Contacts of the helix formed by residues 443 - 474 (chain E) in PDB entry 2BG9
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 443 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309E ARG* 5.2 6.3 - - - -
441E LEU 2.9 12.3 + - - -
442E ILE* 1.3 64.4 - - - +
444E LYS* 1.3 65.1 + - - +
445E VAL 3.3 3.1 - - - -
446E ILE* 4.0 12.3 - - - -
447E ASP* 2.7 39.7 + - - +
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Residues in contact with LYS 444 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442E ILE* 2.6 33.6 + - + +
443E GLY* 1.3 71.4 - - - -
445E VAL* 1.3 62.3 + - + +
447E ASP* 4.0 17.4 + - - +
448E LYS* 2.6 47.2 + - + +
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Residues in contact with VAL 445 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306E VAL* 4.4 20.6 - - + -
309E ARG* 4.2 26.5 - - + +
443E GLY 3.3 0.2 - - - -
444E LYS* 1.3 83.2 - - + +
446E ILE* 1.3 52.8 + - - +
448E LYS* 3.6 3.1 - - - +
449E ALA* 2.7 36.0 + - + +
452E TRP* 4.2 9.3 + - + +
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Residues in contact with ILE 446 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E TYR 4.7 1.1 - - - +
243E PRO* 4.5 31.4 - - + -
244E ALA* 4.8 8.7 - - + +
306E VAL* 4.4 11.7 - - + -
307E SER* 5.1 10.5 - - - -
309E ARG* 2.9 34.7 - - - +
443E GLY* 3.6 11.2 + - - +
444E LYS 3.5 0.2 - - - -
445E VAL* 1.3 76.4 - - - +
447E ASP* 1.3 82.7 + - - +
449E ALA* 2.7 18.1 + - + +
450E CYS* 3.1 11.0 + - - +
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Residues in contact with ASP 447 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244E ALA* 3.7 23.7 - - - +
443E GLY* 2.7 25.4 + - - +
444E LYS* 4.0 13.3 + - - +
446E ILE* 1.3 82.5 - - - +
448E LYS* 1.3 69.1 + - + +
450E CYS* 2.9 33.7 + - - +
451E PHE* 3.5 3.8 + - - +
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Residues in contact with LYS 448 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444E LYS* 2.6 39.3 - - + +
445E VAL* 3.8 3.4 - - - +
446E ILE 3.1 0.2 - - - -
447E ASP* 1.3 83.7 - - + +
449E ALA* 1.3 50.9 + - - +
451E PHE* 3.2 20.4 + - - +
452E TRP* 2.6 68.7 + - + -
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Residues in contact with ALA 449 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E TYR* 5.1 3.6 - - + +
299E ASN* 6.0 0.9 - - - +
303E VAL* 5.6 7.4 - - + -
306E VAL* 4.2 20.0 - - + -
445E VAL* 2.7 22.8 + - + +
446E ILE* 2.7 16.0 + - - +
448E LYS* 1.3 71.3 - - - +
450E CYS* 1.3 57.1 + - - +
452E TRP* 3.0 18.7 - - + +
453E ILE* 3.0 36.7 + - + +
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Residues in contact with CYS 450 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E TYR* 2.5 35.4 + - - -
241E PHE* 2.7 53.5 - - + -
243E PRO* 4.7 1.3 - - - -
244E ALA* 5.1 5.8 - - - -
446E ILE* 3.1 8.5 + - - -
447E ASP* 2.9 16.0 + - - +
449E ALA* 1.3 78.4 - - - +
451E PHE* 1.3 58.0 + - - +
453E ILE* 2.9 11.8 - - - +
454E ALA* 2.8 27.7 + - - +
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Residues in contact with PHE 451 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241E PHE* 4.0 8.2 - + + -
447E ASP 3.5 3.6 + - - +
448E LYS* 3.2 26.3 + - - +
450E CYS* 1.3 77.2 - - - +
452E TRP* 1.4 79.6 + + - +
454E ALA* 3.4 11.2 - - + -
455E LEU* 3.1 44.7 + - + +
