Contacts of the helix formed by residues 218 - 244 (chain A) in PDB entry 1H13
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 218 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A VAL* 5.0 1.0 - - - +
217A THR* 1.3 86.0 + - - +
219A GLN* 1.3 66.7 + - - +
220A ALA* 3.5 11.1 - - - +
221A ASP* 2.2 66.0 + - - +
222A LYS* 3.0 23.3 + - - +
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Residues in contact with GLN 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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217A THR 4.0 1.4 + - - -
218A ASN* 1.3 73.2 - - - +
220A ALA* 1.3 65.2 + - - +
222A LYS* 3.2 11.1 + - + +
223A ASN* 2.9 42.4 + - - +
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Residues in contact with ALA 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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180A LYS* 5.6 0.4 - - - +
218A ASN* 3.3 10.9 + - - +
219A GLN* 1.3 82.0 - - - +
221A ASP* 1.3 60.6 + - - +
223A ASN* 3.3 5.9 + - - +
224A TYR* 2.9 27.3 + - - +
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Residues in contact with ASP 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LYS* 3.1 24.9 + - - -
216A VAL* 3.7 19.3 - - + +
218A ASN* 2.2 46.5 + - - +
220A ALA* 1.3 77.8 - - - +
222A LYS* 1.3 63.9 + - - +
224A TYR* 3.3 6.0 + - - +
225A TRP* 3.0 35.0 + - + +
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Residues in contact with LYS 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ALA* 2.8 36.5 + - + +
214A ASN* 3.5 19.3 + - - +
216A VAL* 2.6 35.2 + - + +
217A THR* 4.3 9.9 - - - +
218A ASN 3.0 17.1 + - - +
219A GLN* 3.6 13.0 - - - +
221A ASP* 1.3 76.6 - - - +
223A ASN* 1.3 63.0 + - - +
225A TRP 3.4 0.2 + - - -
226A ARG* 3.1 21.7 + - - +
404A PHE* 5.5 2.4 - - - -
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Residues in contact with ASN 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A GLN* 2.9 42.4 + - - +
220A ALA* 3.7 6.5 - - - +
222A LYS* 1.3 76.2 - - - +
224A TYR* 1.3 64.3 + - - +
226A ARG* 3.3 7.3 + - - +
227A GLN* 2.9 46.7 + - - +
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Residues in contact with TYR 224 (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 LYS* 3.6 50.6 + - + +
184A MET* 3.4 32.6 - - - +
187A GLN* 3.4 29.8 + - + +
220A ALA 2.9 18.4 + - - +
221A ASP* 3.5 9.6 - - - +
222A LYS 3.3 0.2 - - - -
223A ASN* 1.3 76.2 - - - +
225A TRP* 1.3 88.9 + + - +
227A GLN* 3.2 12.1 + - - +
228A VAL* 3.0 47.0 + - + +
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Residues in contact with TRP 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LEU* 3.7 45.3 - - + +
179A ILE* 3.8 25.4 - - + -
180A LYS* 4.5 6.0 - - + +
184A MET* 4.0 21.8 - - + -
209A TYR* 3.5 37.4 - + + +
212A PHE* 3.8 33.9 - + + -
213A ALA* 3.7 12.1 - - - +
216A VAL* 4.4 13.4 - - + +
221A ASP* 3.0 30.6 + - + +
224A TYR* 1.3 96.0 - + + +
226A ARG* 1.3 61.4 + - - +
228A VAL* 3.3 15.4 + - + +
229A ALA* 2.9 23.2 + - - +
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Residues in contact with ARG 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ASP* 4.4 8.0 - - - +
213A ALA* 3.8 11.1 - - + +
222A LYS 3.1 17.2 + - - +
223A ASN* 3.6 9.0 - - - +
225A TRP* 1.3 75.6 - - - +
227A GLN* 1.3 59.0 + - + +
229A ALA* 3.2 9.5 + - - +
230A THR* 3.0 30.6 + - - -
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Residues in contact with GLN 227 (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 GLN* 2.9 34.9 + - - +
223A ASN* 2.9 40.2 + - - +
224A TYR* 3.5 4.2 - - - +
226A ARG* 1.3 75.3 - - + +
228A VAL* 1.3 65.4 + - - +
230A THR* 3.3 6.7 + - - +
231A LYS* 2.9 32.3 + - + +
