Contacts of the helix formed by residues 196 - 220 (chain A) in PDB entry 3HFV
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 THR 196 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A GLN* 2.7 34.2 + - + +
181A LEU 3.0 8.8 + - - +
182A PHE 3.3 26.5 - - - +
183A GLU* 3.4 19.1 - - - +
191A LYS* 4.3 1.8 - - - -
195A HIS* 1.3 73.1 - - - +
197A MET* 1.3 59.0 + - - +
198A GLU* 3.4 17.6 + - - +
199A ALA* 3.0 19.9 + - - +
200A VAL* 2.9 29.1 + - - +
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Residues in contact with MET 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLU* 4.9 0.6 + - - -
188A SER* 4.9 2.9 - - - +
190A HIS* 4.1 26.9 - - + +
191A LYS* 3.4 38.7 - - + +
196A THR* 1.3 72.3 - - - +
198A GLU* 1.3 74.9 + - - +
200A VAL* 4.3 5.4 - - - +
201A LYS* 2.9 64.8 + - + +
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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
----------------------------------------------------------
170A PHE* 4.3 16.4 - - + -
179A LEU* 4.6 22.0 - - + -
180A GLN 4.9 1.3 - - - +
183A GLU* 4.9 2.1 - - - +
196A THR* 3.4 21.3 - - - +
197A MET* 1.3 88.7 + - - +
199A ALA* 1.3 62.1 + - - +
201A LYS* 3.8 4.9 - - - +
202A LEU* 3.3 27.2 + - - +
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Residues in contact with ALA 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU* 3.9 11.2 - - + +
170A PHE* 4.3 2.0 - - - -
180A GLN 3.8 6.7 - - - +
181A LEU* 3.7 32.1 - - + +
196A THR* 3.0 22.8 + - - +
198A GLU* 1.3 75.3 - - - +
200A VAL* 1.3 65.1 + - - +
202A LEU* 3.2 2.1 + - - -
203A VAL* 3.0 28.9 + - - +
272A ILE* 4.1 10.8 - - + -
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Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A HIS 3.6 20.9 - - - +
191A LYS* 3.8 15.3 - - + -
195A HIS* 3.6 33.7 - - + +
196A THR 2.9 21.3 + - - +
197A MET* 4.0 8.7 - - - +
199A ALA* 1.3 75.0 - - - +
201A LYS* 1.3 58.9 + - + +
203A VAL* 3.9 5.0 - - - +
204A GLU* 2.9 36.5 + - - +
237A PRO* 3.9 19.3 - - + -
257A VAL* 4.3 9.0 - - + -
272A ILE* 5.0 2.7 - - + -
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Residues in contact with LYS 201 (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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190A HIS* 5.2 12.7 - - - +
197A MET* 2.9 55.8 + - + +
198A GLU* 3.8 5.4 - - - +
200A VAL* 1.3 79.1 - - + +
202A LEU* 1.3 68.3 + - + +
204A GLU* 3.9 14.5 + - - +
205A PHE* 3.1 24.6 + - - +
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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
----------------------------------------------------------
169A LEU* 3.6 37.9 - - + +
170A PHE* 4.0 23.8 - - + -
173A ILE* 6.0 5.2 - - + -
198A GLU 3.3 12.9 + - - +
199A ALA 3.2 4.4 + - - +
201A LYS* 1.3 82.4 - - + +
203A VAL* 1.3 63.1 + - - +
205A PHE* 3.3 11.2 + - + +
206A ASP* 2.9 22.5 + - - +
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Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A PHE* 4.3 5.2 - - + -
169A LEU* 3.9 15.0 - - + -
199A ALA 3.0 17.1 + - - +
200A VAL* 3.9 3.6 - - - +
202A LEU* 1.3 75.2 - - - +
204A GLU* 1.3 58.5 + - - +
206A ASP* 3.2 7.7 + - - +
207A LEU* 3.0 24.3 + - - +
257A VAL* 3.9 15.9 - - + -
272A ILE* 3.6 35.7 - - + -
273A GLY 3.9 24.2 - - - +
274A TRP* 3.6 22.2 - - + -
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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
----------------------------------------------------------
190A HIS 5.3 0.7 - - - +
200A VAL* 2.9 28.4 + - - +
201A LYS* 3.9 15.9 + - - +
203A VAL* 1.3 74.4 - - - +
205A PHE* 1.3 66.0 + - - +
207A LEU* 3.4 8.1 + - - +
208A LYS* 3.0 49.4 + - + +
237A PRO* 4.4 4.7 - - - +
