU* 3.0 29.8 + - - +
208A ASP* 2.9 50.4 + - - +
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Residues in contact with PHE 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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77A PHE 4.4 4.7 - - - -
80A ASP* 4.0 25.1 - - + -
81A PHE* 4.1 19.7 - + - -
180A ALA* 3.6 31.0 - - + -
183A GLU* 3.5 29.4 - - + -
184A ALA* 4.5 4.0 - - + -
187A LYS* 3.4 25.8 - - - -
201A ASN 2.8 19.3 + - - +
202A LYS* 3.6 7.2 - - - +
203A ARG 3.2 0.2 - - - -
204A GLN* 1.3 78.5 - - - +
206A GLN* 1.3 72.5 + - - +
208A ASP* 3.2 6.3 + - - +
209A ILE* 3.0 46.5 + - + +
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Residues in contact with GLN 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LYS* 3.0 18.1 + - + +
203A ARG* 3.2 10.5 + - + +
205A PHE* 1.3 97.4 - - - +
207A GLU* 1.3 55.9 + - - +
209A ILE* 3.4 21.1 + - - +
210A LYS* 3.0 27.2 + - - +
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Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ARG* 4.2 6.6 + - - -
203A ARG* 2.9 42.4 + - + +
204A GLN* 3.0 28.0 + - - +
206A GLN* 1.3 75.6 - - - +
208A ASP* 1.3 58.1 + - - +
210A LYS* 3.2 6.9 + - - +
211A VAL* 3.0 39.6 + - + +
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Residues in contact with ASP 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A SER* 2.8 44.1 + - - +
179A ARG* 2.9 50.4 + - - +
180A ALA* 4.4 8.7 - - + -
204A GLN* 2.9 29.6 + - - +
205A PHE* 3.7 6.7 - - - +
207A GLU* 1.3 75.6 - - - +
209A ILE* 1.4 64.2 + - - +
211A VAL* 3.4 2.8 + - - +
212A MET* 3.1 29.5 + - - +
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Residues in contact with ILE 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASP* 3.6 21.3 - - + +
81A PHE* 3.8 21.5 - - + -
180A ALA* 5.7 0.4 - - + -
205A PHE* 3.0 43.9 + - + +
206A GLN* 3.6 26.9 - - - +
208A ASP* 1.4 75.8 - - - +
210A LYS* 1.3 59.3 + - + +
212A MET* 3.2 9.1 + - + +
213A ASN* 2.9 51.4 + - - +
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Residues in contact with LYS 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLN 3.0 16.4 + - - +
207A GLU* 3.2 7.1 + - - +
209A ILE* 1.3 79.0 - - - +
211A VAL* 1.3 56.2 + - - +
213A ASN* 4.5 4.5 - - - +
214A ASP* 2.7 67.4 + - - +
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Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A PRO* 3.8 22.4 - - + +
173A PHE* 4.0 10.8 - - + -
176A SER* 3.5 28.7 - - - +
207A GLU* 3.0 28.4 + - + +
208A ASP 3.7 3.6 - - - +
210A LYS* 1.3 76.4 - - - +
212A MET* 1.3 62.1 + - - +
214A ASP* 4.0 3.8 - - - +
215A LEU* 3.3 23.8 + - + +
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Residues in contact with MET 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE* 3.8 28.9 - - + -
173A PHE* 3.6 35.9 - - + +
176A SER* 4.3 2.0 - - - +
177A MET* 3.6 33.2 - - - +
180A ALA* 3.7 28.3 - - + -
208A ASP 3.1 27.5 + - - +
209A ILE* 3.2 6.9 + - - +
211A VAL* 1.3 79.1 - - - +
213A ASN* 1.3 62.0 + - - +
216A VAL* 3.1 29.6 + - - +
259A ILE* 4.2 21.5 - - + -
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Residues in contact with ASN 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE 4.8 1.7 - - - +
209A ILE* 2.9 40.6 + - - +
210A LYS* 4.0 4.6 - - - +
212A MET* 1.3 74.1 - - - +
214A ASP* 1.3 64.3 + - - +
217A ASP* 2.8 38.4 + - - +
255A ARG* 3.5 51.1 + - - +
256A TYR* 4.6 6.5 + - - -
259A ILE* 3.6 10.6 - - - +
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Residues in contact with ASP 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LYS* 2.7 62.9 + - - +
211A VAL* 4.0 4.8 - - - +
213A ASN* 1.3 74.3 - - - +
215A LEU* 1.4 61.7 + - - +
217A ASP* 4.0 4.6 - - - +
218A LYS* 3.0 25.7 + - - +
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Residues in contact with LEU 215 (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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158A PHE* 4.7 6.1 - - + -
160A TYR* 3.8 43.5 - - + +
162A PHE* 4.3 3.8 - - + -
171A HIS* 3.9 7.4 - - + -
173A PHE* 3.8 34.1 - - + -
211A VAL* 3.3 15.8 + - + +
212A MET 4.1 2.7 - - - +
214A ASP* 1.4 78.2 - - - +
216A VAL* 1.4 65.6 + - - +
218A LYS* 3.2 15.9 + - + +
219A ILE* 3.0 36.6 + - + +
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Residues in contact with VAL 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PHE* 4.1 16.8 - - + -
