Contacts of the helix formed by residues 378 - 403 (chain A) in PDB entry 3OMA
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 LYS 378 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A PHE* 3.9 23.3 - - + -
376A GLU* 3.1 41.4 + - + +
377A LEU* 1.3 80.4 - - - +
379A THR* 1.3 66.5 + - - +
380A PRO* 3.4 5.8 - - + -
381A MET* 3.0 12.6 + - - +
382A LEU* 3.1 10.2 + - - +
448A TYR* 4.6 0.4 - - - +
450A GLU* 3.4 40.7 + - + +
454A LYS* 4.2 2.5 - - - +
531A TRP* 4.4 15.7 - - + -
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Residues in contact with THR 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LYS* 1.3 69.4 - - - +
380A PRO* 1.4 70.7 - - - +
382A LEU* 3.0 20.5 + - - +
383A TRP* 3.2 39.0 + - - +
437A TYR* 3.5 21.5 - - + -
448A TYR* 3.6 9.5 - - - -
450A GLU* 2.8 27.4 + - - -
453A GLY* 3.3 18.9 - - - +
454A LYS* 3.2 20.5 + - - +
457A PHE* 5.2 1.6 - - + -
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Residues in contact with PRO 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A VAL* 3.3 15.6 - - + +
305A PHE* 3.7 27.8 - - + -
378A LYS* 3.5 10.1 - - + -
379A THR* 1.4 90.2 - - - +
381A MET* 1.3 56.3 + - - +
383A TRP* 3.5 10.3 + - + +
384A ALA 3.1 21.1 + - - -
434A ALA* 3.8 22.1 - - - +
437A TYR* 3.9 5.8 - - + -
438A PHE* 3.7 25.4 - - + +
448A TYR* 3.3 15.3 - - - +
531A TRP* 4.0 4.3 - - + -
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Residues in contact with MET 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A VAL* 3.9 5.1 - - - +
302A ILE* 4.1 45.3 - - + +
305A PHE* 3.7 20.1 - - + -
306A ALA* 4.2 13.0 - - + +
370A MET* 4.5 9.0 - - + -
375A ILE* 4.3 14.8 - - + -
376A GLU 3.6 22.7 - - - +
377A LEU* 4.4 6.5 - - + -
378A LYS 3.0 10.8 + - - +
380A PRO* 1.3 79.4 - - - +
382A LEU* 1.3 59.4 + - - +
384A ALA* 3.3 1.4 + - - -
385A LEU* 2.9 61.9 + - + +
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Residues in contact with LEU 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU* 4.1 32.5 - - + +
378A LYS 3.1 11.9 + - - +
379A THR* 3.0 11.7 + - - +
381A MET* 1.3 73.4 - - - +
383A TRP* 1.3 59.2 + - - +
385A LEU* 3.3 7.5 + - + +
386A GLY 2.9 25.6 + - - -
454A LYS* 4.0 31.9 - - + -
457A PHE* 3.1 50.2 - - + -
458A TRP* 4.2 19.3 - - + +
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Residues in contact with TRP 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A THR* 3.2 36.3 + - + +
380A PRO* 3.7 1.3 - - + +
382A LEU* 1.3 74.3 - - - +
384A ALA* 1.3 57.7 + - - +
386A GLY 3.4 0.2 + - - -
387A PHE* 2.8 30.2 + - - +
430A PHE* 3.4 65.8 - + - +
433A PHE* 3.5 37.5 - + + -
434A ALA* 3.7 13.5 - - + -
437A TYR* 3.3 26.8 - + - -
456A HIS* 3.4 28.5 - + - -
457A PHE* 3.6 36.1 - + + +
460A MET* 3.8 18.6 - - + -
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Residues in contact with ALA 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A VAL* 4.4 13.8 - - + +
301A VAL* 3.8 15.0 - - + -
302A ILE* 3.8 26.5 - - + -
380A PRO 3.1 17.8 + - - +
381A MET* 3.6 5.6 - - - +
