Contacts of the helix formed by residues 282 - 305 (chain A) in PDB entry 5AVL
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 282 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A GLN 3.8 1.6 + - - -
281A LEU* 1.3 73.6 - - - +
283A ARG* 1.3 65.5 + - - +
284A GLU* 3.7 10.0 + - - +
285A ASP* 2.7 41.2 + - - +
286A GLN* 3.0 9.8 + - - +
373A GLN* 4.5 12.2 + - - +
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Residues in contact with ARG 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 3.9 12.3 - - - +
281A LEU 3.5 2.6 + - - -
282A SER* 1.3 69.1 - - - +
284A GLU* 1.3 65.0 + - - +
286A GLN* 2.7 56.8 + - - +
287A ILE* 2.8 20.7 + - + +
684B THR* 4.5 5.8 - - + +
691B HIS* 3.9 33.2 + - + +
694B LEU* 3.5 41.8 + - - +
695B GLN* 4.4 12.6 - - - +
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Residues in contact with GLU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A SER* 3.1 9.7 + - - +
283A ARG* 1.3 77.0 - - - +
285A ASP* 1.3 61.0 + - - +
287A ILE* 3.2 6.5 + - - +
288A ALA* 3.0 26.2 + - - +
371A ASN* 5.3 5.7 - - - +
373A GLN* 6.1 1.6 - - + +
682B SER* 3.4 14.4 - - - -
683B LEU* 2.6 38.3 + - + +
684B THR* 2.5 45.1 + - - +
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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
----------------------------------------------------------
281A LEU* 4.2 20.0 - - + +
282A SER* 2.7 27.8 + - - +
284A GLU* 1.3 71.2 - - - +
286A GLN* 1.3 67.1 + - - +
288A ALA* 3.3 3.9 + - - +
289A LEU* 3.0 29.6 + - - +
371A ASN 3.8 3.3 - - - +
372A VAL* 3.4 15.0 - - + +
373A GLN* 2.7 33.8 + - - +
374A ASP* 3.0 32.3 + - - +
378A VAL* 5.4 1.8 - - + -
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Residues in contact with GLN 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A PHE* 3.7 43.1 - - + +
279A LEU* 3.4 27.8 + - - +
281A LEU* 2.9 24.0 + - + +
282A SER 3.0 10.8 + - - +
283A ARG* 2.7 53.3 + - - +
285A ASP* 1.3 77.7 - - - +
287A ILE* 1.3 61.3 + - - +
289A LEU* 3.3 3.0 + - - +
290A LEU* 3.1 29.9 + - - +
694B LEU* 4.0 11.1 - - + +
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Residues in contact with ILE 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ARG* 2.8 20.6 + - + +
284A GLU 3.7 5.8 - - - +
286A GLN* 1.3 73.5 - - - +
288A ALA* 1.3 67.4 + - - +
289A LEU 3.1 0.2 + - - -
291A LYS* 2.8 29.2 + - + +
683B LEU* 4.1 14.6 - - + -
684B THR* 3.7 39.0 - - + +
687B HIS* 3.9 34.3 - - + +
690B LEU* 3.9 16.6 - - + -
691B HIS* 4.2 19.5 - - + +
694B LEU* 3.8 16.6 - - + -
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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
----------------------------------------------------------
284A GLU 3.0 13.1 + - - +
285A ASP* 3.6 9.2 - - - +
287A ILE* 1.3 76.0 - - - +
289A LEU* 1.3 65.2 + - - +
291A LYS* 3.9 3.0 - - - +
292A THR* 3.5 21.5 + - - -
369A ARG* 4.3 5.4 - - - +
370A PRO 3.8 14.2 - - - +
371A ASN 3.8 23.6 - - - +
372A VAL* 4.2 9.0 - - + -
683B LEU* 3.8 15.2 - - + +
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Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A PHE* 4.3 13.2 - - + -
281A LEU* 3.8 29.4 - - + -
285A ASP* 3.0 17.7 + - + +
286A GLN 3.8 3.6 - - - +
287A ILE 3.1 0.2 - - - -
288A ALA* 1.3 78.7 - - - +
290A LEU* 1.3 54.4 + - - +
292A THR* 4.2 0.2 - - - -
293A SER* 2.7 39.6 + - - -
364A ILE* 3.6 21.8 - - + +
365A PHE* 3.8 16.2 - - + -
366A SER 3.5 25.1 - - - +
369A ARG* 4.1 8.3 + - + -
372A VAL* 3.7 21.1 - - + -
378A VAL* 4.0 13.0 - - + -
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ILE* 4.0 21.8 - - + -
269A VAL* 3.9 29.8 - - + -
272A ALA* 3.8 21.3 - - + -
