Contacts of the helix formed by residues 458 - 491 (chain A) in PDB entry 2YEV
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 GLY 458 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A LEU* 4.1 9.6 - - - -
456A ILE 3.4 0.8 + - - -
457A ALA* 1.3 72.5 - - - +
459A TRP* 1.3 65.4 + - - +
460A PRO* 3.4 3.2 - - - +
461A GLU* 3.4 19.1 + - - +
462A LEU* 3.0 34.3 + - - +
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Residues in contact with TRP 459 (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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440A LEU* 3.9 17.0 - - + +
443A LEU* 3.0 31.7 + - + +
444A GLY 3.5 4.5 - - - -
445A MET* 3.3 46.7 - - + +
446A PRO* 3.8 5.2 - - + -
449A TYR* 5.5 3.1 - + - -
452A TYR* 3.5 42.2 - + + -
453A ASN 5.0 0.2 - - - +
456A ILE* 3.3 52.8 - - + +
457A ALA 3.3 6.8 - - - -
458A GLY* 1.3 75.7 - - - +
460A PRO* 1.3 64.8 - - + +
463A ASN* 2.8 41.1 + - - +
22B VAL* 5.0 0.2 - - + -
196B PHE* 3.7 22.9 - + - -
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Residues in contact with PRO 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ALA 4.2 2.9 - - - +
56A PRO* 4.2 25.8 - - + -
452A TYR* 4.0 14.1 - - + +
453A ASN 5.3 0.2 - - - +
454A ALA* 4.6 14.4 - - + +
456A ILE 3.6 10.5 - - - +
458A GLY 3.5 4.7 - - - +
459A TRP* 1.3 96.1 - - + +
461A GLU* 1.3 71.0 + - - +
463A ASN* 3.9 0.7 - - - +
464A LEU* 3.0 31.4 + - - +
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Residues in contact with GLU 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A GLY* 3.5 28.0 + - - +
460A PRO* 1.3 92.5 - - - +
462A LEU* 1.3 64.0 + - + +
464A LEU* 3.3 7.4 + - - +
465A LEU* 3.0 29.4 + - + +
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Residues in contact with LEU 462 (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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436A PRO* 3.6 26.3 - - + +
439A ALA* 3.7 23.1 - - + -
440A LEU* 3.7 25.8 - - + -
443A LEU* 3.6 31.2 - - + -
458A GLY* 3.0 19.3 + - - +
461A GLU* 1.3 79.0 - - + +
463A ASN* 1.3 58.5 + - - +
465A LEU* 3.4 15.3 + - + +
466A SER* 3.0 28.1 + - - -
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Residues in contact with ASN 463 (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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50A ARG* 3.0 32.1 + - - +
53A LEU* 3.3 12.4 - - - +
54A ALA 4.3 1.6 - - - -
380A TYR* 5.5 0.7 - - - -
440A LEU* 3.7 13.6 - - - +
445A MET* 3.6 33.6 - - - +
452A TYR* 3.3 34.7 - - - +
459A TRP* 2.8 29.7 + - - +
460A PRO 4.0 0.7 - - - +
462A LEU* 1.3 74.4 - - - +
464A LEU* 1.3 64.9 + - - +
466A SER* 4.3 1.3 - - - -
467A THR* 3.0 22.0 + - - -
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Residues in contact with LEU 464 (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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54A ALA* 3.7 28.7 + - + +
55A VAL* 5.2 6.7 - - + -
460A PRO 3.0 18.8 + - - +
461A GLU* 3.3 7.6 + - - +
463A ASN* 1.3 73.2 - - - +
465A LEU* 1.3 66.8 + - - +
467A THR* 3.2 4.4 + - + -
468A ILE* 2.9 44.6 + - + +
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Residues in contact with LEU 465 (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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432A LEU* 3.6 26.9 - - + +
436A PRO* 4.2 13.9 - - + -
461A GLU* 3.0 17.4 + - + +
462A LEU* 3.6 22.7 - - + +
464A LEU* 1.3 77.7 - - + +
466A SER* 1.3 63.9 + - - +
468A ILE* 3.0 19.7 + - + +
469A GLY 2.9 18.7 + - - -
