Contacts of the helix formed by residues 273 - 298 (chain A) in PDB entry 1X79
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 273 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A ILE* 5.5 7.9 - - - +
270A THR* 3.4 19.8 - - + +
271A GLU 2.4 23.2 + - - +
272A ASP* 1.3 66.2 - - - +
274A ASP* 1.3 49.7 + - - -
275A GLU* 2.4 27.9 + - - +
276A ALA* 2.5 42.3 + - + +
277A LEU 3.3 3.5 + - - -
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Residues in contact with ASP 274 (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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270A THR* 4.2 1.4 - - - +
272A ASP* 2.6 18.5 + - - +
273A ASN* 1.3 68.9 - - - +
275A GLU* 1.3 65.7 + - + +
277A LEU* 3.6 8.9 - - - +
278A ALA* 3.1 26.0 + - - +
552B GLU* 3.7 22.6 - - - +
553B THR* 5.4 2.3 + - - -
556B GLN* 3.6 18.7 + - - +
554C ARG* 3.3 23.3 + - - +
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Residues in contact with GLU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ASN* 2.4 17.7 + - - +
274A ASP* 1.3 77.5 - - + +
276A ALA* 1.3 63.6 + - - +
278A ALA* 3.1 9.6 + - - +
279A GLU* 3.0 27.4 + - - +
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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
----------------------------------------------------------
211A ILE* 5.6 0.9 - - + -
214A ARG* 3.5 39.1 + - - +
270A THR* 4.3 3.6 - - - +
273A ASN* 2.5 37.9 + - + +
275A GLU* 1.3 70.9 - - - +
277A LEU* 1.3 66.1 + - - +
279A GLU* 2.9 18.5 + - - +
280A ILE* 3.1 17.3 + - - +
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Residues in contact with LEU 277 (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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267A ALA* 4.0 30.3 - - + +
270A THR* 3.2 26.1 + - + +
273A ASN 3.3 2.6 + - - -
274A ASP* 3.6 11.0 - - - +
276A ALA* 1.3 77.1 - - - +
278A ALA* 1.3 62.9 + - - +
280A ILE* 3.0 7.5 + - - +
281A LEU* 3.0 45.1 + - + +
556B GLN* 4.0 24.2 - - + +
560B LEU* 4.5 7.4 - - + -
554C ARG* 4.9 5.4 - - - +
557C VAL* 4.1 20.6 - - + -
561C GLN* 4.2 10.1 - - - +
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ASP 3.1 11.7 + - - +
275A GLU* 3.1 12.5 + - - +
277A LEU* 1.3 79.8 - - - +
279A GLU* 1.3 64.2 + - - +
281A LEU* 3.4 10.1 + - - +
282A GLN* 2.9 24.6 + - - +
552B GLU* 5.1 7.2 - - - +
556B GLN* 4.6 11.4 - - - +
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Residues in contact with GLU 279 (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 ARG* 3.0 31.0 + - - -
215A VAL* 5.7 1.7 - - - +
218A ILE* 3.8 25.6 - - + +
275A GLU* 3.0 15.9 + - + +
276A ALA* 2.9 13.8 + - - +
278A ALA* 1.3 76.6 - - + +
280A ILE* 1.3 66.0 + - - +
282A GLN* 3.4 6.8 + - - +
283A ALA* 3.2 19.9 + - - +
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Residues in contact with ILE 280 (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 ARG* 3.4 35.4 - - + -
218A ILE* 4.2 9.2 - - + -
263A LEU* 3.7 33.9 - - + +
266A LEU* 3.8 23.3 - - + -
267A ALA* 3.9 16.8 - - + +
270A THR* 4.3 6.7 - - - +
276A ALA 3.1 13.4 + - - +
277A LEU* 3.0 13.2 + - - +
279A GLU* 1.3 76.7 - - - +
281A LEU* 1.3 58.6 + - - +
283A ALA* 2.9 11.2 + - - +
284A ASN* 2.9 23.7 + - - +
563B MET* 4.3 6.7 - - + -
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Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ALA* 4.4 1.8 - - + -
277A LEU* 3.0 39.3 + - + +
278A ALA* 4.0 4.0 - - - +
280A ILE* 1.3 80.6 - - - +
282A GLN* 1.3 58.6 + - - +
284A ASN* 3.2 7.2 + - + +
285A ASP* 2.8 33.7 + - - +
556B GLN* 3.9 26.7 - - - +
559B LYS* 4.0 37.6 - - + +
560B LEU* 4.1 16.4 - - + +
563B MET* 3.9 30.3 - - + -
