Contacts of the helix formed by residues 251 - 276 (chain A) in PDB entry 1YGK
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 251 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLN* 4.6 4.1 + - - +
248A HIS* 3.0 24.8 + - + +
249A PRO* 3.4 1.3 - - - +
250A ASN* 1.3 90.5 + - - +
252A LEU* 1.3 54.4 + - - +
253A LYS* 2.7 23.8 + - - +
254A VAL* 2.8 39.2 + - + +
255A ALA* 3.2 12.2 + - - +
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Residues in contact with LEU 252 (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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182A THR* 4.1 11.0 - - + +
183A VAL 4.4 1.8 - - - +
184A VAL* 4.0 14.6 - - + -
203A GLY* 3.8 4.5 - - - +
204A SER* 3.0 52.7 - - - +
205A GLN* 3.1 32.0 - - + +
217A GLN* 4.2 11.4 - - + +
219A ILE* 4.5 7.7 - - + +
241A LEU* 6.0 0.2 - - + -
245A THR* 5.3 8.1 - - + -
248A HIS 5.3 0.2 - - - -
250A ASN 3.8 1.0 + - - -
251A ASN* 1.3 72.0 - - - +
253A LYS* 1.3 63.5 + - - +
255A ALA* 4.1 7.2 - - + -
256A CYS* 3.3 35.7 + - - -
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Residues in contact with LYS 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLN* 3.2 20.1 + - - +
219A ILE* 3.7 24.1 - - + +
251A ASN* 2.7 5.6 + - - +
252A LEU* 1.3 81.1 - - - +
254A VAL* 1.3 63.9 + - + +
255A ALA 2.9 6.5 + - - -
256A CYS* 4.4 1.0 - - - +
257A GLU* 2.6 46.2 + - - +
309A ALA* 5.8 3.8 - - + +
311A VAL* 3.1 30.6 - - + +
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Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A HIS* 3.5 28.7 - - + +
251A ASN* 2.8 40.4 - - + +
253A LYS* 1.3 80.9 - - + +
255A ALA* 1.3 62.5 + - - +
257A GLU* 3.1 24.8 + - - +
258A LYS* 3.5 19.9 + - - +
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Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A LEU* 4.7 1.6 - - + -
244A TRP* 4.2 12.4 - - + +
245A THR* 3.4 41.5 - - + +
248A HIS* 4.2 4.2 - - + -
251A ASN 3.2 12.6 + - - +
252A LEU 3.9 6.3 - - - +
253A LYS 2.9 1.8 + - - -
254A VAL* 1.3 72.2 - - - +
256A CYS* 1.3 60.5 + - - +
257A GLU 2.5 16.4 + - - -
258A LYS* 2.6 17.7 + - - +
259A THR* 3.1 12.4 + - - -
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Residues in contact with CYS 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A VAL* 4.2 14.8 - - - -
219A ILE* 4.5 7.4 - - + -
221A MET* 3.5 30.1 - - + -
237A PHE* 5.3 1.3 - - + -
241A LEU* 4.2 23.5 - - + +
252A LEU* 3.3 36.6 - - - +
253A LYS 3.7 1.9 + - - +
255A ALA* 1.3 78.3 - - - +
257A GLU* 1.3 56.8 + - + +
259A THR* 4.2 1.8 - - - -
260A VAL* 2.7 43.3 + - + +
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Residues in contact with GLU 257 (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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221A MET* 5.0 4.7 - - + +
253A LYS* 2.6 41.6 - - - +
254A VAL* 3.1 27.1 - - - +
255A ALA 2.5 4.6 + - - -
256A CYS* 1.3 77.5 - - + +
258A LYS* 1.3 54.6 + - + +
260A VAL* 4.2 2.6 - - - +
261A SER* 2.2 33.9 + - - -
305A ILE* 5.2 14.0 - - + +
307A VAL* 5.1 13.7 - - - +
308A GLN* 5.8 0.5 + - - -
309A ALA* 4.3 26.5 + - + +
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Residues in contact with LYS 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A TRP* 3.8 40.0 - - + +
248A HIS* 2.8 36.5 + - - +
254A VAL* 3.6 17.7 - - + +
255A ALA 2.6 10.7 + - - +
257A GLU* 1.3 74.3 - - + +
259A THR* 1.3 61.0 + - - +
261A SER* 3.1 8.8 + - - -
262A ALA* 3.0 20.3 + - - +
303A PRO* 3.6 26.7 - - + +
305A ILE* 4.2 28.3 - - + -
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Residues in contact with THR 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A PHE* 3.5 38.8 - - + +
240A MET* 3.4 39.5 + - + +
241A LEU* 3.5 16.8 - - - +
244A TRP* 3.5 13.1 - - - +