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Residues in contact with VAL 228 (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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184A MET* 3.8 15.9 - - + -
187A GLN* 3.7 30.8 - - + +
189A ILE 5.8 0.4 - - - +
209A TYR* 3.5 31.6 - - + -
224A TYR* 3.0 49.8 + - + +
225A TRP* 3.5 14.4 - - + +
227A GLN* 1.3 75.4 - - - +
229A ALA* 1.3 56.9 + - - +
231A LYS* 3.3 1.4 + - - +
232A SER* 2.8 32.3 + - - -
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Residues in contact with ALA 229 (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 PRO* 3.7 11.9 - - - +
209A TYR* 3.7 13.0 - - + +
210A ASP* 3.5 35.4 - - - +
225A TRP 2.9 12.7 + - - +
226A ARG 3.4 9.0 - - - +
227A GLN 3.2 0.2 - - - -
228A VAL* 1.3 76.1 - - - +
230A THR* 1.3 63.6 + - - +
232A SER* 3.2 2.3 + - - -
233A ARG* 3.0 33.0 + - - +
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Residues in contact with THR 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ARG 3.0 13.9 + - - -
227A GLN* 3.3 8.7 + - - -
229A ALA* 1.3 75.9 - - - +
231A LYS* 1.3 60.1 + - + +
233A ARG* 3.3 13.0 + - - +
234A THR* 2.9 36.2 + - - +
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Residues in contact with LYS 231 (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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186A ASN* 3.4 23.1 + - - +
187A GLN* 2.8 41.3 + - + +
188A ILE* 3.7 19.1 - - + +
227A GLN* 2.9 18.8 + - + +
228A VAL 3.9 3.1 - - - +
230A THR* 1.3 79.4 - - + +
232A SER* 1.3 56.4 + - - +
234A THR* 3.3 9.2 + - - +
235A LEU* 2.9 28.4 + - - +
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Residues in contact with SER 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ILE* 4.6 0.9 - - - +
204A HIS* 2.8 41.9 + - - +
206A PRO* 3.4 13.4 - - - +
209A TYR* 3.5 19.3 - - - -
228A VAL* 2.8 19.5 + - - -
229A ALA 3.5 4.5 - - - -
230A THR 3.2 0.2 - - - -
231A LYS* 1.3 75.4 - - - +
233A ARG* 1.3 66.1 + - - +
235A LEU* 3.2 2.1 + - - +
236A LEU* 2.9 26.0 + - - +
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Residues in contact with ARG 233 (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 PRO* 3.5 22.2 - - + +
210A ASP* 2.8 30.1 + - - -
229A ALA* 3.0 22.7 + - - +
230A THR* 3.7 12.7 + - - +
232A SER* 1.3 76.2 - - - +
234A THR* 1.3 56.3 + - - +
236A LEU* 3.3 1.6 + - - +
237A LYS* 2.8 51.0 + - - +
292A ASP* 2.9 38.6 + - - -
296A MET* 3.7 20.3 - - - +
301A TRP* 4.0 21.7 - - + +
302A HIS* 5.0 2.2 - - - -
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Residues in contact with THR 234 (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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230A THR* 2.9 23.0 + - - +
231A LYS* 3.6 9.4 - - - +
232A SER 3.2 0.2 - - - -
233A ARG* 1.3 75.7 - - - +
235A LEU* 1.3 57.6 + - - +
237A LYS* 3.6 15.7 - - - +
238A ASN* 2.8 55.1 + - - +
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Residues in contact with LEU 235 (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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188A ILE* 4.2 8.3 - - + -
199A THR* 4.2 13.0 - - + -
201A PRO* 4.8 6.7 - - + -
204A HIS* 3.6 41.7 - - + +
231A LYS 2.9 17.2 + - - +
232A SER 3.2 4.0 + - - +
234A THR* 1.3 77.1 - - - +
236A LEU* 1.3 68.5 + - + +
238A ASN* 3.6 4.3 - - - +
239A HIS* 2.8 35.8 + - + +
256A SER* 4.2 0.9 - - - +
257A ARG 3.7 8.5 - - - +
258A LEU* 3.6 24.9 - - - +
259A ASP 4.5 0.2 - - - -
260A GLY* 3.6 19.3 - - - +
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Residues in contact with LEU 236 (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 PRO* 4.0 25.8 - - + +
204A HIS* 3.9 30.1 - - + +
206A PRO* 4.0 17.5 - - + -
232A SER 2.9 17.8 + - - +
233A ARG 3.9 1.1 - - - +
235A LEU* 1.3 84.7 - - + +
237A LYS* 1.3 57.2 + - - +