382A LEU 3.3 0.4 - - - -
383A TRP* 1.3 77.6 - - - +
385A LEU* 1.3 57.8 + - - +
387A PHE* 3.3 10.4 - - - +
388A LEU* 3.2 28.6 + - - +
434A ALA* 4.4 3.3 - - + +
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Residues in contact with LEU 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ILE* 4.8 2.0 - - + -
370A MET* 3.3 33.4 - - - -
377A LEU* 3.8 28.7 - - + -
381A MET* 2.9 38.9 + - + +
382A LEU* 3.9 9.9 - - + +
384A ALA* 1.3 72.2 - - - +
386A GLY* 1.3 65.6 + - - +
388A LEU* 3.2 16.2 + - + +
389A PHE* 3.2 21.8 + - - +
76B ILE* 4.3 19.7 - - + +
80B VAL* 3.8 13.7 - - + -
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Residues in contact with GLY 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A LEU 2.9 17.1 + - - -
383A TRP 3.7 1.8 - - - -
385A LEU* 1.3 70.6 - - - +
387A PHE* 1.3 66.0 + - - +
389A PHE* 3.2 3.4 + - - +
390A LEU* 2.9 29.5 + - - +
430A PHE* 3.9 19.3 - - - -
457A PHE* 4.5 5.8 - - - -
461A PHE* 4.6 13.7 - - - -
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Residues in contact with PHE 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A VAL* 4.7 1.8 - - + -
294A ALA* 4.3 14.1 - - + -
295A PHE* 3.4 31.4 - + - -
298A VAL* 3.7 23.1 - - + -
363A ILE* 5.1 0.2 - - + -
366A TRP* 4.0 23.3 - + - -
383A TRP 2.8 17.3 + - - +
384A ALA* 3.3 14.1 - - - +
386A GLY* 1.3 72.9 - - - +
388A LEU* 1.3 65.1 + - + +
391A PHE* 2.8 54.6 + + + +
426A LEU 4.3 8.3 - - - -
427A GLY* 3.0 40.2 - - - -
428A ALA 4.3 0.7 - - - -
430A PHE* 3.8 6.3 - - + -
431A GLY 4.3 4.7 - - - +
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Residues in contact with LEU 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A VAL* 4.4 0.4 - - + -
302A ILE* 3.9 20.9 - - + -
363A ILE* 4.2 15.6 - - + +
366A TRP* 3.4 48.5 - - + -
367A ILE* 4.6 8.7 - - + -
370A MET* 4.6 3.8 - - - -
384A ALA 3.2 12.1 + - - +
385A LEU* 3.2 20.7 + - + +
387A PHE* 1.3 84.2 - - + +
389A PHE* 1.3 60.2 + - - +
392A THR* 2.7 33.1 + - - -
72B VAL* 4.7 1.3 - - - +
76B ILE* 3.8 29.8 - - + -
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Residues in contact with PHE 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A LEU 3.2 9.4 + - - +
386A GLY* 3.7 7.6 - - - +
388A LEU* 1.3 79.2 - - - +
390A LEU* 1.3 91.6 + - + +
392A THR* 3.4 7.3 + - - -
393A VAL* 3.1 44.4 + - + +
461A PHE* 4.0 23.1 - + + -
465A ASN* 4.5 6.7 - - - -
69B THR* 5.9 2.6 - - - -
72B VAL* 5.5 1.3 - - - -
73B THR* 3.1 41.7 - - + -
76B ILE* 4.3 10.2 - - + +
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Residues in contact with LEU 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A GLY 2.9 16.5 + - - +
389A PHE* 1.3 100.6 - - + +
391A PHE* 1.3 61.4 + - - +
393A VAL* 3.2 4.6 + - - +
394A GLY 3.0 23.7 + - - -
422A TYR* 3.7 24.6 - - + +
426A LEU* 3.2 33.9 - - + +
430A PHE* 3.6 37.7 - - + -
461A PHE* 4.0 11.0 - - + -
464A ALA* 6.0 0.2 - - + -
465A ASN* 3.5 24.0 - - - +
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Residues in contact with PHE 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HEA 3.9 36.3 - - + -