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Residues in contact with GLN 282 (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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278A ALA 2.9 18.3 + - - +
279A GLU* 3.6 8.3 - - - +
280A ILE 3.1 0.2 - - - -
281A LEU* 1.3 75.6 - - - +
283A ALA* 1.3 58.8 + - - +
285A ASP* 3.0 21.9 - - - +
286A ASN* 2.8 64.2 + - - +
559B LYS* 5.2 1.8 + - - +
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Residues in contact with ALA 283 (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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218A ILE* 4.4 19.1 - - + -
221A VAL* 3.9 20.6 - - + +
222A ASN* 4.2 8.5 - - - +
263A LEU* 4.9 7.2 - - + -
279A GLU 3.2 9.7 + - - +
280A ILE* 2.9 10.7 + - - +
282A GLN* 1.3 77.4 - - - +
284A ASN* 1.3 65.6 + - - +
286A ASN* 3.0 12.5 + - - +
287A LEU* 2.8 25.7 + - - +
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Residues in contact with ASN 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ARG* 3.6 18.5 + - - -
263A LEU* 4.4 16.1 - - + +
264A PHE* 4.5 3.3 - - - -
280A ILE 2.9 8.9 + - - +
281A LEU* 3.5 8.7 - - - +
283A ALA* 1.3 76.3 - - - +
285A ASP* 1.3 52.0 + - - +
287A LEU* 3.2 5.9 + - - +
288A THR* 2.7 46.3 + - - -
559B LYS* 5.1 1.4 + - - +
562B LEU* 4.2 8.7 - - - +
563B MET* 3.4 43.6 - - + +
566B GLN* 3.1 23.4 + - - +
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Residues in contact with ASP 285 (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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281A LEU 2.8 17.9 + - - +
282A GLN* 3.0 26.8 - - - +
284A ASN* 1.3 76.6 + - - +
286A ASN* 1.3 65.2 + - - +
288A THR* 3.1 8.3 + - - -
289A GLN* 3.0 23.8 + - - +
559B LYS* 2.7 39.2 + - - +
562B LEU* 5.2 9.2 - - - +
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Residues in contact with ASN 286 (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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222A ASN* 3.6 21.3 + - - +
225A VAL* 3.4 29.9 - - + +
282A GLN* 2.8 48.9 + - - +
283A ALA* 3.0 7.8 + - - +
285A ASP* 1.3 73.3 - - - +
287A LEU* 1.3 61.7 + - - +
289A GLN* 3.5 19.0 + - - +
290A VAL 3.2 15.9 + - - -
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Residues in contact with LEU 287 (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 VAL* 4.3 11.0 - - + -
225A VAL* 4.1 8.4 - - + +
256A CYS* 3.8 38.4 - - + +
259A MET* 4.3 8.1 - - + -
260A ARG* 4.3 14.6 - - + +
263A LEU* 3.5 30.3 - - + -
283A ALA 2.8 16.3 + - - +
284A ASN* 3.4 5.8 - - - +
286A ASN* 1.3 76.8 - - - +
288A THR* 1.3 67.5 + - - +
290A VAL* 3.0 17.4 + - + +
291A ILE* 2.9 39.7 + - + +
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Residues in contact with THR 288 (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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260A ARG* 2.7 22.9 + - - +
284A ASN* 2.7 33.8 + - - -
285A ASP* 3.5 6.9 - - - -
287A LEU* 1.3 72.2 - - - +
289A GLN* 1.3 53.9 + - - +
291A ILE* 3.1 6.4 + - + +
292A ASN* 2.8 55.1 + - - +
562B LEU* 4.4 7.8 - - + +
566B GLN* 3.2 22.2 + - - +
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Residues in contact with GLN 289 (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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225A VAL* 5.0 5.3 - - - +
229A THR* 5.8 1.4 + - - +
285A ASP 3.0 14.7 + - - +
286A ASN* 3.6 23.4 + - - +
287A LEU 3.1 0.2 - - - -
288A THR* 1.3 80.1 - - - +
290A VAL* 1.3 60.9 + - - +
292A ASN* 3.4 9.7 + - - +
293A LEU* 3.1 28.1 + - + +
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Residues in contact with VAL 290 (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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225A VAL* 3.5 27.1 - - + +
228A LEU* 3.5 37.4 - - + +