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Residues in contact with SER 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 3.2 24.8 + - - -
432A LEU 3.5 12.7 + - - -
433A THR* 2.7 26.3 + - - -
436A PRO* 4.4 2.4 - - - +
437A GLN* 3.0 24.0 + - - -
440A LEU* 5.4 0.9 - - - -
462A LEU 3.0 17.5 + - - -
463A ASN* 3.6 2.0 - - - -
464A LEU 3.3 0.2 - - - -
465A LEU* 1.3 75.1 - - - +
467A THR* 1.3 58.1 + - - +
469A GLY* 3.2 3.5 + - - -
470A ALA 3.0 22.7 + - - -
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Residues in contact with THR 467 (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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50A ARG* 2.5 54.5 + - + +
54A ALA* 3.5 19.0 - - + -
463A ASN 3.0 16.1 + - - -
464A LEU* 3.2 6.9 + - + -
466A SER* 1.3 73.5 - - - +
468A ILE* 1.3 65.1 + - + +
470A ALA* 3.2 2.1 + - - +
471A TYR* 3.1 47.8 + - + +
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Residues in contact with ILE 468 (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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432A LEU* 3.8 14.6 - - + -
464A LEU* 2.9 41.5 + - + +
465A LEU* 3.5 18.6 - - + +
467A THR* 1.3 75.6 - - + +
469A GLY* 1.3 63.5 + - - +
471A TYR* 3.1 13.5 + - + +
472A ILE* 3.1 29.2 + - + +
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Residues in contact with GLY 469 (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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429A GLY* 3.8 5.5 - - - -
432A LEU* 3.6 27.7 - - - +
433A THR* 2.9 15.8 + - - -
465A LEU 2.9 10.5 + - - -
466A SER 3.2 2.4 + - - -
468A ILE* 1.3 77.8 - - - +
470A ALA* 1.3 57.1 + - - +
472A ILE* 2.9 23.6 + - - +
473A LEU* 3.0 10.2 + - - +
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Residues in contact with ALA 470 (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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46A SER* 5.1 4.3 - - - +
47A LEU* 3.4 20.8 - - + +
50A ARG* 3.8 29.2 - - + -
433A THR* 2.9 14.8 + - + +
466A SER 3.0 10.6 + - - +
467A THR 3.2 8.9 + - - +
469A GLY* 1.3 74.3 - - - +
471A TYR* 1.3 57.0 + - + +
473A LEU* 3.2 11.6 + - + +
474A GLY 3.0 21.8 + - - -
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Residues in contact with TYR 471 (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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47A LEU* 3.7 29.4 - - + -
50A ARG* 5.7 0.2 - - + -
51A THR* 2.6 38.1 + - - +
467A THR* 3.1 35.2 + - + +
468A ILE* 3.5 13.9 - - + +
469A GLY 3.1 0.4 - - - -
470A ALA* 1.3 79.7 - - + +
472A ILE* 1.3 55.6 + - + +
474A GLY* 3.1 4.1 + - - +
475A LEU* 3.0 30.0 + - - +
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Residues in contact with ILE 472 (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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425A LEU* 3.7 37.7 - - + +
428A VAL* 4.5 17.5 - - + -
429A GLY* 3.8 9.9 - - - +
432A LEU* 4.1 21.1 - - + -
468A ILE* 3.1 20.3 + - + +
469A GLY* 2.9 9.3 + - - +
471A TYR* 1.3 74.4 - - + +
473A LEU* 1.3 60.2 + - - +
475A LEU* 3.2 16.6 + - + +
476A GLY* 3.0 23.6 + - - -
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Residues in contact with LEU 473 (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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391A MET* 3.9 23.6 - - + -
426A PHE* 3.5 53.6 - - + +
429A GLY* 3.8 7.9 - - - -
430A TYR* 3.6 9.6 - - - +
433A THR* 3.8 22.9 - - + +
434A PHE* 4.6 9.2 - - + -
469A GLY 3.0 11.2 + - - +
470A ALA* 3.4 11.7 - - + +
472A ILE* 1.3 74.1 - - - +
474A GLY* 1.3 65.5 + - - +
