Contacts of the helix formed by residues 277 - 304 (chain A) in PDB entry 3WAJ
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 SER 277 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A TYR* 2.7 23.8 + - - -
265A ALA 2.8 7.8 - - - +
268A TYR* 4.1 8.3 - - - -
270A GLY 3.2 22.2 - - - -
272A SER* 3.0 29.5 + - - -
275A PHE 3.0 6.6 + - - -
276A TYR* 1.3 73.8 - - - +
278A PRO* 1.3 67.5 - - - +
279A PHE 3.4 4.9 + - - -
280A GLN* 2.7 22.9 + - - +
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Residues in contact with PRO 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ALA* 3.2 19.3 - - + +
266A PHE* 4.1 25.8 - - + -
268A TYR 4.3 6.3 - - - +
270A GLY 3.5 11.9 - - - +
271A PHE* 3.5 22.2 - - + -
277A SER* 1.3 86.8 - - - +
279A PHE* 1.3 64.0 + - - +
280A GLN 3.2 0.4 - - - -
281A LEU* 3.2 9.6 + - + +
282A LEU* 2.9 28.6 + - + +
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Residues in contact with PHE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A PHE* 3.7 22.9 - + - -
271A PHE* 3.8 23.4 - + + -
272A SER 3.4 24.9 - - - +
273A THR* 3.7 26.2 - - + -
277A SER* 3.1 13.8 + - - +
278A PRO* 1.3 78.6 - - - +
280A GLN* 1.3 69.4 + - + +
282A LEU* 3.1 16.8 + - + +
283A VAL* 2.9 38.3 + - + +
331A PHE* 4.3 29.4 - + - -
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Residues in contact with GLN 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A VAL* 4.3 7.4 - - + -
216A GLY* 3.1 33.4 + - - +
219A PHE* 3.7 17.9 - - + -
261A TYR* 3.1 29.9 + - + +
272A SER 3.3 14.5 + - - +
273A THR 3.7 9.5 - - - -
275A PHE 2.8 21.8 + - - -
276A TYR* 4.7 0.2 - - - +
277A SER* 2.7 32.2 + - - +
278A PRO 3.2 0.2 - - - -
279A PHE* 1.3 78.9 - - + +
281A LEU* 1.3 57.1 + - - +
283A VAL* 3.1 10.7 + - - +
284A LEU* 3.0 31.9 + - + +
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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
----------------------------------------------------------
258A ALA* 3.6 31.6 - - + +
261A TYR* 3.3 21.0 - - + -
262A LEU* 3.7 33.0 - - + -
265A ALA* 3.9 13.0 - - + -
266A PHE* 4.2 11.2 - - + -
278A PRO* 3.2 13.4 + - + +
280A GLN* 1.3 75.2 - - - +
282A LEU* 1.3 64.6 + - + +
284A LEU* 3.3 3.7 + - - +
285A LEU* 2.9 52.0 + - + +
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Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PHE* 4.2 27.6 - - + -
278A PRO* 2.9 22.0 + - + +
279A PHE* 3.1 17.5 + - + +
281A LEU* 1.3 82.6 - - + +
283A VAL* 1.3 55.7 + - + +
285A LEU* 4.6 9.6 - - + -
286A GLY* 2.7 34.0 + - - -
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A PHE* 4.0 27.8 - - + +
222A ALA* 3.9 22.7 - - + -
223A PRO* 4.7 5.8 - - + -
279A PHE* 2.9 50.5 + - + +
280A GLN* 3.1 8.3 + - - +
282A LEU* 1.3 77.1 - - + +
284A LEU* 1.3 57.1 + - + +
286A GLY* 3.9 0.6 - - - -
287A SER* 2.9 35.6 + - - +
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Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ILE* 4.2 13.7 - - + -
209A GLY* 5.7 0.4 - - - -
212A VAL* 4.2 18.4 - - + -
219A PHE* 4.8 10.5 - - + -
221A ILE* 5.7 0.2 - - + -
222A ALA* 4.1 22.4 - - + -
254A PHE* 3.6 19.9 - - + +
257A SER* 3.6 42.4 - - - +
258A ALA* 4.0 10.3 - - + -
261A TYR* 4.1 19.1 - - + -
280A GLN* 3.0 17.0 + - + +
281A LEU 4.0 1.6 - - - +
283A VAL* 1.3 80.4 - - + +
285A LEU* 1.3 60.0 + - - +
287A SER* 3.6 2.8 + - - -
288A ALA* 3.2 15.9 + - - +
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ALA* 5.8 3.4 - - - +
258A ALA* 4.0 19.3 - - + -
281A LEU* 2.9 41.6 + - + +
282A LEU* 4.0 10.3 - - + +
