Contacts of the helix formed by residues 404 - 433 (chain A) in PDB entry 2HBH
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 LEU 404 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A GLY 4.0 14.1 - - - +
403A ARG* 1.3 87.4 - - + +
405A LEU* 1.3 65.8 + - + +
406A TYR 3.4 2.5 - - - -
407A ALA* 3.7 11.5 + - + +
408A LYS* 3.1 56.7 + - + +
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Residues in contact with LEU 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 4.1 30.5 - - + +
353A LEU* 3.8 22.2 - - + -
357A GLU* 3.6 9.0 - - - +
395A ILE* 3.6 24.9 - - + -
399A HIS* 3.3 33.7 - - + +
401A GLY 5.3 0.2 - - - +
402A GLY* 3.3 19.7 + - - +
404A LEU* 1.3 78.7 - - + +
406A TYR* 1.3 66.6 + - - +
408A LYS* 3.0 10.7 + - + +
409A MET* 2.8 24.6 + - - +
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Residues in contact with TYR 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A CYS* 3.4 46.4 + - - +
391A LEU* 4.1 23.1 - - + -
392A GLN* 3.4 52.6 + - + +
395A ILE* 3.7 16.3 - - + +
402A GLY 4.4 2.3 + - - +
403A ARG 5.5 4.0 - - - +
404A LEU 3.4 0.6 - - - -
405A LEU* 1.3 78.4 - - - +
407A ALA* 1.3 61.0 + - + +
409A MET* 3.0 6.6 + - - +
410A ILE* 2.9 49.9 + - + +
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Residues in contact with ALA 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A LEU* 3.7 13.7 + - + +
405A LEU 3.3 0.4 - - - -
406A TYR* 1.3 82.9 - - - +
408A LYS* 1.3 58.8 + - + +
410A ILE* 3.5 5.8 + - - +
411A GLN* 2.9 29.9 + - - +
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Residues in contact with LYS 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 3.7 33.6 - - + +
404A LEU* 3.1 52.3 + - + +
405A LEU* 3.0 12.6 + - + +
407A ALA* 1.3 78.0 - - + +
409A MET* 1.3 58.0 + - - +
411A GLN* 3.4 9.0 - - - +
412A LYS* 3.1 34.5 + - - +
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Residues in contact with MET 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 4.4 5.2 - - + -
353A LEU* 3.8 30.1 - - + -
357A GLU* 3.0 39.5 - - + +
361A LEU* 3.6 35.9 - - + +
391A LEU* 3.6 33.9 - - + -
395A ILE* 3.8 15.5 - - - -
405A LEU* 2.8 15.3 + - + +
406A TYR* 3.4 8.1 - - - +
408A LYS* 1.3 74.7 - - - +
410A ILE* 1.3 64.9 - - + +
412A LYS* 3.2 23.3 + - - +
413A LEU* 3.5 4.3 + - - +
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Residues in contact with ILE 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A LEU* 5.5 1.1 - - + -
364A ILE* 5.0 2.5 - - + -
388A CYS* 4.5 14.4 - - - -
391A LEU* 5.3 6.5 - - + -
406A TYR* 2.9 54.4 + - + +
407A ALA* 4.0 5.4 - - - +
409A MET* 1.3 74.2 - - - +
411A GLN* 1.3 66.9 + - - +
413A LEU* 3.1 39.0 + - + +
414A ALA* 3.7 3.8 + - - +
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Residues in contact with GLN 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ALA 2.9 18.9 + - - +
408A LYS* 3.4 9.9 - - - +
409A MET 3.2 0.2 - - - -
410A ILE* 1.3 78.4 - - - +
412A LYS* 1.3 66.8 + - + +
414A ALA* 2.9 30.7 + - - +
415A ASP* 3.4 25.6 + - - +
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Residues in contact with LYS 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU* 5.7 0.4 - - + -
344A PHE* 3.7 31.0 + - + +
347A GLY* 3.8 35.7 - - - -
348A LEU* 4.0 12.0 - - + +
351A LEU* 4.4 15.5 - - + -
361A LEU* 4.6 10.8 - - + -
408A LYS* 3.1 23.9 + - - +
409A MET* 3.2 13.7 + - - +
411A GLN* 1.3 80.7 - - - +
413A LEU* 1.3 62.2 + - + +
415A ASP* 3.2 22.5 + - - +
416A LEU* 3.2 26.1 + - - +
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Residues in contact with LEU 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A GLU* 4.8 0.7 - - - +
361A LEU* 4.0 19.1 - - + +
364A ILE* 3.9 24.0 - - + -
365A CYS* 3.6 38.4 - - + -
368A SER* 5.6 2.9 - - - +
384A GLN* 5.5 4.5 - - - +
409A MET 3.9 9.2 - - - +
410A ILE* 3.3 30.5 - - + +
411A GLN 3.1 0.6 - - - -
412A LYS* 1.3 78.1 - - - +
414A ALA* 1.3 61.6 + - - +
416A LEU* 3.3 25.1 + - + +
