Contacts of the helix formed by residues 195 - 217 (chain A) in PDB entry 4U1D
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 ARG 195 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A THR* 4.8 6.5 + - - +
155A LEU* 3.6 27.1 - - - +
156A ARG* 3.5 32.9 - - - +
189A PHE* 4.0 15.7 - - + -
190A CYS* 2.9 21.1 + - + +
193A TYR* 3.2 38.3 + - + +
194A GLN* 1.3 67.9 - - - +
196A LYS* 1.3 58.0 + - - +
197A ASN 3.4 2.2 - - - -
198A GLU* 3.1 47.1 + - + +
199A PHE* 2.8 29.4 + - - +
250A LEU* 4.9 0.4 - - - -
479C SER* 5.3 2.8 + - - -
492C ALA 5.2 12.6 - - - -
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Residues in contact with LYS 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A GLN* 2.9 43.1 + - - +
195A ARG* 1.3 68.5 - - - +
197A ASN* 1.3 61.6 + - - +
199A PHE* 3.3 3.2 + - - +
200A LYS* 2.9 35.4 + - - +
250A LEU* 3.1 34.5 + - + -
251A GLU* 4.8 8.7 + - - +
252A LEU* 3.7 33.2 - - + +
218B SER* 3.9 25.1 - - - -
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Residues in contact with ASN 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ARG 3.4 0.4 - - - -
196A LYS* 1.3 77.4 - - - +
198A GLU* 1.3 66.3 + - + +
200A LYS* 3.4 13.4 + - - +
201A ARG* 3.1 21.7 + - - +
214B ASN 4.2 2.6 - - - +
215B TYR* 3.2 58.2 + - + +
218B SER* 3.5 16.9 + - - -
219B LYS* 3.2 26.8 - - - +
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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
----------------------------------------------------------
156A ARG* 3.0 24.8 + - - +
159A TRP* 3.2 56.5 - - + +
189A PHE* 4.0 1.4 - - - -
190A CYS* 4.4 1.1 - - - -
195A ARG* 3.1 54.4 + - + +
196A LYS 3.2 0.4 - - - -
197A ASN* 1.3 77.5 - - + +
199A PHE* 1.3 54.5 + - - +
201A ARG* 3.1 8.7 + - - +
202A LEU* 2.7 35.0 + - - +
476C ASP* 4.8 4.0 - - - +
479C SER* 4.7 5.1 - - - -
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Residues in contact with PHE 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A MET* 4.3 17.0 - - + -
190A CYS* 3.7 24.1 - - + -
195A ARG 2.8 17.4 + - - +
196A LYS 3.3 3.1 + - - +
198A GLU* 1.3 77.0 - - - +
200A LYS* 1.3 57.5 + - - +
202A LEU* 3.0 14.4 + - + +
203A ALA* 2.8 30.8 + - + +
243A GLN* 3.4 26.5 - - + -
246A VAL* 3.6 27.1 - - + -
247A SER* 3.2 35.9 - - - -
250A LEU* 4.3 9.9 - - + -
252A LEU* 3.7 19.3 - - + -
255A GLU* 4.2 11.0 - - + -
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Residues in contact with LYS 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LYS 2.9 20.2 + - - +
197A ASN* 3.5 14.4 - - - +
199A PHE* 1.3 79.2 - - - +
201A ARG* 1.3 61.7 + - - +
203A ALA* 3.6 2.9 + - - +
204A GLU* 3.3 21.7 + - - +
252A LEU* 4.0 35.2 - - + +
254A HIS* 5.7 4.9 - - - +
255A GLU* 4.1 28.8 - - + +
258A ARG* 5.2 6.9 - - - +
214B ASN* 4.5 18.8 + - + +
217B GLN* 5.1 8.3 - - - +
218B SER* 4.1 21.1 - - - -
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Residues in contact with ARG 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TRP* 4.6 8.5 - - + -
163A ARG* 5.3 3.6 - - - +
197A ASN 3.1 14.3 + - - +
198A GLU* 3.4 10.1 - - - +
199A PHE 3.1 0.2 - - - -
200A LYS* 1.3 76.5 - - - +
202A LEU* 1.3 59.2 + - - +
204A GLU* 3.3 6.4 + - + +
205A MET* 2.9 37.1 + - + +
340C ILE* 4.3 5.9 - - - +
341C PRO* 3.4 24.5 + - - +
342C SER* 4.2 11.4 + - - +
343C ILE* 4.3 22.5 + - - +
474C VAL 3.4 20.3 + - - -
475C GLU* 3.5 24.5 + - - +
476C ASP* 3.4 33.8 + - - +
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Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TRP* 3.9 12.1 - - + -
166A LEU* 3.6 30.7 - - + -
183A VAL* 4.8 1.8 - - + +
186A THR* 3.5 25.8 - - + +
187A MET* 3.7 34.8 - - + +
190A CYS* 4.6 1.8 - - - -
198A GLU 2.7 17.8 + - - +
199A PHE* 3.3 19.3 - - + +