239A HIS* 3.2 4.1 + - + +
240A PHE* 2.9 42.1 + - + -
285A VAL* 4.2 19.7 - - + -
288A ASN* 5.6 1.6 - - + -
289A VAL* 4.6 9.9 - - + -
301A TRP* 3.8 25.8 - - + -
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Residues in contact with LYS 237 (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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233A ARG* 2.8 41.4 + - - +
234A THR* 3.6 15.3 - - + +
236A LEU* 1.3 74.9 - - - +
238A ASN* 1.3 60.7 + - - +
240A PHE* 3.4 3.6 + - - +
241A THR* 3.0 32.9 + - - +
301A TRP* 3.2 58.5 - - + +
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Residues in contact with ASN 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A THR* 2.8 43.1 + - - +
235A LEU* 3.6 5.6 - - - +
237A LYS* 1.3 77.1 - - - +
239A HIS* 1.3 63.0 + - - +
241A THR* 3.2 8.3 + - - -
242A LYS* 2.9 29.8 + - + +
258A LEU 5.3 1.2 + - - -
259A ASP* 3.4 30.4 + - - +
260A GLY* 4.3 2.0 - - - -
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Residues in contact with HIS 239 (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 PRO* 3.6 26.1 - - + +
235A LEU* 2.8 24.6 + - + +
236A LEU* 3.6 9.0 - - + +
238A ASN* 1.3 72.9 - - - +
240A PHE* 1.3 63.2 + + + +
242A LYS* 3.1 2.6 + - - +
243A VAL* 2.9 32.6 + - + +
252A PRO* 3.4 22.3 - - + +
253A THR* 3.0 44.8 + - - -
256A SER* 3.6 9.7 + - - -
260A GLY* 2.8 32.2 + - - +
262A PRO* 3.9 13.5 - - + -
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Residues in contact with PHE 240 (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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236A LEU* 2.9 34.7 + - + +
237A LYS* 4.0 4.9 - - - +
239A HIS* 1.3 75.8 - + + +
241A THR* 1.3 65.1 + - - +
243A VAL* 3.5 13.6 + - + +
244A SER* 3.1 23.4 + - - -
250A ASN 4.6 6.3 - - - -
252A PRO* 4.0 26.0 - - + -
285A VAL* 3.6 32.8 - - + -
286A ILE* 3.9 14.1 - - + -
289A VAL* 4.0 10.5 - - + -
301A TRP* 4.6 5.4 - + + +
305A ALA* 3.6 48.7 - - + -
308A LYS* 5.6 0.9 - - - -
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Residues in contact with THR 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LYS* 3.0 15.7 + - - +
238A ASN* 3.5 12.9 + - - -
240A PHE* 1.3 75.7 - - - +
242A LYS* 1.3 67.7 + - + +
244A SER* 3.3 20.6 + - - +
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Residues in contact with LYS 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A ASN* 2.9 16.3 + - - +
239A HIS 3.6 3.8 - - - +
241A THR* 1.3 81.8 - - + +
243A VAL* 1.3 60.2 + - - +
244A SER 3.6 4.3 + - - +
246A SER 5.4 0.3 - - - +
247A PRO* 5.2 3.6 - - - +
248A HIS* 3.8 13.5 - - - -
259A ASP* 3.6 21.1 + - - +
260A GLY 3.5 10.8 - - - +
261A SER* 3.4 41.8 + - - +
262A PRO* 4.0 9.2 - - + -
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Residues in contact with VAL 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A HIS* 2.9 33.5 + - + +
240A PHE* 3.7 23.8 - - + +
242A LYS* 1.3 75.2 - - - +
244A SER* 1.3 60.0 + - - +
245A GLY 4.2 0.2 - - - -
248A HIS* 3.7 14.6 - - + -
249A TRP 3.4 6.2 + - - -
250A ASN* 2.7 35.1 + - - -
251A LEU 3.4 34.3 - - - +
252A PRO* 4.2 2.5 - - + -
253A THR* 4.3 2.0 - - + -
262A PRO* 3.7 26.2 - - + -
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Residues in contact with SER 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A PHE 3.1 12.9 + - - -
241A THR* 3.3 19.6 + - - +
242A LYS 4.3 2.9 - - - +
243A VAL* 1.3 76.5 - - - +
245A GLY* 1.3 69.0 + - - +
246A SER 3.8 6.6 - - - +
250A ASN* 3.2 7.6 - - - +
308A LYS* 3.1 31.3 + - - +
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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
------------------------------------------------------------
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