417A ARG* 3.4 17.3 + - - +
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Residues in contact with ALA 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A ILE 3.7 3.6 + - - +
411A GLN* 2.9 23.3 + - - +
413A LEU* 1.3 75.6 - - - +
415A ASP* 1.3 66.2 + - - +
416A LEU 3.0 1.6 - - - -
417A ARG* 3.0 25.3 + - - +
418A SER* 3.5 8.8 + - - -
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Residues in contact with ASP 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A PHE* 3.9 16.4 - - + -
411A GLN* 3.5 26.9 - - - +
412A LYS* 3.2 40.9 + - - +
414A ALA* 1.3 76.3 - - - +
416A LEU* 1.3 61.4 + - - +
418A SER* 3.4 9.0 + - - -
419A LEU* 3.1 29.0 + - + +
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Residues in contact with LEU 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A GLU* 3.4 38.6 - - + +
300A MET* 4.2 14.3 - - + +
301A LEU* 3.8 33.9 - - + -
344A PHE* 3.6 28.5 - - + -
365A CYS* 4.0 8.7 - - - -
412A LYS 3.2 16.8 + - - +
413A LEU* 3.3 18.6 - - + +
414A ALA 3.0 0.2 - - - -
415A ASP* 1.3 76.4 - - - +
417A ARG* 1.3 55.2 + - - +
419A LEU* 3.8 10.1 - - + +
420A ASN* 2.7 36.6 + - - +
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Residues in contact with ARG 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A GLU* 3.1 21.4 + - - -
368A SER* 3.4 23.0 + - - -
370A ASP* 2.7 49.5 + - - -
371A ARG* 3.3 20.2 - - - +
413A LEU* 3.6 14.7 + - - +
414A ALA* 3.0 11.4 + - - +
416A LEU* 1.3 78.9 - - - +
418A SER* 1.3 57.1 + - - +
420A ASN* 3.3 2.9 + - - +
421A GLU* 2.8 31.1 + - - +
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Residues in contact with SER 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ALA 3.5 9.4 + - - -
415A ASP* 3.4 10.8 + - - -
416A LEU 3.3 0.6 - - - -
417A ARG* 1.3 75.8 - - - +
419A LEU* 1.3 62.6 + - - +
421A GLU* 3.3 6.4 + - - +
422A GLU* 2.9 30.7 + - - +
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Residues in contact with LEU 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A MET* 3.8 26.0 - - + -
337A LEU* 3.5 21.1 - - + +
340A PRO* 3.4 33.7 - - + -
341A LEU* 3.5 14.6 - - + +
344A PHE* 3.8 37.9 - - + -
415A ASP* 3.1 17.8 + - + +
416A LEU* 3.8 12.8 - - + +
418A SER* 1.3 79.9 - - - +
420A ASN* 1.3 57.3 + - - +
422A GLU* 3.4 1.5 + - + -
423A HIS* 2.9 32.5 + - - +
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Residues in contact with ASN 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A SER 2.9 27.0 + - - +
296A ILE* 3.7 23.7 - - - +
297A GLU* 2.7 28.9 + - + +
300A MET* 5.0 0.4 - - - -
371A ARG* 3.8 3.2 - - - +
416A LEU 2.7 22.8 + - - +
417A ARG* 3.3 6.6 - - - +
419A LEU* 1.3 73.7 - - - +
421A GLU* 1.3 57.3 + - - +
423A HIS* 3.2 4.0 + - - +
424A SER* 2.8 37.2 + - - -
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Residues in contact with GLU 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A ARG 2.8 20.0 + - - +
418A SER* 3.5 7.9 - - - +
420A ASN* 1.3 71.8 - - - +
422A GLU* 1.3 65.4 + - - +
424A SER* 3.2 15.5 + - - -
425A LYS* 3.1 35.2 + - + +
428A ARG* 5.4 3.5 + - - -
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Residues in contact with GLU 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A GLU* 3.4 28.6 - - + +
337A LEU* 3.7 21.8 - - + -
418A SER 2.9 16.8 + - - +
419A LEU* 3.8 5.2 - - + +
421A GLU* 1.3 76.4 - - - +
423A HIS* 1.3 64.2 + - - +
425A LYS* 3.1 34.8 + - - +
426A GLN* 3.0 54.8 + - - +
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Residues in contact with HIS 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ILE* 3.3 40.8 - - + +
300A MET* 5.6 0.2 - - + -
333A HIS* 3.5 20.6 - + - -
337A LEU* 3.9 21.5 - - + +
419A LEU 2.9 17.6 + - - +
420A ASN* 3.5 6.2 + - - +
422A GLU* 1.3 77.2 - - - +
424A SER* 1.3 56.0 + - - +
425A LYS 3.2 0.2 + - - -
426A GLN* 3.3 1.7 + - - +
427A TYR* 2.7 51.9 + + + +
448A PHE* 4.2 22.5 - + - -
500A XE4 3.1 36.6 + - + +