284A LEU* 1.3 72.3 - - - +
286A GLY* 1.3 67.7 + - - +
288A ALA* 3.0 18.9 + - + +
289A VAL* 3.1 18.5 + - + +
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Residues in contact with GLY 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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282A LEU 2.7 22.2 + - - -
283A VAL* 3.9 0.9 - - - -
285A LEU* 1.3 71.7 - - - +
287A SER* 1.3 55.8 + - - +
289A VAL* 2.9 13.1 + - - +
290A ILE* 2.8 35.6 + - - +
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Residues in contact with SER 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ALA* 3.5 17.5 - - - +
223A PRO* 5.4 0.2 - - - +
226A LEU* 3.5 16.3 - - - +
254A PHE* 3.6 35.3 - - - -
283A VAL* 2.9 24.8 + - - +
284A LEU 3.7 2.7 - - - -
286A GLY* 1.3 75.4 - - - +
288A ALA* 1.3 62.4 + - - +
290A ILE* 3.4 11.4 + - - +
291A ALA* 3.0 24.4 + - - +
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A VAL* 3.7 16.1 - - + +
254A PHE* 3.7 18.1 - - + +
255A ALA* 4.1 15.7 - - + +
284A LEU 3.2 10.5 + - - +
285A LEU* 3.0 16.2 + - + +
287A SER* 1.3 79.1 - - - +
289A VAL* 1.3 62.8 + - + +
291A ALA* 3.5 5.7 + - - +
292A ALA* 3.1 20.8 + - - +
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU* 3.3 15.7 - - + +
286A GLY* 2.9 10.4 + - - +
288A ALA* 1.3 75.0 - - + +
290A ILE* 1.3 63.9 + - + +
292A ALA* 2.9 11.2 + - + +
293A ALA* 2.9 27.9 + - + +
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Residues in contact with ILE 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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226A LEU* 4.0 22.4 - - + -
286A GLY 2.8 29.5 + - - +
287A SER* 3.6 9.6 - - - +
289A VAL* 1.3 73.3 - - + +
291A ALA* 1.3 63.8 + - - +
293A ALA* 2.9 9.1 + - - +
294A PHE* 2.9 50.4 + - + -
323A LEU* 4.4 3.6 - - + -
327A ILE* 3.4 46.9 - - + -
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LEU* 4.5 0.6 - - + +
229A MET* 3.8 15.5 - - + -
247A SER* 3.6 9.4 - - - +
250A ALA* 3.7 28.7 - - + -
251A VAL* 3.7 17.0 - - + +
254A PHE* 4.6 1.1 - - + -
287A SER 3.0 14.7 + - - +
288A ALA 3.6 5.8 - - - +
289A VAL 3.3 0.2 - - - -
290A ILE* 1.3 79.8 - - - +
292A ALA* 1.3 56.5 + - - +
294A PHE* 3.2 4.7 + - - +
295A TYR* 2.9 24.1 + - - +
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A VAL* 3.5 16.3 - - + +
288A ALA 3.1 12.7 + - - +
289A VAL* 2.9 14.4 + - + +
291A ALA* 1.3 73.8 - - - +
293A ALA* 1.3 65.7 + - - +
295A TYR* 3.3 10.7 + - + +
296A GLN* 3.1 22.5 + - - +
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Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A VAL* 2.9 12.7 + - + +
290A ILE* 2.9 11.6 + - - +
292A ALA* 1.3 73.0 - - - +
294A PHE* 1.3 55.6 + - - +
296A GLN* 3.3 8.1 + - - +
297A ILE* 2.8 40.6 + - + +
323A LEU* 4.2 25.8 - - + -
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Residues in contact with PHE 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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226A LEU* 4.8 6.5 - - + -
229A MET* 3.5 33.4 - - + -
230A PHE* 3.9 23.1 - + + -
233A PHE* 3.5 47.9 - + + -
247A SER* 3.8 4.9 - - - +
290A ILE* 2.9 45.5 + - + -
291A ALA 3.3 7.9 - - - +
293A ALA* 1.3 75.5 - - - +
295A TYR* 1.3 65.1 + - - +
297A ILE* 3.1 7.8 + - + +
298A GLU* 3.0 19.4 + - - +
320A VAL* 3.7 31.0 - - + -
323A LEU* 4.7 9.9 - - + -
324A THR* 5.2 4.5 - - + -
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Residues in contact with TYR 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LYS* 3.5 46.4 + - + +
247A SER* 3.7 12.5 - - - -
