Contacts of the helix formed by residues 372 - 402 (chain A) in PDB entry 3KMR
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 HIS 372 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A SER 5.4 0.4 - - - -
370A ARG* 3.5 44.8 + - + +
371A PRO* 1.3 85.1 - - + +
373A MET* 1.3 71.2 + - + +
374A PHE 3.5 1.3 - - - -
375A PRO* 3.4 16.2 - - + +
376A LYS* 3.4 23.1 - - + +
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Residues in contact with MET 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 3.8 38.6 - - + +
363A VAL* 3.6 21.3 - - + -
367A ARG* 3.8 18.6 - - - +
370A ARG* 3.3 57.4 + - + +
371A PRO 3.3 1.0 - - - -
372A HIS* 1.3 83.1 - - + +
374A PHE* 1.3 59.6 + - - +
376A LYS* 3.2 5.4 + - + +
377A MET* 2.8 49.6 + - + +
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Residues in contact with PHE 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LEU* 3.6 24.7 - - + -
359A LEU* 3.8 28.5 - - + -
360A LYS* 3.6 52.5 - - + -
363A VAL* 4.0 8.8 - - + +
364A ARG* 3.4 31.8 - - - +
371A PRO 4.5 0.8 + - - -
373A MET* 1.3 78.7 - - - +
375A PRO* 1.4 62.2 - - + +
377A MET* 3.3 7.5 + - - +
378A LEU* 3.1 59.0 + - + +
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Residues in contact with PRO 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ARG* 4.3 3.6 - - - +
371A PRO 3.9 8.1 - - - +
372A HIS* 3.4 23.6 - - + +
374A PHE* 1.4 96.9 - - + +
376A LYS* 1.3 56.9 + - - +
378A LEU* 3.3 15.5 + - + +
379A MET* 3.1 35.7 + - + +
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Residues in contact with LYS 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 4.8 14.4 - - + +
372A HIS* 3.4 20.9 - - + +
373A MET* 3.2 12.7 + - + +
375A PRO* 1.3 78.2 - - - +
377A MET* 1.3 64.8 + - - +
379A MET* 3.7 13.5 + - + +
380A LYS* 3.6 36.3 + - - +
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Residues in contact with MET 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 4.5 4.2 - - + +
321A MET* 3.7 51.1 - - + -
325A GLU* 4.2 3.4 - - - +
329A LEU* 3.5 19.5 - - + +
359A LEU* 4.1 16.4 - - + -
363A VAL* 3.6 22.9 - - + -
367A ARG* 3.7 16.2 - - - +
373A MET* 2.8 46.5 + - + +
374A PHE* 3.3 11.4 - - - +
376A LYS* 1.3 76.9 - - - +
378A LEU* 1.3 62.7 + - - +
380A LYS* 3.1 25.4 + - - +
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Residues in contact with LEU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A LEU* 4.7 3.8 - - + -
332A ILE* 5.1 0.4 - - + -
356A LEU* 3.8 29.2 - - + -
359A LEU* 4.8 7.4 - - + -
374A PHE* 3.1 53.3 + - + +
375A PRO* 3.3 15.9 + - + +
377A MET* 1.3 76.6 - - + +
379A MET* 1.3 70.7 + - + +
380A LYS 3.1 0.2 - - - -
381A ILE* 3.0 38.5 + - + +
382A THR* 3.7 2.8 + - - -
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Residues in contact with MET 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A PRO* 3.1 17.3 + - + +
376A LYS* 3.7 13.2 + - + +
377A MET 3.3 0.4 - - - -
378A LEU* 1.3 87.7 - - + +
380A LYS* 1.3 60.2 + - - +
381A ILE 3.2 0.4 - - - -
382A THR* 3.3 25.0 + - - +
383A ASP* 2.9 38.5 + - - +
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Residues in contact with LYS 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A PHE* 3.5 27.2 - - + -
315A GLN* 3.3 42.1 + - - +
316A LEU* 4.3 11.9 - - + -
319A LEU* 3.8 28.0 - - + +
329A LEU* 4.1 14.1 - - + -
376A LYS* 3.6 34.1 - - - +
377A MET* 3.1 17.4 + - + +
379A MET* 1.3 78.0 - - - +
381A ILE* 1.3 52.5 + - - +
383A ASP* 3.4 13.4 + - - +
384A LEU* 2.7 36.2 + - - +
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Residues in contact with ILE 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ASP* 4.8 0.7 - - - +
329A LEU* 3.7 28.0 - - + -
332A ILE* 3.4 34.3 - - + -
333A CYS* 3.4 35.2 - - - +
378A LEU* 3.0 21.4 + - + +
380A LYS* 1.3 75.1 - - - +
382A THR* 1.3 61.9 + - - +
384A LEU* 3.2 7.4 + - - +
385A ARG* 2.8 48.2 + - - +
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Residues in contact with THR 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LEU 3.7 2.1 + - - -