288A TYR* 6.3 0.7 - + - -
291A VAL* 3.9 20.4 - - + -
295A PHE* 3.5 22.7 - + - -
359A THR* 3.5 28.0 - - + -
363A ILE* 4.2 16.6 - - + -
366A TRP* 6.0 0.2 - + - -
387A PHE* 2.8 43.8 + + + +
388A LEU* 4.5 1.1 - - - +
390A LEU* 1.3 77.0 - - - +
392A THR* 1.3 59.3 + - - +
394A GLY 3.4 0.7 + - - +
395A GLY* 2.8 25.8 + - - -
422A TYR 4.6 6.1 - - - -
423A VAL* 4.0 24.9 - - + -
426A LEU 4.3 1.6 + - - -
427A GLY* 4.8 1.6 - - - -
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Residues in contact with THR 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HEA 4.1 27.3 - - + +
363A ILE* 3.8 17.8 - - - +
388A LEU 2.7 23.1 + - - -
389A PHE 3.5 5.6 - - - -
390A LEU 3.2 0.4 - - - -
391A PHE* 1.3 79.4 - - - +
393A VAL* 1.3 62.1 + - - +
396A VAL* 3.0 28.3 + - + +
68B ILE* 4.7 0.9 - - + -
69B THR* 3.8 29.4 - - + -
72B VAL* 3.9 19.0 - - + +
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Residues in contact with VAL 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TRD 4.3 20.4 - - + -
389A PHE* 3.1 38.8 + - + +
390A LEU* 3.2 9.1 + - - +
392A THR* 1.3 73.3 - - - +
394A GLY* 1.3 62.1 + - - +
396A VAL* 3.4 19.6 - - - +
397A THR* 3.5 12.3 + - - +
422A TYR* 3.7 32.3 - - + -
469A PHE* 4.7 7.4 - - + -
472A HIS* 4.6 7.6 - - + -
69B THR* 4.7 15.0 - - + +
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Residues in contact with GLY 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LEU 3.0 11.3 + - - -
391A PHE 3.8 0.2 - - - -
393A VAL* 1.3 76.5 - - - +
395A GLY* 1.3 57.2 + - - +
397A THR* 3.0 13.0 + - - -
398A GLY 3.1 4.2 + - - -
419A HIS* 2.8 27.5 + - - -
422A TYR* 3.6 22.8 - - - +
423A VAL* 3.5 17.5 - - - -
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Residues in contact with GLY 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HEA 3.5 50.2 - - - +
391A PHE* 2.8 18.8 + - - -
392A THR 3.3 0.4 + - - -
394A GLY* 1.3 73.8 - - - +
396A VAL* 1.3 56.2 + - - +
398A GLY* 3.2 3.8 + - - -
399A ILE 3.1 19.9 + - - -
423A VAL* 3.7 4.4 - - - +
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Residues in contact with VAL 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HEA 4.4 21.3 - - + -
3A TRD 4.1 6.1 - - + -
392A THR* 3.0 21.8 + - + +
393A VAL 3.4 8.7 - - - +
395A GLY* 1.3 72.8 - - - +
397A THR* 1.3 63.3 + - - +
399A ILE* 3.1 10.6 + - - +
400A VAL* 3.1 26.7 + - - +
65B ILE* 3.7 35.2 - - + +
68B ILE* 4.3 17.0 - - + -
69B THR* 3.6 28.3 - - + -
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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
----------------------------------------------------------
3A TRD 4.1 17.3 - - + -
393A VAL 3.5 13.4 + - - +
394A GLY* 3.0 16.7 + - - -
396A VAL* 1.3 74.4 - - - +
398A GLY* 1.3 64.3 + - - +
399A ILE 3.1 0.4 - - - -
400A VAL* 3.3 9.0 + - - +
401A LEU* 3.0 28.7 + - - +
415A TYR* 3.5 28.0 - - + +
419A HIS* 3.5 21.6 - - - +
472A HIS* 3.7 24.0 + - + +
65B ILE* 4.6 2.0 - - + -