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Residues in contact with TRP 452 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299E ASN* 5.1 4.5 - - - +
445E VAL* 4.2 12.5 + - + +
448E LYS* 2.6 45.8 + - + +
449E ALA* 3.0 31.5 - - + +
450E CYS 3.1 0.2 - - - -
451E PHE* 1.4 86.0 - + - +
453E ILE* 1.3 61.1 + - + +
455E LEU* 4.3 1.0 - - - +
456E LEU* 2.9 30.7 + - - +
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Residues in contact with ILE 453 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237E VAL* 3.2 31.6 - - + -
240E TYR* 2.7 51.4 - - + -
299E ASN* 3.1 33.4 - - - +
303E VAL* 5.5 0.9 - - + -
449E ALA* 3.3 14.4 - - + +
450E CYS 2.9 16.2 - - - +
452E TRP* 1.3 71.9 - - + +
454E ALA* 1.3 74.1 + - - +
456E LEU* 3.4 13.9 - - + +
457E LEU* 2.3 43.9 + - + +
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Residues in contact with ALA 454 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237E VAL* 5.2 0.7 - - + -
241E PHE* 4.2 11.0 - - + -
450E CYS 2.8 16.1 + - - +
451E PHE* 3.3 21.3 - - + +
453E ILE* 1.3 87.9 - - + +
455E LEU* 1.3 52.5 + - - +
457E LEU* 2.7 29.3 - - - +
458E PHE* 2.7 16.8 + - - +
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Residues in contact with LEU 455 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451E PHE* 3.1 38.3 + - + +
452E TRP 4.5 0.9 - - - +
454E ALA* 1.3 79.2 - - - +
456E LEU* 1.3 52.2 + - - +
458E PHE* 3.1 26.2 + - + -
459E SER* 2.7 36.4 + - - +
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Residues in contact with LEU 456 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E TYR* 5.7 1.1 - - + -
295E VAL* 4.5 6.3 - - + -
299E ASN* 3.8 25.6 - - + +
452E TRP 2.9 22.4 + - - +
453E ILE* 3.4 17.3 - - + +
455E LEU* 1.3 77.5 - - - +
457E LEU* 1.3 60.2 + - + +
459E SER* 2.5 23.8 + - - +
460E LEU* 2.7 54.7 + - + +
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Residues in contact with LEU 457 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E SER* 3.7 30.7 - - - +
234E SER* 6.0 0.2 - - - -
236E VAL* 5.6 2.7 - - + -
237E VAL* 3.6 30.3 - - + -
240E TYR* 5.9 2.2 - - + -
453E ILE* 2.3 35.8 + - + +
454E ALA* 2.7 11.7 - - - +
456E LEU* 1.3 72.9 - - + +
458E PHE* 1.3 57.3 - - - +
460E LEU* 3.3 9.1 + - + +
461E GLY* 2.8 29.3 + - - -
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Residues in contact with PHE 458 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454E ALA 2.7 13.6 + - - +
455E LEU* 3.4 28.0 - - + +
457E LEU* 1.3 76.5 - - - +
459E SER* 1.3 52.3 + - - +
461E GLY* 5.1 0.7 - - - -
462E THR* 2.6 64.3 + - + -
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Residues in contact with SER 459 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455E LEU* 2.7 19.2 + - - -
456E LEU* 2.5 36.8 + - - +
458E PHE* 1.3 73.1 - - - +
460E LEU* 1.3 58.0 + - - +
461E GLY 3.1 1.3 - - - -
462E THR* 4.3 4.3 - - - -
463E LEU* 2.5 38.7 + - - +
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Residues in contact with LEU 460 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291E PHE* 5.5 3.4 - - + -
292E VAL* 4.4 30.0 - - + +
295E VAL* 3.4 46.4 - - + -
296E ILE* 4.8 3.8 - - + +
456E LEU* 2.7 53.9 + - + +
457E LEU* 3.8 9.6 - - + +
459E SER* 1.3 73.3 + - - +
461E GLY* 1.3 57.8 + - - +
463E LEU* 3.6 12.8 - - + +
