Contacts of the helix formed by residues 439 - 468 (chain D) in PDB entry 2HVH
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 ASP 439 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438D PRO* 1.3 75.2 - - - +
440D GLU* 1.3 74.2 + - - +
441D PRO* 3.3 21.8 - - + +
442D VAL* 2.9 15.3 + - + -
443D LEU 2.9 19.1 + - - -
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Residues in contact with GLU 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D LEU* 4.4 13.1 - - + +
345D PHE* 3.9 19.8 - - + -
347D ARG* 2.7 55.0 + - - +
438D PRO 3.6 2.1 + - - -
439D ASP* 1.3 75.2 + - - +
441D PRO* 1.3 71.6 - - + +
443D LEU* 3.6 9.4 - - + +
444D ALA* 2.8 23.4 + - - +
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Residues in contact with PRO 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D PHE* 5.0 2.4 - - + -
303D LEU* 5.2 7.4 - - + -
439D ASP* 3.3 26.2 - - - +
440D GLU* 1.3 94.7 - - + +
442D VAL* 1.3 65.7 + - + +
444D ALA* 3.7 5.4 - - + +
445D GLU* 3.1 24.0 + - - +
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Residues in contact with VAL 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428D VAL* 4.6 14.6 - - + +
438D PRO* 3.9 24.2 - - + -
439D ASP* 2.9 17.3 + - + +
441D PRO* 1.3 80.1 - - + +
443D LEU* 1.3 64.1 + - - +
445D GLU* 3.3 5.6 + - - +
446D HIS* 3.1 21.4 + - + +
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Residues in contact with LEU 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333D VAL* 3.8 37.0 - - + +
334D GLY* 4.8 0.2 - - - -
345D PHE* 4.3 15.9 - - + -
429D TYR* 4.0 23.1 - - + +
437D VAL* 4.1 19.5 - - + -
438D PRO* 4.2 14.7 - - + +
439D ASP 2.9 11.7 + - - +
440D GLU* 3.6 11.7 - - + +
442D VAL* 1.3 78.1 - - - +
444D ALA* 1.3 63.6 + - - +
446D HIS* 3.2 6.8 + - + +
447D LEU* 3.0 47.6 + - + +
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Residues in contact with ALA 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D PHE* 3.8 18.8 - - + -
303D LEU* 4.3 8.1 - - + -
345D PHE* 3.6 39.4 - - + -
440D GLU 2.8 20.8 + - - +
441D PRO 3.7 3.6 - - - +
443D LEU* 1.3 74.3 - - - +
445D GLU* 1.3 62.7 + - - +
447D LEU* 3.4 1.6 + - - +
448D VAL* 3.0 28.1 + - - +
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Residues in contact with GLU 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D LYS 4.4 6.2 - - - +
298D LYS* 5.3 0.6 - - - -
299D MET* 5.0 9.4 + - + +
301D PHE* 4.0 21.8 - - + -
441D PRO 3.1 16.1 + - - +
442D VAL* 3.9 5.3 - - - +
444D ALA* 1.3 76.2 - - - +
446D HIS* 1.3 58.8 + - - +
448D VAL* 3.3 3.1 + - + +
449D ARG* 2.9 66.4 + - + +
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Residues in contact with HIS 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422D VAL* 4.9 0.6 - - - +
423D ARG* 3.2 35.2 + - - +
425D ASP* 2.8 27.9 + - - -
428D VAL* 3.5 41.1 - - + +
429D TYR* 3.5 24.0 - - - -
442D VAL* 3.1 12.9 + - + +
443D LEU* 3.6 8.3 - - + +
445D GLU* 1.3 80.5 - - - +
447D LEU* 1.3 63.7 + - + +
449D ARG* 3.4 7.0 + - - +
450D LYS* 3.1 47.4 + - + +
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Residues in contact with LEU 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D VAL* 4.1 7.5 - - + +
321D GLU* 3.5 29.6 - - + +
334D GLY* 3.6 36.6 - - - +