173A PHE* 3.7 22.2 - - + -
212A MET 3.1 17.1 + - - +
215A LEU* 1.4 76.5 - - + +
217A ASP* 1.3 58.2 + - - +
219A ILE* 3.3 2.0 + - - +
220A ILE* 2.9 29.0 + - + +
255A ARG* 3.5 38.4 - - + +
258A ILE* 3.9 39.0 - - + -
259A ILE* 4.2 7.0 - - + -
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Residues in contact with ASP 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ASN* 2.8 29.9 + - - +
214A ASP* 4.0 5.2 - - - +
216A VAL* 1.3 71.2 - - - +
218A LYS* 1.3 57.7 + - - +
220A ILE* 3.4 8.6 + - - +
221A ALA* 2.8 32.2 + - - +
251A ASP 5.0 1.2 - - - +
252A GLU* 5.6 0.9 - - - -
255A ARG* 2.7 53.0 + - - +
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Residues in contact with LYS 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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214A ASP 3.0 19.4 + - - +
215A LEU* 3.5 15.7 - - + +
217A ASP* 1.3 77.4 - - - +
219A ILE* 1.3 64.2 + - + +
221A ALA* 3.4 5.8 + - - +
222A ASP* 2.8 59.1 + - - +
136B ASP* 4.6 23.2 - - - +
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Residues in contact with ILE 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PHE* 3.6 48.0 - - + +
160A TYR* 3.8 28.5 - - + -
215A LEU* 3.0 28.6 + - + +
216A VAL 3.3 4.0 + - - +
218A LYS* 1.3 84.6 - - + +
220A ILE* 1.3 57.7 + - - +
222A ASP* 3.4 18.1 + - + +
223A ARG* 3.0 31.1 + - + +
234A LEU* 4.2 9.6 - - + -
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Residues in contact with ILE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A VAL* 2.9 24.6 + - + +
217A ASP* 3.7 7.9 - - - +
219A ILE* 1.3 75.5 - - + +
221A ALA* 1.3 57.7 + - - +
223A ARG* 3.1 4.2 + - - +
224A LYS* 2.9 36.7 + - + +
234A LEU* 3.8 24.9 - - + -
238A LEU* 4.6 11.1 - - + +
251A ASP* 3.7 38.6 - - + +
254A ILE* 3.9 7.6 - - + -
255A ARG* 3.6 37.9 - - + +
258A ILE* 4.2 5.8 - - + -
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Residues in contact with ALA 221 (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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217A ASP 2.8 20.9 + - - +
218A LYS* 3.6 7.2 - - - +
220A ILE* 1.3 73.4 - - - +
222A ASP* 1.3 60.2 + - - +
224A LYS* 3.5 8.8 + - - +
225A ALA* 3.0 28.1 + - - +
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Residues in contact with ASP 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LYS* 2.8 57.2 + - - +
219A ILE* 3.7 17.1 - - + +
221A ALA* 1.3 75.0 - - - +
223A ARG* 1.3 58.0 + - - +
225A ALA* 3.4 6.7 + - - +
226A SER* 2.9 31.2 + - - -
135B ALA* 6.0 1.9 - - - +
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Residues in contact with ARG 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PHE 3.4 17.2 + - - -
159A ASN* 3.5 14.6 - - - +
219A ILE* 3.0 20.0 + - - +
220A ILE 3.6 3.8 - - - +
222A ASP* 1.3 73.7 - - - +
224A LYS* 1.3 65.8 + - - +
226A SER* 3.4 4.5 + - - -
227A GLY* 3.1 21.0 + - - -
228A GLU* 3.3 41.1 + - - +
230A SER* 4.2 8.1 - - - -
232A ASP* 2.8 41.2 + - - -
234A LEU* 3.8 16.9 - - + +
235A THR* 3.1 20.5 + - - +
238A LEU* 3.5 23.7 - - + +
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Residues in contact with LYS 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ILE* 2.9 21.9 + - + +
221A ALA* 3.7 8.1 - - - +
223A ARG* 1.3 78.9 - - - +
225A ALA* 1.3 60.2 + - - +
226A SER 3.6 0.2 + - - -
227A GLY* 3.8 6.9 + - - -
238A LEU* 3.9 26.9 - - + -
251A ASP* 2.7 42.8 + - - +
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Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ALA 3.0 17.4 + - - +
222A ASP* 3.7 7.4 - - - +
223A ARG 3.3 0.2 - - - -
224A LYS* 1.3 78.3 - - - +
226A SER* 1.3 61.6 + - - +
227A GLY 3.6 0.3 + - - -
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Residues in contact with SER 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ASP 2.9 15.2 + - - -
223A ARG* 3.4 9.9 + - - -
224A LYS 3.4 0.2 - - - -
225A ALA* 1.3 78.9 - - - +
227A GLY* 1.3 59.8 + - - +
228A GLU* 3.1 29.8 + - - +
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Residues in contact with GLY 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ARG 3.1 10.5 + - - -
224A LYS 3.8 5.2 + - - -
225A ALA 3.4 3.2 + - - -
226A SER* 1.3 77.0 + - - +
228A GLU* 1.3 55.6 + - - +
229A GLN* 2.8 29.5 + - - +
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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