255A ALA 3.1 7.0 + - - -
256A CYS* 3.6 9.0 - - - -
258A LYS* 1.3 73.7 - - - +
260A VAL* 1.3 69.6 + - - +
262A ALA* 3.0 15.5 + - - +
263A MET* 3.1 13.6 + - + +
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Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A MET* 3.3 34.1 - - + -
223A MET* 3.1 47.9 - - + +
237A PHE* 4.2 12.3 - - + -
256A CYS* 2.7 34.7 + - + +
257A GLU 4.2 2.0 - - - +
259A THR* 1.3 75.3 - - - +
261A SER* 1.3 64.7 + - - +
263A MET* 3.0 23.4 + - - +
264A HIS* 3.4 4.5 + - - +
307A VAL* 4.5 14.1 - - + +
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Residues in contact with SER 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A GLU 2.2 30.5 + - - -
258A LYS* 3.3 9.3 - - - -
259A THR 3.0 0.8 - - - -
260A VAL* 1.3 78.0 - - - +
262A ALA* 1.3 62.6 + - - +
264A HIS* 3.1 16.0 + - - +
265A HIS* 3.0 17.4 + - - -
303A PRO* 4.4 4.0 - - - -
304A GLU 4.7 2.5 - - - -
305A ILE* 3.8 19.1 - - - +
306A VAL* 3.8 25.0 + - - +
307A VAL* 4.2 12.9 + - - +
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Residues in contact with ALA 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A MET* 3.4 32.3 - - + -
244A TRP* 5.6 0.2 - - - +
258A LYS 3.0 11.6 + - - +
259A THR* 3.0 9.2 + - - +
261A SER* 1.3 75.4 - - - +
263A MET* 1.3 61.9 + - - +
265A HIS* 3.3 15.8 + - - +
266A VAL* 3.1 28.1 + - + +
299A ASP* 4.5 7.4 - - - +
300A ILE* 4.7 1.3 - - - -
303A PRO* 4.5 14.7 - - + +
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Residues in contact with MET 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A MET* 4.9 13.2 - - + -
233A THR* 3.6 13.5 - - + +
236A LEU* 3.7 26.2 - - + +
237A PHE* 3.1 60.6 - - + +
240A MET* 5.3 2.4 - - - +
259A THR* 3.1 12.5 + - + +
260A VAL* 3.0 18.8 + - - +
262A ALA* 1.3 77.8 - - - +
264A HIS* 1.4 58.8 + - - +
266A VAL* 3.5 1.7 + - - -
267A LEU* 2.9 53.7 + - + +
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Residues in contact with HIS 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A MET* 5.7 7.5 - - + +
224A HIS* 5.0 25.1 + - + -
226A VAL* 5.1 7.4 - - + -
260A VAL 3.4 4.0 + - - +
261A SER* 3.1 13.0 + - - +
263A MET* 1.4 76.3 - - - +
265A HIS* 1.3 66.4 + - + +
267A LEU* 3.4 4.4 + - - +
268A GLN* 2.4 64.0 + - + +
306A VAL* 5.2 17.6 - - + +
307A VAL* 6.1 3.1 - - + -
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Residues in contact with HIS 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A SER* 3.0 28.7 + - - -
262A ALA* 3.3 16.9 + - - +
264A HIS* 1.3 85.0 + - + +
266A VAL* 1.3 66.4 + - - +
267A LEU 3.0 0.5 + - - -
268A GLN* 3.8 1.0 - - - -
269A ARG* 3.0 29.7 + - - +
299A ASP* 3.4 45.3 + - + +
303A PRO* 5.0 1.1 - - + -
304A GLU* 3.7 50.5 + - + -
306A VAL* 4.7 8.4 - - + +
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Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LEU* 3.9 24.0 - - + -
240A MET* 5.3 0.2 - - + -
262A ALA* 3.1 16.2 + - + +
263A MET 3.8 4.5 - - - +
265A HIS* 1.3 79.8 - - + +
267A LEU* 1.3 61.5 + - + +
269A ARG* 3.8 2.3 - - - +
270A THR* 2.3 40.9 + - - +
291A LEU* 4.4 14.1 - - + -
292A ARG 4.5 4.6 + - - +
293A MET* 5.1 1.8 - - - -
296A SER* 3.7 26.3 + - - +
300A ILE* 3.6 33.0 - - + +
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Residues in contact with LEU 267 (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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223A MET* 5.5 8.1 - - + -
226A VAL* 5.1 13.0 - - + -
230A PHE* 4.0 26.9 - - + -
233A THR* 4.0 26.7 - - + -
236A LEU* 5.3 0.4 - - + -
263A MET* 2.9 44.2 + - + +
264A HIS* 4.2 3.8 - - + +
265A HIS 3.0 1.0 + - - -
266A VAL* 1.3 87.6 - - + +
268A GLN* 1.3 51.7 + - - +
269A ARG 2.9 4.7 - - - -
270A THR* 2.8 7.2 + - - -
271A ILE* 2.5 38.2 + - - +
291A LEU* 4.2 13.0 - - + -