379A MET* 3.3 35.8 + - - +
381A ILE* 1.3 78.9 - - - +
383A ASP* 1.3 65.2 + - - +
385A ARG* 3.4 7.6 + - + +
386A SER* 3.1 22.7 + - - -
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Residues in contact with ASP 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A PHE* 3.9 15.2 - - + -
315A GLN* 4.5 9.0 - - - +
379A MET* 2.9 30.4 + - - +
380A LYS* 3.5 25.7 + - - +
382A THR* 1.3 79.6 - - - +
384A LEU* 1.3 56.2 + - - +
386A SER* 3.3 7.7 + - - -
387A ILE* 3.0 37.3 + - + +
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Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ASP* 3.2 40.6 - - - +
270A ILE* 3.8 27.8 - - + +
271A LEU* 4.0 20.2 - - + +
312A PHE* 3.8 26.5 - - + -
329A LEU* 5.2 2.9 - - + -
333A CYS* 4.2 22.4 - - - -
380A LYS 2.7 20.9 + - - +
381A ILE* 3.4 6.7 - - - +
383A ASP* 1.3 74.2 - - - +
385A ARG* 1.3 51.7 + - - +
387A ILE* 3.2 7.4 + - + +
388A SER* 2.7 35.5 + - - -
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Residues in contact with ARG 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ASP* 3.4 12.3 + - - +
333A CYS 5.3 0.6 + - - -
336A CYS* 3.3 26.9 - - - -
338A ASP* 3.3 24.0 + - - -
339A ARG* 3.1 36.4 - - - +
381A ILE* 2.8 32.1 + - - +
382A THR* 3.6 9.7 - - + +
384A LEU* 1.3 74.1 - - - +
386A SER* 1.3 57.6 + - - +
388A SER* 3.1 5.8 + - - +
389A ALA* 3.0 30.4 + - + +
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Residues in contact with SER 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU* 6.0 1.7 - - - +
382A THR* 3.1 11.1 + - - -
383A ASP* 3.4 11.0 - - - -
385A ARG* 1.3 78.2 - - - +
387A ILE* 1.3 64.6 + - - +
389A ALA* 3.3 8.6 + - - +
390A LYS* 3.3 34.9 + - - +
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Residues in contact with ILE 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ILE* 3.9 23.5 - - + +
305A LEU* 4.1 7.9 - - + +
308A LEU* 3.9 31.4 - - + +
309A VAL* 3.9 20.6 - - + +
312A PHE* 3.7 39.0 - - + -
383A ASP* 3.0 23.9 + - + +
384A LEU* 3.2 8.7 + - + +
386A SER* 1.3 77.0 - - - +
388A SER* 1.3 58.8 + - - +
390A LYS* 3.2 8.5 + - - +
391A GLY* 2.8 24.4 + - - -
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Residues in contact with SER 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU* 3.9 25.8 - - - +
267A ASP* 2.9 37.8 + - - -
270A ILE* 4.6 4.0 - - - -
384A LEU 2.7 14.8 + - - -
385A ARG* 3.1 12.8 + - - +
387A ILE* 1.3 74.6 - - - +
389A ALA* 1.3 56.4 + - - +
391A GLY* 3.5 3.9 - - - +
392A ALA* 2.9 27.4 + - - +
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Residues in contact with ALA 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ARG* 3.0 15.9 + - + +
386A SER* 3.5 8.3 - - - +
387A ILE 3.2 0.2 - - - -
388A SER* 1.3 76.2 + - - +
390A LYS* 1.3 63.9 + - + +
392A ALA* 3.3 8.4 + - - +
393A GLU* 3.3 26.1 + - - +
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Residues in contact with LYS 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PRO 6.1 0.7 - - - +
305A LEU* 3.5 21.6 - - + +
308A LEU* 3.7 28.9 - - + +
386A SER* 3.3 22.5 + - - +
387A ILE* 3.2 7.0 + - - +
389A ALA* 1.3 75.9 - - + +
391A GLY* 1.3 60.1 + - - +
393A GLU* 3.2 23.9 + - - +
394A ARG* 2.9 22.7 + - - +
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Residues in contact with GLY 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A EQN 3.7 2.3 - - - +
266A LEU* 3.7 15.3 - - - -
305A LEU* 3.5 20.6 - - - +
387A ILE 2.8 15.8 + - - -
388A SER* 3.3 5.4 + - - -
389A ALA 3.2 0.4 - - - -
390A LYS* 1.3 77.4 - - - +
392A ALA* 1.3 55.4 + - - +
394A ARG* 2.9 4.0 + - - +
395A VAL* 2.9 30.5 + - - +
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Residues in contact with ALA 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU* 3.9 4.8 - - + +
388A SER 2.9 12.8 + - - +
389A ALA* 3.3 10.7 + - - +
391A GLY* 1.3 71.9 - - - +
393A GLU* 1.3 65.8 + - + +
395A VAL* 3.5 12.3 + - - +
396A ILE* 3.5 26.3 + - - +