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Residues in contact with SER 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A ASN* 2.8 27.1 + - - -
421A GLU* 3.3 21.0 - - - -
423A HIS* 1.3 80.2 + - - +
425A LYS* 1.3 56.9 + - - +
427A TYR* 3.8 5.6 - - - +
428A ARG* 2.9 44.9 + - - +
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Residues in contact with LYS 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A GLU* 5.9 0.4 - - - +
421A GLU* 3.1 23.4 + - + +
422A GLU* 3.2 38.7 + - - +
424A SER* 1.3 78.6 - - - +
426A GLN* 1.3 64.8 + - + +
428A ARG* 2.9 31.2 + - - +
429A SER* 3.2 11.3 + - - -
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Residues in contact with GLN 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A GLY 4.2 5.7 - - - +
333A HIS* 2.7 41.7 + - + +
334A THR* 2.8 45.9 + - + +
336A GLU* 3.8 0.2 - - - +
337A LEU* 3.2 26.2 - - - +
422A GLU* 3.0 34.8 + - - +
423A HIS 4.5 0.4 - - - -
425A LYS* 1.3 78.8 - - - +
427A TYR* 1.3 60.3 + - - +
429A SER* 3.6 8.1 + - - -
430A LEU* 3.3 21.1 + - - +
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Residues in contact with TYR 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A HIS* 4.0 4.4 - - - -
423A HIS* 2.7 36.9 + + + +
424A SER* 3.8 5.8 - - - +
426A GLN* 1.3 71.1 - - - +
428A ARG* 1.3 59.1 + - - +
430A LEU* 3.2 9.4 + - + +
431A SER* 2.8 49.0 + - - -
440A LEU* 3.1 35.2 - - + +
444A VAL* 3.7 27.3 + - + +
445A LEU* 3.7 12.3 - - - +
448A PHE* 3.4 39.9 - + + -
449A GLY* 4.6 2.7 - - - -
500A XE4 3.2 27.1 - - + +
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Residues in contact with ARG 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A GLU* 5.4 3.6 + - - -
424A SER* 2.9 31.3 + - - +
425A LYS* 2.9 18.9 + - - +
427A TYR* 1.3 79.1 - - - +
429A SER* 1.3 62.7 + - - +
431A SER* 2.8 22.2 + - - +
432A PHE* 3.0 47.3 + - + -
450A SER* 5.3 11.9 + - - -
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Residues in contact with SER 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A LYS 3.2 11.9 + - - -
426A GLN* 3.7 9.0 + - - -
428A ARG* 1.3 77.6 - - - +
430A LEU* 1.3 65.8 + - - +
432A PHE* 3.2 20.7 + - - +
433A GLN* 3.5 19.6 + - - +
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Residues in contact with LEU 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LEU* 3.6 31.0 - - + -
255A LEU* 4.5 8.5 - - + -
331A ALA 3.8 9.0 - - - +
332A GLY* 4.3 12.3 - - - +
333A HIS* 4.7 4.7 - - - +
426A GLN 3.3 9.5 + - - +
427A TYR* 3.2 14.3 + - + +
429A SER* 1.3 79.7 - - - +
431A SER* 1.3 63.0 + - - +
433A GLN* 3.0 30.0 + - - +
436A HIS* 3.7 24.3 - - + +
437A SER 4.1 1.0 + - - -
440A LEU* 4.8 8.3 - - + -
500A XE4 3.8 35.2 - - + +
----------------------------------------------------------
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Residues in contact with SER 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A TYR* 2.8 43.1 + - - -
428A ARG* 2.8 19.2 + - - +
430A LEU* 1.3 74.5 - - - +
432A PHE* 1.3 69.0 + - - +
433A GLN 3.5 0.2 + - - -
434A PRO* 5.2 0.2 - - - +
437A SER* 3.5 27.3 + - - +
440A LEU* 4.8 4.0 - - - +
445A LEU* 5.2 2.9 - - - -
----------------------------------------------------------
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Residues in contact with PHE 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ARG* 3.0 55.9 + - + -
429A SER* 3.6 10.8 - - - +
430A LEU 3.1 0.6 - - - -
431A SER* 1.3 83.7 - - - +
433A GLN* 1.3 61.4 + - + +
434A PRO* 2.9 14.6 - - - +
----------------------------------------------------------
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Residues in contact with GLN 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ARG* 3.4 24.2 - - - +
429A SER* 3.5 15.6 + - - +
430A LEU* 3.0 9.3 + - - +
432A PHE* 1.3 80.0 - - + +
434A PRO* 1.3 57.0 - - - +
435A GLU* 3.2 17.8 + - - +
436A HIS* 2.8 43.5 + - - +
437A SER* 2.9 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