248A LEU* 3.5 42.6 - - + +
251A VAL* 5.4 0.9 - - + -
291A ALA 2.9 13.3 + - - +
292A ALA* 3.4 15.3 - - + +
294A PHE* 1.3 76.0 - - - +
296A GLN* 1.3 59.7 + - + +
298A GLU* 3.2 8.6 + - - +
299A LYS* 3.0 55.9 + - + +
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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
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292A ALA 3.1 10.3 + - - +
293A ALA* 3.5 10.5 - - - +
295A TYR* 1.3 80.2 - - + +
297A ILE* 1.3 65.3 + - - +
299A LYS* 3.1 33.3 + - - +
300A TRP* 2.9 77.3 + - + +
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Residues in contact with ILE 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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233A PHE* 4.4 2.5 - - + -
293A ALA* 2.8 28.5 + - + +
294A PHE* 3.1 13.4 + - + +
296A GLN* 1.3 72.1 - - - +
298A GLU* 1.3 62.7 + - - +
300A TRP* 3.3 21.7 + - + +
301A ASN* 3.0 18.4 + - - +
306A PHE* 3.6 13.4 - - + -
316A MET* 3.4 30.1 - - + +
319A ALA* 4.2 21.8 - - + +
320A VAL* 4.0 24.5 - - + -
323A LEU* 4.4 18.4 - - + -
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Residues in contact with GLU 298 (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 PHE* 3.7 7.2 - - + -
243A ARG* 2.6 52.9 + - + +
244A LYS* 3.4 27.1 - - + +
294A PHE 3.0 12.0 + - - +
295A TYR 3.2 8.5 + - - +
297A ILE* 1.3 77.2 - - - +
299A LYS* 1.3 56.6 + - - +
301A ASN* 3.1 10.7 + - - +
302A ASP* 2.8 57.5 + - - +
316A MET* 3.3 18.5 - - - +
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Residues in contact with LYS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LYS* 3.7 21.1 - - + +
295A TYR* 3.0 51.3 + - + +
296A GLN* 3.1 32.8 + - - +
298A GLU* 1.3 74.7 - - - +
300A TRP* 1.3 58.8 + - - +
302A ASP* 3.3 8.0 + - - +
303A VAL* 3.0 31.1 + - - +
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Residues in contact with TRP 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLN* 2.9 51.3 + - + +
297A ILE* 3.6 22.7 - - + +
299A LYS* 1.3 73.4 - - + +
301A ASN* 1.3 64.3 + - - +
303A VAL* 3.2 11.1 - - + +
305A PHE* 2.9 66.4 + + + +
306A PHE* 3.9 16.7 + + + -
319A ALA* 6.1 1.3 - - + -
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Residues in contact with ASN 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ARG* 4.2 3.8 + - - -
297A ILE 3.0 13.1 + - - +
298A GLU* 3.2 30.0 - - - +
300A TRP* 1.3 77.1 - - - +
302A ASP* 1.3 65.2 + - - +
304A GLY* 3.1 14.7 + - - -
306A PHE* 3.6 26.2 - - + +
312A GLY 5.1 4.9 + - - -
313A ARG* 5.7 4.2 + - - +
316A MET* 4.0 22.0 - - + +
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Residues in contact with ASP 302 (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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244A LYS* 3.4 28.8 - - - +
298A GLU* 2.8 48.5 + - - +
299A LYS* 3.8 4.9 - - - +
301A ASN* 1.3 76.9 - - - +
303A VAL* 1.3 59.6 + - - +
304A GLY* 3.6 0.3 + - - -
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LYS 3.0 17.1 + - - +
300A TRP* 3.2 26.9 - - + +
302A ASP* 1.3 77.2 - - - +
304A GLY* 1.3 58.4 + - - +
305A PHE* 3.6 12.8 - - + +
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Residues in contact with GLY 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ASN 3.1 13.3 + - - -
302A ASP 3.3 0.6 - - - -
303A VAL* 1.3 80.3 - - - +
305A PHE* 1.3 60.8 + - - +
306A PHE 3.4 2.2 - - - -
307A GLU* 3.1 17.7 + - - +
308A ARG* 2.9 29.2 + - - +
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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