201A ARG* 1.3 74.0 - - - +
203A ALA* 1.3 58.1 + - - +
205A MET* 3.2 14.4 + - + +
206A LEU* 2.9 43.0 + - + +
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Residues in contact with ALA 203 (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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187A MET* 6.0 0.2 - - - -
199A PHE* 2.8 18.6 + - + +
200A LYS 3.8 3.1 - - - +
202A LEU* 1.3 79.3 - - - +
204A GLU* 1.3 63.3 + - - +
206A LEU* 3.2 6.6 + - - +
207A ARG* 3.1 28.8 + - - +
243A GLN* 3.8 29.7 - - + +
255A GLU* 3.3 29.4 - - + +
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Residues in contact with GLU 204 (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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200A LYS 3.3 14.3 + - - +
201A ARG* 3.8 7.0 - - + +
202A LEU 3.3 0.6 - - - -
203A ALA* 1.3 78.8 - - - +
205A MET* 1.3 63.6 + - - +
207A ARG* 3.1 35.1 + - - +
208A GLN* 3.0 22.3 + - - +
255A GLU* 5.4 0.3 - - - +
258A ARG* 5.0 7.3 + - - -
343C ILE* 3.6 27.6 - - + +
344C GLY 4.9 2.0 + - - +
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Residues in contact with MET 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TRP* 4.4 9.9 - - + -
163A ARG* 4.2 26.7 - - + +
166A LEU* 4.6 12.3 - - + -
167A ASP* 5.4 2.2 - - - +
201A ARG* 2.9 22.8 + - + +
202A LEU* 3.5 30.7 - - + +
204A GLU* 1.3 77.8 - - - +
206A LEU* 1.3 62.4 + - + +
208A GLN* 3.3 11.1 + - - +
209A HIS* 3.0 49.0 + - + +
341C PRO* 4.2 28.7 - - + -
342C SER 5.8 3.8 - - - +
343C ILE 4.8 5.3 + - - +
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Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU* 4.8 4.5 - - + -
179A TYR* 3.3 24.5 - - + +
183A VAL* 3.9 24.9 - - + -
187A MET* 3.5 30.7 - - + -
202A LEU* 2.9 35.1 + - + +
203A ALA* 3.5 7.4 - - - +
204A GLU 3.2 0.2 - - - -
205A MET* 1.3 75.9 - - + +
207A ARG* 1.3 64.8 + - + +
209A HIS* 3.3 10.0 + - + +
210A LEU* 3.1 16.6 + - - +
239A GLN* 5.1 1.6 - - - +
240A ARG* 3.5 31.7 + - - +
243A GLN* 3.6 13.7 - - - +
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Residues in contact with ARG 207 (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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203A ALA 3.1 29.0 + - - +
204A GLU* 3.1 41.5 + - - +
206A LEU* 1.3 76.1 - - + +
208A GLN* 1.3 64.7 + - - +
210A LEU* 3.1 7.0 + - - +
211A ASP* 3.0 31.3 + - - +
240A ARG* 5.3 3.8 - - - +
243A GLN* 3.3 14.6 - - - +
255A GLU* 2.6 33.1 + - - -
258A ARG* 3.2 29.9 - - - +
259A SER* 3.4 3.8 + - - -
262A ASP* 2.7 37.0 + - - +
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Residues in contact with GLN 208 (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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170A ARG* 6.0 2.0 - - - +
204A GLU* 3.0 12.6 + - - +
205A MET* 3.6 13.0 - - - +
207A ARG* 1.3 76.5 - - - +
209A HIS* 1.3 66.7 + - + +
211A ASP* 3.4 9.2 + - + +
212A ALA* 3.1 23.1 + - + +
341C PRO* 5.8 0.7 - - - +
342C SER* 3.2 23.6 - - - +
343C ILE 3.7 0.7 - - - +
344C GLY* 3.1 47.6 + - - +
360C LYS* 5.9 2.8 - - - +
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Residues in contact with HIS 209 (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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166A LEU* 3.8 27.1 - - + -
167A ASP* 4.3 5.4 + - - -
170A ARG* 3.7 37.0 + - + +
171A ASN* 3.1 29.4 - - - +
179A TYR* 2.7 31.9 + + + +
205A MET* 3.0 39.1 + - + +
206A LEU* 3.4 12.3 - - + +
207A ARG 3.1 0.2 - - - -
208A GLN* 1.3 83.5 - - + +
210A LEU* 1.3 61.9 + - - +
212A ALA* 3.3 2.4 + - - +
213A ALA* 3.2 11.6 + - - +
240A ARG* 5.7 0.7 - - - +
341C PRO* 6.1 0.4 - - - +