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Residues in contact with GLN 268 (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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224A HIS* 5.3 7.5 + - - -
226A VAL* 4.9 14.5 - - + +
264A HIS* 2.4 63.6 + - + +
265A HIS* 3.8 0.9 - - - +
267A LEU* 1.3 71.9 - - - +
269A ARG* 1.3 50.3 + - - +
271A ILE* 4.0 20.7 - - + +
272A LYS* 2.5 55.2 + - + +
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Residues in contact with ARG 269 (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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265A HIS* 3.0 26.3 + - - +
266A VAL 3.8 3.1 - - - +
267A LEU 2.9 0.8 - - - -
268A GLN* 1.3 77.1 - - - +
270A THR* 1.3 58.4 + - - +
272A LYS* 3.4 6.1 - - + +
273A CYS* 2.8 38.9 + - - +
292A ARG* 4.4 9.0 - - + +
295A GLN* 3.7 40.1 + - + +
296A SER* 2.8 37.6 + - - +
298A LYS* 5.6 2.8 - - - +
299A ASP* 2.3 32.3 + - - +
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Residues in contact with THR 270 (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 PHE* 3.9 12.1 - - + -
266A VAL 2.3 27.3 + - - -
267A LEU* 3.1 10.1 - - - -
269A ARG* 1.3 75.1 - - - +
271A ILE* 1.3 53.9 + - - +
273A CYS* 3.9 0.9 - - - +
274A ALA* 2.5 40.5 + - + +
288A GLN 4.6 1.7 - - - +
289A LEU* 2.9 34.3 - - - +
290A GLU 3.5 14.8 - - - +
291A LEU* 3.9 9.0 - - + +
292A ARG* 3.6 22.3 + - + +
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Residues in contact with ILE 271 (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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226A VAL* 3.5 28.0 - - + -
227A ASP* 4.1 20.0 - - - +
228A ALA* 4.6 9.0 - - + -
230A PHE* 3.8 11.4 - - + -
267A LEU 2.5 23.0 + - - +
268A GLN* 4.0 27.8 - - + +
270A THR* 1.3 71.6 - - - +
272A LYS* 1.3 73.0 + - + +
274A ALA* 3.0 10.9 + - + -
275A LYS* 2.9 49.9 + - + +
284A PRO* 5.3 2.7 - - + -
289A LEU* 5.1 3.8 - - + -
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Residues in contact with LYS 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A GLN* 2.5 44.5 + - + +
269A ARG* 3.4 9.0 - - + +
270A THR 3.3 0.4 - - - -
271A ILE* 1.3 83.1 - - + +
273A CYS* 1.3 63.0 + - - +
275A LYS* 3.4 9.5 + - - +
276A ALA* 3.1 20.3 + - - +
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Residues in contact with CYS 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ARG* 2.8 22.3 + - - +
270A THR 4.0 1.3 - - - +
272A LYS* 1.3 71.8 - - - +
274A ALA* 1.3 68.4 + - - +
276A ALA* 3.0 24.7 + - - +
277A LYS* 3.4 9.0 + - - +
292A ARG* 3.4 47.6 - - - +
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Residues in contact with ALA 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A THR 2.5 31.8 + - - +
271A ILE* 3.0 21.5 + - + +
273A CYS* 1.3 74.5 - - - +
275A LYS* 1.3 58.0 + - - +
277A LYS* 3.4 14.4 + - - +
284A PRO* 4.1 5.0 - - + +
288A GLN* 3.7 35.2 + - - +
289A LEU* 3.8 22.2 - - + -
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Residues in contact with LYS 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ASP* 4.6 14.8 - - - +
271A ILE* 2.9 48.5 + - + +
272A LYS* 4.2 9.1 + - - +
274A ALA* 1.3 67.9 - - - +
276A ALA* 1.3 50.2 - - - +
277A LYS 2.3 21.6 + - - -
278A SER* 2.6 5.8 + - - -
279A GLY* 2.5 37.9 + - - +
280A GLU* 3.6 23.5 + - - +
282A VAL 5.5 3.4 - - - +
284A PRO* 4.2 21.1 - - + -
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Residues in contact with ALA 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LYS 3.1 14.3 + - - +
273A CYS* 3.0 20.8 + - - +
275A LYS* 1.3 72.9 - - - +
277A LYS* 1.3 58.3 + - - +
278A SER 3.5 2.1 + - - -
279A GLY* 4.0 8.3 + - - +
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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