278A PHE* 3.8 14.8 - - + -
286A GLN 3.1 15.4 + - - +
287A ILE 4.1 0.9 - - - +
289A LEU* 1.3 73.7 - - - +
291A LYS* 1.3 67.9 + - - +
293A SER* 3.5 7.9 - - - +
294A ALA* 3.0 29.4 + - + +
364A ILE* 4.7 5.6 - - + -
442A ILE* 5.3 0.8 - - - +
690B LEU* 4.1 18.6 - - + -
694B LEU* 3.9 24.0 - - + -
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Residues in contact with LYS 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ILE* 2.8 27.3 + - + +
288A ALA* 3.9 4.7 - - - +
290A LEU* 1.3 73.5 - - - +
292A THR* 1.3 66.3 + - + +
294A ALA* 4.2 5.0 + - - +
295A ILE* 5.3 0.5 + - - +
441A GLU 3.5 2.4 + - - -
442A ILE* 2.9 52.2 + - - +
443A TRP* 4.6 7.3 + - - -
444A ASP 4.9 6.9 + - - -
683B LEU* 4.6 15.5 - - + -
686B ARG* 5.4 2.0 - - - +
687B HIS* 3.0 43.5 + - + +
690B LEU* 4.3 2.3 - - + +
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Residues in contact with THR 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ALA 3.5 11.5 + - - -
289A LEU 3.6 2.0 + - - -
290A LEU 3.2 0.2 - - - -
291A LYS* 1.3 85.8 - - - +
293A SER* 1.3 62.1 + - - +
294A ALA 3.4 0.7 - - - -
295A ILE* 4.0 14.3 - - + +
296A GLU* 3.9 6.1 - - - +
369A ARG* 3.9 36.6 + - - +
370A PRO* 4.2 22.9 + - + +
418A SER* 4.3 7.9 + - - +
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Residues in contact with SER 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ILE* 5.2 0.3 - - - +
289A LEU 2.7 24.6 + - - -
290A LEU* 3.5 9.5 - - - +
292A THR* 1.3 78.0 - - - +
294A ALA* 1.3 67.3 + - - +
295A ILE 3.3 1.1 - - - -
296A GLU* 2.8 14.3 + - - +
297A VAL* 2.9 15.7 + - - +
363A SER* 4.0 2.5 - - - -
364A ILE* 3.6 35.9 - - - +
369A ARG* 3.5 22.8 - - - +
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Residues in contact with ALA 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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265A VAL* 5.0 6.7 - - + -
268A ILE* 3.6 24.6 - - + +
290A LEU* 3.0 19.1 + - + +
291A LYS 4.4 2.5 - - - +
292A THR 3.4 1.0 - - - -
293A SER* 1.3 77.5 + - - +
295A ILE* 1.3 57.9 + - - +
297A VAL* 3.2 2.0 + - - -
298A MET* 2.8 39.3 + - + +
442A ILE* 3.9 26.2 - - + -
443A TRP* 4.9 0.2 - - - +
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Residues in contact with ILE 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LYS 5.3 0.6 + - - +
292A THR* 4.0 11.4 - - + +
294A ALA* 1.3 76.4 - - - +
296A GLU* 1.3 55.3 + - - +
298A MET* 3.2 12.4 + - - +
299A LEU* 2.7 54.3 + - + +
335A PHE* 4.6 0.9 - - + -
418A SER* 3.6 27.6 - - - +
421A HIS* 3.7 40.6 - - + +
443A TRP* 4.1 19.3 - - + +
501A 4KQ 3.3 28.3 - - + +
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Residues in contact with GLU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A THR 3.9 2.4 - - - +
293A SER 2.8 8.3 + - - +
295A ILE* 1.3 77.5 - - + +
297A VAL* 1.3 58.9 + - - +
299A LEU* 3.2 2.1 + - + -
300A LEU* 2.9 33.3 + - - +
363A SER* 3.0 15.8 + - - +
369A ARG* 2.7 45.2 + - - -
411A LEU* 5.5 0.7 - - - +
414A LEU* 3.6 45.5 - - + +
415A ARG* 3.6 13.9 + - - +
418A SER* 3.4 27.2 + - - +
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Residues in contact with VAL 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ILE* 3.8 28.9 - - + -
293A SER* 2.9 20.6 + - - +
294A ALA 3.7 6.3 - - - +
296A GLU* 1.3 74.8 - - - +
298A MET* 1.3 58.5 + - - +
300A LEU* 3.0 9.6 + - - +
301A GLU* 2.8 34.8 + - + +
360A ILE* 3.8 46.9 - - + +
363A SER* 4.8 4.3 - - - +
364A ILE* 4.1 20.2 - - + -
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Residues in contact with MET 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ALA* 3.4 39.5 - - + +
264A SER* 3.5 20.9 - - - +