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Residues in contact with GLU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ALA 3.3 15.3 + - - +
390A LYS* 3.2 25.1 + - - +
392A ALA* 1.3 77.2 - - + +
394A ARG* 1.3 60.8 + - - +
396A ILE* 3.3 24.7 + - + +
397A THR* 3.3 18.1 + - - +
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Residues in contact with ARG 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A EQN 4.2 7.4 - - + -
219A SER 3.9 12.5 + - - -
298A HIS 5.1 0.4 + - - -
301A GLY* 2.8 32.2 + - - +
302A PHE 3.7 11.2 + - - +
303A GLY* 4.0 8.5 - - - -
304A PRO* 3.8 28.9 - - + +
305A LEU* 3.7 19.7 - - + -
390A LYS 2.9 13.2 + - - +
391A GLY 2.9 8.0 + - - +
393A GLU* 1.3 73.8 - - - +
395A VAL* 1.3 66.1 + - - +
397A THR* 3.2 25.1 + - - -
398A LEU* 2.9 42.5 + - + +
401A GLU* 3.3 26.6 + - - -
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Residues in contact with VAL 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A EQN 3.8 30.9 - - + +
266A LEU* 4.5 2.7 - - + -
391A GLY 2.9 18.1 + - - +
392A ALA* 3.6 15.7 - - - +
394A ARG* 1.3 76.7 - - - +
396A ILE* 1.3 63.6 + - + +
398A LEU* 3.9 2.9 - - - +
399A LYS* 3.1 35.1 + - + +
406A MET* 4.1 9.0 - - + +
410A ILE* 6.1 0.7 - - + -
414A LEU* 3.9 33.7 - - + +
415A GLU* 3.6 24.0 - - - +
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Residues in contact with ILE 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ALA 3.5 17.7 - - - +
393A GLU* 3.3 17.7 + - + +
394A ARG 3.2 0.2 - - - -
395A VAL* 1.3 79.8 - - + +
397A THR* 1.3 66.6 + - + +
399A LYS* 3.4 34.2 + - - +
400A MET* 3.7 26.8 + - + +
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Residues in contact with THR 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PRO* 5.6 0.7 - - - +
393A GLU* 3.3 12.6 + - + +
394A ARG* 3.2 38.2 + - - -
396A ILE* 1.3 83.4 - - + +
398A LEU* 1.3 60.9 + - - +
400A MET* 3.3 29.0 + - + +
401A GLU* 3.5 11.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A EQN 3.6 34.5 - - + -
220A LEU* 3.8 26.2 - - + -
225A TRP* 3.9 17.5 - - + -
301A GLY* 3.7 17.5 - - - +
394A ARG* 2.9 44.6 + - - +
395A VAL 3.9 3.4 - - - +
397A THR* 1.3 72.7 + - - +
399A LYS* 1.3 58.9 - - - +
400A MET 3.1 2.0 - - - -
401A GLU* 2.9 23.4 + - + +
402A ILE* 2.9 28.5 + - + +
406A MET* 4.0 7.0 - - + -
----------------------------------------------------------
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Residues in contact with LYS 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A VAL* 3.1 22.4 + - + +
396A ILE* 3.4 33.5 + - - +
397A THR 3.4 0.4 - - - -
398A LEU* 1.3 76.4 - - - +
400A MET* 1.3 61.7 + - + +
401A GLU 3.5 0.2 + - - -
402A ILE* 4.0 21.1 - - + +
404A GLY 4.8 4.7 - - - +
406A MET* 3.7 23.3 - - + +
415A GLU* 3.1 41.1 - - - +
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Residues in contact with MET 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ILE* 3.7 36.1 + - + +
397A THR* 3.3 22.4 + - + +
398A LEU 3.1 0.4 - - - -
399A LYS* 1.3 77.5 - - + +
401A GLU* 1.3 62.1 + - + +
402A ILE 4.7 1.7 - - - +
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Residues in contact with GLU 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A SER* 2.7 41.3 + - - +
220A LEU* 3.9 20.0 - - + +
394A ARG* 3.3 35.0 + - - -
397A THR 3.5 9.0 + - - +
398A LEU* 2.9 13.3 + - + +
400A MET* 1.3 81.0 - - + +
402A ILE* 1.3 62.7 + - - +
403A PRO* 3.8 2.4 - - - +
----------------------------------------------------------
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Residues in contact with ILE 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LEU* 3.8 17.9 - - + -
225A TRP* 3.6 46.4 - - + +
398A LEU* 2.9 30.0 + - + +
399A LYS* 4.0 16.4 - - - +
400A MET 4.7 1.7 - - - +
401A GLU* 1.3 78.7 - - - +
403A PRO* 1.4 74.0 - - + +
404A GLY 3.5 10.9 + - - +
405A SER* 3.7 33.0 - - - +
406A MET* 3.8 13.2 - - + +
----------------------------------------------------------
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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