335D ILE* 4.0 2.9 - - - +
336D ALA* 3.6 20.9 - - + +
345D PHE* 4.1 8.5 - - + -
429D TYR* 3.5 24.9 - - - +
443D LEU* 3.0 27.1 + - + +
444D ALA 4.0 3.1 - - - +
446D HIS* 1.3 79.6 - - + +
448D VAL* 1.3 61.0 + - - +
450D LYS* 3.2 14.5 + - - +
451D ALA* 3.0 18.5 + - - +
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Residues in contact with VAL 448 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D MET* 4.0 11.0 - - + -
301D PHE* 3.7 39.3 - - + -
336D ALA* 3.9 8.7 - - + -
338D VAL* 4.2 2.8 - - + +
343D ARG* 3.8 32.8 - - + -
344D PHE 4.1 21.1 - - - +
345D PHE* 4.5 2.0 - - + -
444D ALA 3.0 21.1 + - - +
445D GLU* 3.8 3.6 - - + +
447D LEU* 1.3 75.7 - - - +
449D ARG* 1.3 51.6 + - + +
451D ALA* 3.1 4.0 + - - +
452D ALA* 2.7 32.6 + - - +
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Residues in contact with ARG 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D LYS* 3.4 26.5 + - - +
298D LYS 3.8 18.0 + - - -
299D MET* 3.9 24.7 - - + +
419D TYR* 4.7 0.5 + - - -
421D ALA* 3.0 49.0 + - - +
422D VAL* 3.9 15.5 - - + +
423D ARG* 5.2 6.1 - - - +
445D GLU* 2.9 48.2 + - + +
446D HIS* 3.7 7.9 - - - +
448D VAL* 1.3 76.3 - - + +
450D LYS* 1.3 57.2 + - - +
452D ALA* 3.5 7.6 - - - +
453D ALA* 2.8 28.9 + - - +
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Residues in contact with LYS 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D VAL* 4.3 11.4 - - + -
321D GLU* 2.7 40.2 + - - -
410D VAL* 4.1 33.5 - - + +
422D VAL* 4.0 13.0 - - + -
423D ARG 5.1 0.7 - - - +
425D ASP* 2.8 26.7 + - - +
446D HIS* 3.1 37.6 + - + +
447D LEU* 3.2 15.0 + - - +
449D ARG* 1.3 73.5 - - - +
451D ALA* 1.3 61.2 + - - +
453D ALA* 3.5 1.2 - - - +
454D ILE* 2.9 36.3 + - - +
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Residues in contact with ALA 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D ALA* 3.2 28.9 - - - +
319D VAL* 3.8 17.8 - - + +
336D ALA* 4.1 12.6 - - + -
338D VAL* 3.6 17.4 - - + +
447D LEU 3.0 12.6 + - - +
448D VAL 3.5 7.9 - - - +
450D LYS* 1.3 74.2 - - - +
452D ALA* 1.3 65.7 + - - +
454D ILE* 3.5 2.0 + - - -
455D TRP* 3.0 19.4 + - - +
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Residues in contact with ALA 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D MET* 3.6 31.6 - - + -
338D VAL* 3.9 12.5 - - + +
343D ARG* 4.6 6.7 - - - +
419D TYR* 4.0 6.3 - - - +
448D VAL 2.7 20.1 + - - +
449D ARG 3.5 5.2 - - - +
451D ALA* 1.3 75.5 - - - +
453D ALA* 1.3 63.3 + - - +
455D TRP* 3.2 7.2 + - - +
456D GLU* 3.0 26.4 + - + +
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Residues in contact with ALA 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D VAL* 3.8 20.2 - - + -
414D ALA* 4.9 0.4 - - + -
419D TYR* 3.7 32.1 + - + -
422D VAL* 4.7 5.6 - - + -
449D ARG 2.8 18.0 + - - +
450D LYS* 3.5 5.8 - - - +
452D ALA* 1.3 75.8 - - - +
454D ILE* 1.3 63.9 + - - +
456D GLU* 3.0 3.5 + - - +
457D LEU* 2.9 35.0 + - + +
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Residues in contact with ILE 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D ALA* 4.2 3.1 - - + -
318D LEU 4.6 1.3 - - - +
319D VAL* 4.2 20.4 - - + -
369D SER* 3.6 37.8 - - - +
370D MET* 3.7 9.2 - - - +
371D PHE* 3.7 31.9 - - + +