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Residues in contact with LEU 210 (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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206A LEU 3.1 10.9 + - - +
207A ARG* 3.1 10.3 + - - +
209A HIS* 1.3 74.9 - - - +
211A ASP* 1.3 67.0 + - - +
213A ALA* 3.3 6.0 + - + +
214A ASN* 3.0 33.0 + - - +
227A LEU* 3.8 17.3 - - + -
236A TYR* 3.6 37.2 - - + -
240A ARG* 4.1 16.5 - - - +
266A LEU* 3.8 32.5 - - + -
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Residues in contact with ASP 211 (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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207A ARG* 3.0 19.6 + - - +
208A GLN* 3.9 8.3 - - + +
209A HIS 3.4 0.2 - - - -
210A LEU* 1.3 77.2 - - - +
212A ALA* 1.3 65.0 + - - +
214A ASN* 3.2 13.4 + - - +
215A TYR* 3.1 22.2 + - - +
350B ARG* 5.1 13.1 + - - +
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Residues in contact with ALA 212 (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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170A ARG* 4.4 7.2 - - - +
171A ASN* 3.4 25.4 - - - +
208A GLN* 3.1 14.3 + - + +
209A HIS* 3.6 4.0 - - - +
210A LEU 3.2 0.2 - - - -
211A ASP* 1.3 76.7 - - - +
213A ALA* 1.3 61.0 - - - +
215A TYR* 3.3 7.5 + - - +
216A GLN* 3.1 37.6 + - - +
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Residues in contact with ALA 213 (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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171A ASN* 4.4 7.8 + - - +
209A HIS 3.2 10.4 + - - +
210A LEU* 3.4 16.6 - - + +
211A ASP 3.2 0.4 - - - -
212A ALA* 1.3 79.1 - - - +
214A ASN* 1.3 62.4 + - - +
216A GLN* 3.2 8.3 + - - +
217A GLN* 3.2 27.0 + - - +
225A VAL* 4.3 21.3 - - + +
227A LEU* 3.7 22.2 - - + -
236A TYR* 5.4 1.3 - - - +
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Residues in contact with ASN 214 (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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210A LEU* 3.0 25.6 + - - +
211A ASP* 3.2 15.3 + - - +
213A ALA* 1.3 79.3 - - - +
215A TYR* 1.3 61.3 + - - +
217A GLN* 3.7 16.8 + - - +
218A SER* 4.9 2.3 + - - -
227A LEU* 3.5 21.4 - - - +
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Residues in contact with TYR 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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211A ASP 3.1 12.2 + - - +
212A ALA* 3.7 10.1 - - - +
213A ALA 3.2 0.2 - - - -
214A ASN* 1.3 77.3 - - - +
216A GLN* 1.3 74.7 + - + +
217A GLN 3.4 0.6 + - - -
218A SER* 4.1 9.9 + - - -
219A LYS* 4.0 21.6 - - - +
345B TYR* 5.3 15.7 - + - -
349C LEU* 4.9 22.1 - - + +
350C ARG* 3.6 25.5 + - + +
353C ARG* 2.4 41.6 + - - -
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Residues in contact with GLN 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ARG* 5.7 2.8 - - - +
171A ASN* 4.3 16.9 + - - +
212A ALA* 3.1 29.0 + - - +
213A ALA* 3.2 5.9 + - - +
215A TYR* 1.3 88.9 - - + +
217A GLN* 1.3 65.5 + - - +
218A SER 3.3 2.2 - - - -
219A LYS* 3.2 26.5 + - + +
220A SER 4.2 1.0 + - - -
224A LEU* 3.3 44.7 - - + +
225A VAL 5.6 2.5 + - - +
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Residues in contact with GLN 217 (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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213A ALA 3.2 15.5 + - - +
214A ASN* 3.7 15.5 - - - +
215A TYR 3.4 0.8 - - - -
216A GLN* 1.3 77.7 - - - +
218A SER* 1.3 58.3 + - - +
219A LYS 3.1 5.4 + - - -
220A SER* 3.9 7.1 + - - -
224A LEU* 6.4 0.2 - - - -
225A VAL 2.8 18.9 + - - +
226A ASP* 3.3 19.4 + - - +
227A LEU* 2.5 43.2 + - + +
228A SER* 4.0 7.5 + - - -
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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