239A PHE* 3.6 31.4 - - + -
257A VAL* 4.7 10.3 - - + +
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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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201A LYS 3.1 18.6 + - - +
202A LEU* 3.5 11.4 - - + +
204A GLU* 1.3 77.7 - - - +
206A ASP* 1.3 68.4 + - - +
208A LYS* 3.4 5.5 + - + +
209A GLN* 3.0 63.9 + - + +
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Residues in contact with ASP 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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162A ARG* 4.3 5.2 + - - -
164A PHE* 3.3 27.6 - - + -
169A LEU* 6.1 0.2 - - + -
202A LEU 2.9 13.4 + - - +
203A VAL 3.2 8.7 + - - +
205A PHE* 1.3 81.3 - - + +
207A LEU* 1.3 61.5 + - - +
209A GLN* 3.8 3.9 - - - +
210A THR* 2.5 41.1 + - - -
213A ARG* 5.6 4.2 + - - -
274A TRP* 2.7 28.9 + - - +
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Residues in contact with LEU 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 VAL 3.0 15.3 + - - +
204A GLU* 3.6 7.9 - - - +
206A ASP* 1.3 79.4 - - - +
208A LYS* 1.3 66.5 + - + +
210A THR* 3.3 2.4 + - - -
211A LEU* 3.0 40.0 + - + +
239A PHE* 4.4 11.7 - - + -
255A CYS* 3.5 21.1 - - + -
256A GLY* 3.5 39.7 - - - +
257A VAL* 5.9 0.2 - - + -
274A TRP* 3.6 44.1 - - + +
275A ALA 4.1 1.1 - - - +
276A PHE* 4.1 7.2 - - + -
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Residues in contact with LYS 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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204A GLU* 3.0 42.9 + - + +
205A PHE* 4.0 5.2 - - + +
207A LEU* 1.3 83.2 - - + +
209A GLN* 1.3 58.3 + - + +
212A THR* 2.6 38.5 + - - +
227A TRP* 3.6 59.3 - - + +
239A PHE* 3.7 33.9 - - + -
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Residues in contact with GLN 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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205A PHE* 3.0 59.8 + - + +
206A ASP* 3.8 4.5 - - - +
208A LYS* 1.3 77.9 + - + +
210A THR* 1.3 61.9 + - - +
212A THR* 3.1 13.2 + - - +
213A ARG* 2.8 58.7 + - - +
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Residues in contact with THR 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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60A HIS* 3.8 6.0 + - - +
61A PHE* 3.8 32.8 - - + -
64A GLN* 6.0 1.1 - - + -
206A ASP* 2.5 35.1 + - - -
207A LEU 3.5 3.6 - - - -
209A GLN* 1.3 77.3 - - - +
211A LEU* 1.3 64.6 + - + -
213A ARG* 3.4 25.3 + - - +
214A LEU* 2.9 25.9 + - - +
274A TRP* 4.1 16.1 - - + -
276A PHE* 5.5 2.0 - - + -
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Residues in contact with LEU 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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61A PHE* 6.0 0.2 - - + -
207A LEU* 3.0 33.3 + - + +
210A THR* 1.3 80.1 - - - +
212A THR* 1.3 57.3 + - - +
214A LEU* 3.6 14.6 + - + +
215A MET* 2.9 34.2 + - + +
227A TRP* 3.7 26.0 - - + -
241A MET* 4.9 2.2 - - - -
253A LEU* 3.8 40.6 - - + -
255A CYS* 4.1 5.6 - - - -
276A PHE* 3.4 40.4 - - + -
278A LEU* 5.0 0.9 - - + -
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Residues in contact with THR 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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208A LYS* 2.6 26.1 + - - +
209A GLN* 3.6 14.7 + - - +
211A LEU* 1.3 74.8 - - - +
213A ARG* 1.3 62.0 + - + +
215A MET* 3.3 5.8 + - - +
216A ALA* 2.9 34.8 + - + +
225A ILE* 4.1 18.7 - - + +
227A TRP* 3.5 17.2 + - - -
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Residues in contact with ARG 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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60A HIS* 3.8 11.7 + - + -