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Residues in contact with GLY 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HEA 3.3 30.1 - - - +
394A GLY 3.1 10.9 + - - -
395A GLY 3.2 5.8 + - - -
397A THR* 1.3 77.8 + - - +
399A ILE* 1.3 55.2 + - - +
401A LEU* 3.3 2.1 + - - +
402A SER 3.1 22.0 + - - -
419A HIS* 3.4 26.2 + - - -
----------------------------------------------------------
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Residues in contact with ILE 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HEA 3.7 54.7 - - + -
352A THR 4.4 1.1 - - - +
353A MET* 4.2 20.2 - - + -
356A ALA* 3.8 21.5 - - + +
395A GLY 3.1 13.7 + - - +
396A VAL* 3.1 9.6 + - - +
398A GLY* 1.3 75.2 - - - +
400A VAL* 1.3 63.7 + - - +
402A SER* 2.5 26.3 + - - +
403A GLN* 3.6 12.3 + - + +
61B ILE* 5.3 3.4 - - + -
65B ILE* 5.2 5.4 - - + -
112B LEU* 4.3 11.4 - - + -
115B ILE* 4.9 12.1 - - + -
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Residues in contact with VAL 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A VAL 3.1 14.5 + - - +
397A THR* 3.4 7.4 - - - +
399A ILE* 1.3 75.4 - - - +
401A LEU* 1.3 56.3 + - - +
403A GLN* 3.1 32.2 + - - +
406A VAL* 4.0 12.9 - - + +
410A TYR* 3.7 32.8 - - + -
415A TYR* 3.7 15.9 - - + +
58B ASP* 4.1 7.2 - - - +
61B ILE* 3.8 23.1 - - + -
62B LEU* 5.7 0.7 - - - +
65B ILE* 3.6 23.6 - - + -
----------------------------------------------------------
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Residues in contact with LEU 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HEA 3.4 35.4 - - + +
336A TYR* 3.5 3.8 - - - -
397A THR 3.0 20.2 + - - +
398A GLY* 3.7 5.2 - - - +
399A ILE 3.3 0.2 - - - -
400A VAL* 1.3 73.8 - - - +
402A SER* 1.3 63.1 + - - +
407A ASP* 3.3 35.0 - - - +
410A TYR* 3.5 35.2 - - + -
415A TYR* 3.8 15.3 - - + -
416A VAL* 3.9 16.2 - - + -
419A HIS* 3.7 35.0 - - + -
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Residues in contact with SER 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HEA 3.1 10.5 + - - -
336A TYR* 2.7 24.0 + - - -
349A MET* 3.4 12.1 - - - +
352A THR* 3.5 33.9 - - - -
353A MET* 3.8 8.8 - - - +
398A GLY 3.1 9.7 + - - -
399A ILE* 2.5 25.8 + - - +
401A LEU* 1.3 77.1 - - - +
403A GLN* 1.3 69.6 + - - +
404A ALA 3.1 4.9 + - - -
----------------------------------------------------------
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Residues in contact with GLN 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A MET* 3.1 14.1 - - - +
353A MET* 3.2 26.3 - - - +
399A ILE* 3.6 8.9 + - + +
400A VAL 3.1 14.3 + - - +
401A LEU 4.1 1.3 - - - -
402A SER* 1.3 95.9 + - - +
404A ALA* 1.3 55.1 + - - +
405A SER* 3.1 4.5 - - - +
406A VAL* 2.8 35.4 + - + +
407A ASP* 2.8 12.6 + - - +
61B ILE* 3.8 20.2 - - + -
115B ILE* 3.5 15.1 - - + +
119B SER* 2.7 38.0 + - - +
----------------------------------------------------------
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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