476A GLY* 3.1 2.3 + - - +
477A GLY* 2.8 19.8 + - - -
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Residues in contact with GLY 474 (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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47A LEU* 4.5 20.2 - - - +
470A ALA 3.0 14.0 + - - -
471A TYR* 3.1 6.7 + - - -
473A LEU* 1.3 74.6 - - - +
475A LEU* 1.3 62.1 + - - +
477A GLY* 2.9 12.6 + - - -
478A LEU* 3.1 18.2 + - - +
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Residues in contact with LEU 475 (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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425A LEU* 4.2 16.4 - - + -
471A TYR 3.0 17.8 + - - +
472A ILE* 3.4 20.4 - - + +
474A GLY* 1.3 73.7 - - - +
476A GLY* 1.3 64.9 + - - +
478A LEU* 3.0 24.4 + - + +
479A VAL* 3.0 24.4 + - + +
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Residues in contact with GLY 476 (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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422A HIS* 3.5 6.6 - - - -
425A LEU* 3.7 28.8 - - - +
426A PHE* 3.8 14.6 - - - -
472A ILE 3.0 12.4 + - - -
473A LEU 3.1 4.9 + - - -
475A LEU* 1.3 74.5 - - - +
477A GLY* 1.3 56.4 + - - +
479A VAL* 3.2 2.7 + - - +
480A TRP* 2.8 29.5 + - - +
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Residues in contact with GLY 477 (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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39A PHE* 6.2 0.2 - - - -
426A PHE* 3.8 7.4 - - - -
473A LEU 2.8 13.2 + - - -
474A GLY* 2.9 6.6 + - - -
476A GLY* 1.3 73.6 - - - +
478A LEU* 1.3 65.0 + - - +
480A TRP* 3.2 15.6 + - - +
481A ILE* 3.0 30.6 + - - +
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Residues in contact with LEU 478 (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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474A GLY 3.1 11.1 + - - +
475A LEU* 3.0 27.9 + - + +
477A GLY* 1.3 74.6 - - - +
479A VAL* 1.3 64.3 + - + +
481A ILE* 3.2 10.9 + - + +
482A TYR* 2.9 24.5 + - - +
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Residues in contact with VAL 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LEU* 3.8 16.8 - - + +
421A LEU* 3.9 21.8 - - + -
422A HIS* 3.8 24.7 - - - +
425A LEU* 3.7 19.7 - - + -
475A LEU* 3.0 16.8 + - + +
476A GLY* 3.5 7.4 - - - +
478A LEU* 1.3 76.7 - - + +
480A TRP* 1.3 54.7 + - - +
482A TYR* 3.5 7.7 + - + +
483A THR* 2.7 39.9 + - - +
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Residues in contact with TRP 480 (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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36A PHE* 3.6 52.3 - + + -
39A PHE* 3.8 23.3 - + - -
40A ALA* 4.3 11.9 - - + -
399A PHE* 3.4 18.0 - + - -
402A LEU* 3.6 6.3 - - + +
403A TYR* 3.8 9.2 - - - -
422A HIS* 3.3 37.4 - + + +
426A PHE* 5.4 0.2 - + - -
476A GLY 2.8 11.0 + - - +
477A GLY* 3.2 16.1 + - - +
479A VAL* 1.3 77.7 - - - +
481A ILE* 1.3 79.7 + - + +
483A THR* 3.3 5.8 + - - -
484A MET* 3.2 56.0 + - + +
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Residues in contact with ILE 481 (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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40A ALA* 5.4 6.5 - - + -
477A GLY 3.0 20.5 + - - +
478A LEU* 3.7 10.5 - - + +
480A TRP* 1.3 97.2 - - + +
482A TYR* 1.3 66.6 + - - +
484A MET* 3.3 18.0 + - + +
485A TRP* 3.0 25.3 + - + +
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Residues in contact with TYR 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LEU* 3.7 35.7 - - + -