64A GLN* 3.8 27.3 - - - +
68A ARG* 3.4 37.0 - - - +
71A THR* 5.6 3.6 + - - +
206A ASP* 5.6 4.4 + - - -
209A GLN* 2.8 55.0 + - + +
210A THR* 3.8 29.7 + - - +
212A THR* 1.3 71.8 - - + +
214A LEU* 1.3 52.8 + - - +
216A ALA* 3.0 9.7 + - - +
217A HIS* 2.8 33.3 + - - +
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Residues in contact with LEU 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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57A VAL* 4.2 27.1 - - + -
60A HIS* 3.5 44.3 - - + +
61A PHE* 4.8 7.6 - - + -
210A THR* 2.9 19.4 + - + +
211A LEU* 3.6 21.1 - - + +
213A ARG* 1.3 77.5 - - - +
215A MET* 1.3 71.2 + - + +
217A HIS* 2.9 18.2 + - + +
218A LEU* 3.1 27.5 + - + +
276A PHE* 4.9 1.3 - - + -
278A LEU* 4.6 16.4 - - + -
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Residues in contact with MET 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 LEU* 2.9 23.3 + - + +
212A THR* 3.7 6.5 - - + +
214A LEU* 1.3 88.8 - - + +
216A ALA* 1.3 57.3 + - - +
218A LEU* 3.3 10.3 + - - -
219A PHE* 3.0 55.7 + - + +
223A LEU* 4.0 19.5 - - + -
225A ILE* 5.1 2.7 - - + -
241A MET* 3.4 31.0 - - + -
243A ILE* 4.5 0.4 - - + -
252A VAL* 4.4 2.5 - - + -
253A LEU* 4.0 26.7 - - + -
278A LEU* 4.8 3.8 - - + -
283A LEU* 4.2 24.7 - - + -
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Residues in contact with ALA 216 (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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212A THR* 2.9 21.2 + - + +
213A ARG* 3.0 9.2 + - - +
215A MET* 1.3 77.2 - - - +
217A HIS* 1.3 57.2 + - - +
220A GLY* 2.8 43.0 + - - +
221A ASP* 5.2 4.9 - - + +
223A LEU* 4.4 7.2 - - + +
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Residues in contact with HIS 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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56A ARG* 3.2 48.2 + - - +
59A GLU* 4.4 10.0 + - + -
60A HIS* 3.9 26.9 + - + +
63A LYS* 4.7 15.6 + - - -
213A ARG 2.8 11.2 + - - +
214A LEU* 2.9 15.2 + - + +
216A ALA* 1.3 79.5 - - - +
218A LEU* 1.3 73.3 + - + +
220A GLY* 3.9 3.1 + - - -
313A ASN* 3.5 25.5 + - - -
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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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53A ILE* 4.9 9.9 - - + +
56A ARG* 3.4 58.7 + - + +
57A VAL* 4.4 11.7 - - + +
214A LEU* 3.1 30.2 + - + +
215A MET* 3.3 18.6 + - - +
217A HIS* 1.3 86.2 - - + +
219A PHE* 1.3 69.9 + - + +
283A LEU* 4.8 13.0 - - + -
287A LEU* 3.3 24.0 - - + +
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Residues in contact with PHE 219 (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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215A MET* 3.0 44.7 + - - +
218A LEU* 1.3 84.9 - - + +
220A GLY* 1.3 68.8 + - - +
222A GLU* 4.0 12.6 + - - +
223A LEU* 3.8 27.4 - - + -
243A ILE* 3.9 12.6 - - + -
283A LEU* 3.8 24.5 - - + -
286A ILE* 4.0 15.3 - - + -
287A LEU* 3.6 44.6 - - + -
315A LYS* 6.0 1.9 + - - -
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Residues in contact with GLY 220 (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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216A ALA* 2.8 23.1 + - - +
217A HIS 3.9 3.5 + - - -
218A LEU 3.6 2.2 - - - -
219A PHE* 1.3 79.9 - - - +
221A ASP* 1.3 54.0 + - - -
222A GLU* 2.7 18.0 + - - -
223A LEU* 3.3 16.1 - - - +
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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) + - + + + + + -
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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