392D PHE* 4.7 7.4 - - + -
394D LEU* 3.9 24.7 - - + -
410D VAL* 4.4 6.5 - - + -
450D LYS 2.9 21.3 + - - +
451D ALA* 3.7 4.7 - - - +
452D ALA 3.3 0.2 - - - -
453D ALA* 1.3 74.4 - - - +
455D TRP* 1.3 65.2 + - - +
457D LEU* 3.1 11.9 + - - +
458D GLU* 3.3 15.1 + - - +
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Residues in contact with TRP 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D LYS* 3.8 42.4 - - + -
316D ALA* 3.7 22.2 - - - -
317D ALA* 3.6 19.7 - - + -
338D VAL* 3.7 24.8 - - + +
339D ASN* 4.0 6.2 + - - -
340D GLU* 4.0 21.7 - - + +
369D SER* 5.3 3.1 - - - -
451D ALA 3.0 18.9 + - - +
452D ALA* 3.3 5.8 - - - +
454D ILE* 1.3 77.8 - - - +
456D GLU* 1.3 78.2 + - + +
458D GLU* 4.3 11.3 + - - +
459D ARG 5.4 0.3 + - - -
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Residues in contact with GLU 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419D TYR* 4.0 27.8 - - + +
452D ALA* 3.0 13.9 + - + +
453D ALA 3.0 7.8 + - - +
455D TRP* 1.3 96.4 - - + +
457D LEU* 1.3 60.2 + - - +
458D GLU 3.5 0.4 + - - -
459D ARG* 4.4 2.7 + - - +
460D PRO* 3.4 18.2 - - - +
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Residues in contact with LEU 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392D PHE* 4.9 0.9 - - - -
394D LEU* 4.4 20.0 - - + -
414D ALA* 3.6 36.1 - - + +
417D LYS* 3.9 26.2 - - + +
419D TYR* 4.0 21.5 - - + -
453D ALA* 2.9 23.1 + - + +
454D ILE* 3.1 3.3 + - - +
456D GLU* 1.3 79.2 - - - +
458D GLU* 1.3 65.0 + - - +
459D ARG 3.2 3.3 + - - -
460D PRO* 3.3 11.7 - - + +
461D PHE* 3.1 43.2 + - + -
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Residues in contact with GLU 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A ARG* 5.7 1.2 + - - -
315D LYS* 3.1 26.2 + - - -
369D SER* 2.6 27.9 + - - -
391D SER* 4.8 5.2 + - - +
392D PHE* 3.7 35.7 - - + +
454D ILE 3.3 13.7 + - - +
455D TRP* 4.5 9.7 - - - +
456D GLU 3.5 1.4 - - - -
457D LEU* 1.3 76.6 - - - +
459D ARG* 1.3 60.9 + - - +
461D PHE* 3.9 1.2 - - - +
462D LEU* 2.9 55.8 + - + +
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Residues in contact with ARG 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ARG* 5.3 16.6 + - - +
467A ARG* 6.3 0.6 - - - +
455D TRP 5.4 0.4 + - - -
456D GLU 4.4 2.8 + - - +
458D GLU* 1.3 79.7 + - - +
460D PRO* 1.3 76.2 - - + +
462D LEU* 3.1 33.5 + - - +
463D ASP* 2.9 59.5 + - - +
466D ARG* 5.9 0.2 - - - +
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Residues in contact with PRO 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417D LYS* 4.1 25.8 + - + +
456D GLU 3.4 13.0 - - - +
457D LEU* 3.3 30.7 - - + +
459D ARG* 1.3 96.4 - - + +
461D PHE* 1.3 59.8 + - - +
463D ASP* 3.3 9.1 + - + +
464D GLU* 3.1 22.0 + - - +
467D ARG* 5.5 0.5 + - - -
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Residues in contact with PHE 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392D PHE* 4.1 12.3 - - + -
394D LEU* 3.8 21.5 - - + -
397D ALA* 3.9 17.9 - - + -
398D ALA* 3.8 20.9 - - + -
401D LEU* 3.5 29.3 - - + +
413D ALA* 3.5 26.7 - - + -
416D MET* 4.2 9.4 - - + -
417D LYS* 3.5 31.9 - - + +
457D LEU* 3.1 39.7 + - + +
458D GLU 3.9 2.7 - - - +
460D PRO* 1.3 75.4 - - - +
462D LEU* 1.3 58.8 + - - +