478A LEU 2.9 17.4 + - - +
479A VAL* 3.7 8.3 - - + +
481A ILE* 1.3 75.8 - - - +
483A THR* 1.3 54.8 + - - +
485A TRP* 3.1 28.0 + + - +
486A LYS* 2.8 55.6 + - + +
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Residues in contact with THR 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A TYR* 4.3 23.2 + - + +
414A TYR* 4.3 15.2 - - + +
415A ASP 4.4 3.4 + - - +
418A LEU* 3.1 46.8 + - + +
419A GLY 4.3 8.7 - - - +
479A VAL* 2.7 23.9 + - - +
480A TRP* 3.5 8.2 - - - -
481A ILE 3.2 0.2 - - - -
482A TYR* 1.3 75.6 - - - +
484A MET* 1.3 63.0 + - + +
486A LYS* 3.7 2.0 + - - +
487A SER* 3.1 23.7 + - - -
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Residues in contact with MET 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 6.3 0.2 - - - -
402A LEU* 4.2 8.3 - - + -
403A TYR* 5.7 4.3 - - + +
406A TRP* 3.7 40.1 - - + -
480A TRP* 3.2 62.1 + - + +
481A ILE* 3.3 20.2 + - + +
483A THR* 1.3 76.3 - - + +
485A TRP* 1.3 65.7 + - - +
487A SER* 3.3 2.6 + - - -
488A LEU* 3.0 31.0 + - + +
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Residues in contact with TRP 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A ILE* 3.0 22.0 + - + +
482A TYR* 3.5 26.0 - + - +
484A MET* 1.3 76.6 - - - +
486A LYS* 1.3 82.9 + - + +
488A LEU* 3.1 9.7 + - + +
489A ARG* 3.0 70.0 + - + +
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Residues in contact with LYS 486 (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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415A ASP* 4.2 22.0 + - + +
418A LEU* 3.7 22.9 - - + -
482A TYR* 2.8 42.9 + - + +
483A THR* 3.9 4.3 - - - +
485A TRP* 1.3 87.8 - - + +
487A SER* 1.3 58.8 + - - +
489A ARG* 3.2 2.6 + - - -
490A SER* 2.8 48.3 + - - +
491A GLY 3.6 2.3 + - - -
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Residues in contact with SER 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A TRP* 2.9 29.7 + - - -
412A ARG* 3.6 12.8 - - - +
413A MET 2.7 27.6 + - - -
414A TYR* 3.9 10.5 - - - +
415A ASP 5.7 0.4 - - - +
483A THR 3.1 19.3 + - - -
484A MET 3.5 5.4 - - - -
485A TRP 3.2 0.2 - - - -
486A LYS* 1.3 77.6 - - - +
488A LEU* 1.3 58.9 + - - +
491A GLY* 2.9 26.6 + - - +
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Residues in contact with LEU 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A TRP* 3.8 27.4 - - + -
410A THR* 3.9 23.6 - - + +
412A ARG* 4.5 16.9 + - + +
484A MET* 3.0 23.0 + - + +
485A TRP* 3.7 6.3 - - - +
487A SER* 1.3 78.0 - - - +
489A ARG* 1.3 61.2 + - - +
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Residues in contact with ARG 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A TRP* 3.0 62.1 + - + +
486A LYS* 3.9 3.8 - - - +
488A LEU* 1.3 80.1 - - - +
490A SER* 1.3 67.0 + - - +
491A GLY 3.9 0.7 - - - -
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Residues in contact with SER 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A LYS* 2.8 36.3 + - - +
489A ARG* 1.3 86.3 + - - +
491A GLY* 1.3 61.4 + - - +
492A PRO* 4.0 2.3 - - - +
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Residues in contact with GLY 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ARG* 3.2 20.4 + - - +
413A MET 3.7 9.4 - - - -
486A LYS 3.6 1.0 + - - -
487A SER* 2.9 22.9 + - - -
489A ARG 3.9 0.6 - - - -
490A SER* 1.3 79.7 - - - +
492A PRO* 1.3 78.0 - - - +
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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).
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