265A VAL* 3.5 21.1 - - + +
268A ILE* 4.0 3.6 - - + -
294A ALA* 2.8 19.9 + - + +
295A ILE* 3.3 13.2 - - - +
297A VAL* 1.3 76.1 - - - +
299A LEU* 1.3 56.4 + - - +
301A GLU* 3.3 7.4 + - - +
302A THR* 2.8 32.4 + - - -
443A TRP* 3.6 33.0 - - + -
501A 4KQ 3.8 29.0 - - + +
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Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ILE* 2.7 41.2 + - + +
296A GLU* 3.7 5.2 - - - +
297A VAL 3.2 0.2 - - - -
298A MET* 1.3 73.3 - - - +
300A LEU* 1.3 59.8 + - - +
302A THR* 3.5 4.5 - - - +
303A SER* 3.0 27.5 + - - -
335A PHE* 4.7 4.5 - - + -
339A ILE* 4.0 24.9 - - + -
342A PHE* 3.8 11.4 - - + -
343A SER* 5.3 0.3 + - - -
414A LEU* 3.8 15.9 - - + +
417A LEU* 3.8 38.1 - - + +
418A SER* 4.6 0.9 - - - +
501A 4KQ 3.7 30.5 - - + -
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Residues in contact with LEU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLU 2.9 19.5 + - - +
297A VAL* 3.0 10.5 + - - +
299A LEU* 1.3 76.1 - - - +
301A GLU* 1.3 58.8 + - - +
303A SER* 2.9 19.0 + - - -
304A ARG* 3.0 15.6 + - - +
342A PHE* 4.3 2.2 - - + -
346A MET* 3.6 29.6 - - + -
356A PHE* 3.6 15.3 - - + +
359A LEU* 4.1 21.5 - - + +
360A ILE* 3.8 43.1 - - + +
363A SER* 4.6 3.4 - - - -
410A LYS* 5.8 0.4 - - + -
411A LEU* 5.2 2.7 - - + -
414A LEU* 3.6 23.3 - - + -
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Residues in contact with GLU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLN* 3.5 23.0 + - - -
264A SER* 5.4 3.6 - - - +
267A GLU* 5.6 3.4 - - - +
268A ILE* 6.1 0.9 - - + -
297A VAL* 2.8 29.5 + - + +
298A MET* 3.7 6.7 - - - +
300A LEU* 1.3 73.8 - - - +
302A THR* 1.3 63.1 + - - +
304A ARG* 2.9 24.2 + - - +
305A ARG* 2.5 60.7 + - - +
315A PHE* 5.0 2.0 - - - -
360A ILE* 3.6 8.7 - - + +
501A 4KQ 4.0 23.1 - - + -
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Residues in contact with THR 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A MET 2.8 22.3 + - - -
299A LEU* 3.5 10.8 - - - -
300A LEU 3.2 0.2 - - - -
301A GLU* 1.3 76.9 - - - +
303A SER* 1.3 63.8 + - - +
304A ARG 3.1 0.9 + - - -
305A ARG* 3.2 12.8 + - - -
306A TYR 3.6 7.3 + - - -
313A ILE* 3.8 33.8 - - + +
315A PHE* 3.7 16.6 - - + -
326A PHE* 4.7 0.9 - - + -
339A ILE* 4.0 24.5 - - + -
343A SER* 4.2 3.6 - - - +
501A 4KQ 3.3 25.6 - - + +
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Residues in contact with SER 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU 3.0 13.3 + - - -
300A LEU* 2.9 18.7 + - - -
302A THR* 1.3 76.9 - - - +
304A ARG* 1.3 60.1 + - - +
306A TYR* 3.6 14.1 + - - +
342A PHE* 4.2 7.0 - - - -
343A SER* 3.8 33.7 - - - +
346A MET* 3.3 32.3 - - - +
347A ASN* 5.0 7.4 + - - -
356A PHE* 3.9 5.9 - - - -
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Residues in contact with ARG 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLN* 3.0 30.2 + - - +
300A LEU 3.0 16.2 + - - +
301A GLU* 2.9 33.0 + - - +
302A THR 3.1 0.4 - - - -
303A SER* 1.3 78.5 - - - +
305A ARG* 1.3 82.8 + - - +
306A TYR 3.4 5.1 + - - +
347A ASN* 5.8 1.2 + - - -
353A ASP* 3.2 33.9 + - - +
356A PHE* 3.6 55.8 - - + +
360A ILE* 4.6 2.6 - - - +
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Residues in contact with ARG 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLU* 5.8 0.6 + - - -
301A GLU* 2.5 53.0 + - - +
302A THR* 3.2 7.7 + - - +
304A ARG* 1.3 93.8 - - - +
306A TYR* 1.3 59.0 + - - -
307A ASN* 3.8 1.0 - - - +
313A ILE* 3.6 7.1 - - + -
314A THR* 2.9 59.1 + - - +
315A PHE* 4.7 4.0 - - + -
501A 4KQ 2.9 45.0 + - - +
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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