229A THR* 3.6 30.3 - - + +
232A VAL* 4.9 3.4 - - + -
256A CYS* 5.7 0.4 - - - -
286A ASN 3.2 2.7 + - - +
287A LEU* 3.0 29.4 - - + +
289A GLN* 1.3 78.6 - - + +
291A ILE* 1.3 65.1 + - + +
293A LEU* 3.5 7.4 - - + +
294A TYR* 3.1 22.7 + - - +
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Residues in contact with ILE 291 (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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228A LEU* 5.9 0.4 - - + -
253A TYR* 3.5 30.0 - - + +
256A CYS* 4.0 17.9 - - + +
257A GLU* 4.4 7.6 - - + -
260A ARG* 4.1 32.1 - - - +
287A LEU* 2.9 39.7 + - + +
288A THR* 3.4 9.4 - - + +
290A VAL* 1.3 78.8 - - + +
292A ASN* 1.3 66.5 + - - +
294A TYR* 3.9 1.6 - - - +
295A LYS* 3.2 48.1 + - - +
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Residues in contact with ASN 292 (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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288A THR* 2.8 39.9 + - - +
289A GLN* 3.8 7.5 - - - +
291A ILE* 1.3 82.0 - - - +
293A LEU* 1.3 69.7 + - - +
295A LYS* 3.5 15.2 + - - +
296A GLN* 3.1 41.5 + - - +
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Residues in contact with LEU 293 (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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229A THR* 4.4 17.5 - - + -
232A VAL* 3.9 29.2 - - + -
233A MET* 4.2 27.4 - - + -
289A GLN* 3.1 19.3 + - + +
290A VAL* 3.5 9.0 - - - +
292A ASN* 1.3 76.4 - - - +
294A TYR* 1.3 63.6 + - - +
296A GLN* 2.9 20.2 + - - +
297A LEU* 2.9 29.4 + - + +
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Residues in contact with TYR 294 (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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228A LEU* 4.5 2.2 - - + -
232A VAL* 4.2 18.2 - - + -
249A MET* 3.5 28.9 - - + -
250A LYS* 3.0 32.6 - - - +
253A TYR* 3.5 62.9 - + + -
254A GLN* 5.1 1.0 + - - -
290A VAL* 3.1 15.4 + - + +
291A ILE 3.9 1.6 - - - +
292A ASN 3.4 0.2 - - - -
293A LEU* 1.3 80.8 - - - +
295A LYS* 1.3 63.7 + - + +
298A VAL* 2.9 56.9 + - + +
299A ARG 3.4 5.2 + - - -
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Residues in contact with LYS 295 (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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253A TYR* 3.4 24.6 + - + +
260A ARG* 5.7 1.8 - - - +
291A ILE* 3.2 33.9 + - - +
292A ASN* 3.9 16.1 + - - +
294A TYR* 1.3 81.4 - - + +
296A GLN* 1.3 58.8 + - + +
299A ARG* 2.8 51.3 + - - +
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Residues in contact with GLN 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ASN* 3.1 36.4 + - - +
293A LEU* 2.9 12.8 + - - +
295A LYS* 1.3 80.6 - - + +
297A LEU* 1.3 70.8 + - + +
299A ARG* 3.9 14.6 - - - +
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Residues in contact with LEU 297 (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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232A VAL* 4.2 26.2 - - + +
233A MET* 4.6 17.0 - - - -
235A HIS* 5.8 1.7 + - - +
236A SER* 6.2 3.8 - - - -
293A LEU* 2.9 30.4 + - + +
296A GLN* 1.3 91.4 - - + +
298A VAL* 1.3 60.1 + - + +
299A ARG* 2.9 11.6 + - - +
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Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A VAL* 4.2 15.3 - - + -
235A HIS* 4.6 18.4 - - + +
246A GLU* 4.8 10.5 - - - +
249A MET* 3.1 42.4 - - + -
250A LYS* 4.9 2.0 - - + -
294A TYR* 2.9 46.5 + - + +
297A LEU* 1.3 70.8 - - + +
299A ARG* 1.3 70.3 + - - +
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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) + - + + + + + -
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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