464D GLU* 3.1 4.4 + - - +
465D LEU* 2.9 33.3 + - + +
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Residues in contact with LEU 462 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A ARG* 4.5 22.2 - - - +
392D PHE* 4.2 10.5 - - + -
458D GLU* 2.9 46.7 + - + +
459D ARG* 3.6 31.2 - - - +
461D PHE* 1.3 76.8 - - - +
463D ASP* 1.3 63.3 + - - +
465D LEU* 3.9 9.2 - - + +
466D ARG* 3.1 24.4 + - - +
471D ASP* 5.0 10.0 - - + +
474D LEU* 4.1 25.8 - - + -
475D VAL* 5.3 3.4 - - + -
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Residues in contact with ASP 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459D ARG* 2.9 53.3 + - - +
460D PRO* 3.7 8.1 - - + +
461D PHE 3.2 0.2 - - - -
462D LEU* 1.3 77.3 - - - +
464D GLU* 1.3 61.0 + - - +
466D ARG* 3.4 37.3 + - - +
467D ARG* 3.1 29.9 + - - +
----------------------------------------------------------
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Residues in contact with GLU 464 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401D LEU* 3.8 31.2 - - + +
417D LYS* 2.7 33.6 + - - +
460D PRO 3.1 11.1 + - - +
461D PHE 3.1 7.8 + - - +
463D ASP* 1.3 74.8 - - - +
465D LEU* 1.3 65.3 + - - +
467D ARG* 3.3 31.9 + - - +
468D ASN* 3.1 32.8 + - - +
772D TYR* 4.9 5.0 + - - -
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Residues in contact with LEU 465 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392D PHE* 5.1 0.2 - - + -
397D ALA* 4.2 14.8 - - + +
400D LEU* 4.0 19.5 - - + -
401D LEU* 3.5 26.0 - - + +
461D PHE 2.9 20.7 + - - +
462D LEU* 3.9 14.8 - - + +
464D GLU* 1.3 75.1 - - - +
466D ARG* 1.3 62.9 + - - +
468D ASN* 2.9 8.2 + - - -
470D GLN* 2.8 58.2 + - + +
471D ASP* 3.9 5.4 - - + +
474D LEU* 3.6 35.4 - - + -
----------------------------------------------------------
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Residues in contact with ARG 466 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ARG 5.6 0.4 - - - -
467A ARG 3.9 17.5 - - - +
468A ASN* 5.3 1.1 - - - -
469A GLU* 3.0 51.2 + - - +
459D ARG* 5.9 0.2 - - - +
462D LEU 3.1 16.6 + - - +
463D ASP* 3.4 46.8 + - - +
465D LEU* 1.3 76.6 - - - +
467D ARG* 1.3 82.6 + - - +
469D GLU* 3.2 19.6 + - - +
471D ASP* 4.0 22.2 - - + +
1H GLC 3.6 12.5 + - - -
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Residues in contact with ARG 467 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417D LYS* 4.9 4.2 - - - +
460D PRO 5.5 0.4 + - - -
463D ASP* 3.1 29.7 + - - +
464D GLU* 3.3 42.9 + - - +
466D ARG* 1.3 93.3 - - - +
468D ASN* 1.3 64.1 + - - +
469D GLU* 3.3 2.0 + - - +
770D ARG* 5.4 0.2 + - - -
----------------------------------------------------------
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Residues in contact with ASN 468 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401D LEU* 4.2 12.1 + - - +
464D GLU* 3.1 23.3 + - - +
465D LEU 2.9 9.6 + - - +
467D ARG* 1.3 80.8 - - - +
469D GLU* 1.3 69.2 + - - +
470D GLN* 3.5 29.7 + - - +
768D HIS* 4.4 6.1 - - - +
770D ARG* 3.1 50.0 + - - +
772D TYR* 4.1 6.5 + - - -
----------------------------------------------------------
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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