464E ALA* 2.9 30.7 + - - +
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Residues in contact with GLY 461 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292E VAL* 6.1 1.1 - - - -
457E LEU 2.8 17.2 + - - -
458E PHE* 3.8 1.1 - - - -
460E LEU* 1.3 75.0 - - - +
462E THR* 1.3 58.2 + - - +
464E ALA* 3.0 4.0 + - - -
465E ILE* 2.6 46.3 + - - +
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Residues in contact with THR 462 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458E PHE* 2.6 58.5 + - + -
459E SER* 3.9 4.3 - - - -
461E GLY* 1.3 70.4 - - - +
463E LEU* 1.3 63.8 + - - +
465E ILE* 4.9 7.0 - - + +
466E PHE* 2.7 47.3 + - + +
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Residues in contact with LEU 463 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288E PHE* 5.8 2.7 - - + -
291E PHE* 3.6 36.3 - - + -
292E VAL* 5.3 2.7 - - + -
459E SER 2.5 32.3 + - - +
460E LEU* 3.6 12.6 - - + +
462E THR* 1.3 69.6 - - - +
464E ALA* 1.3 61.9 + - + +
466E PHE* 4.2 5.8 - - + +
467E LEU* 3.1 42.6 + - + +
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Residues in contact with ALA 464 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288E PHE* 4.6 17.1 - - + -
292E VAL* 4.0 23.1 - - + -
460E LEU 2.9 18.1 + - - +
461E GLY* 3.0 4.0 + - - +
463E LEU* 1.3 76.6 - - + +
465E ILE* 1.3 57.8 + - + +
466E PHE 3.1 1.1 - - - -
467E LEU* 2.9 6.9 + - - +
468E THR* 2.6 39.3 + - - +
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Residues in contact with ILE 465 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461E GLY* 2.6 31.6 + - - +
462E THR* 4.8 4.9 - - + +
464E ALA* 1.3 73.5 - - + +
466E PHE* 1.3 54.5 - - - +
468E THR* 3.1 11.4 + - - +
469E GLY* 2.7 30.5 + - - -
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Residues in contact with PHE 466 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462E THR* 2.7 44.1 + - + +
463E LEU* 4.8 4.9 - - + -
465E ILE* 1.3 76.9 - - - +
467E LEU* 1.3 70.8 + - + +
469E GLY* 2.9 16.8 + - - -
470E HIS* 3.0 13.0 + - + +
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Residues in contact with LEU 467 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288E PHE* 3.8 33.9 - - + -
463E LEU* 3.1 36.1 + - + +
464E ALA* 2.9 5.2 + - - +
466E PHE* 1.3 89.5 - - + +
468E THR* 1.3 63.2 + - - +
469E GLY 2.9 1.3 - - - -
470E HIS* 2.7 31.9 + - + +
471E LEU* 2.8 16.6 + - - +
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Residues in contact with THR 468 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E PHE* 5.7 4.5 - - + -
219E LEU* 6.5 0.4 - - + -
285E TYR* 4.8 20.1 - - + -
288E PHE* 4.9 15.0 - - - +
464E ALA* 2.6 30.3 + - - +
465E ILE* 3.7 10.2 - - - -
467E LEU* 1.3 72.7 - - - +
469E GLY* 1.3 64.2 + - - +
471E LEU* 4.0 4.8 - - - +
472E ASN* 3.5 22.3 + - + +
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Residues in contact with GLY 469 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465E ILE 2.7 15.1 + - - -
466E PHE* 2.9 8.9 + - - -
468E THR* 1.3 78.4 - - - +
470E HIS* 1.3 55.7 + - - +
472E ASN* 3.8 7.1 - - - +
473E GLN* 2.9 31.3 + - - +
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Residues in contact with HIS 470 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466E PHE* 3.0 9.0 + - + +
467E LEU* 2.7 28.2 + - + +
469E GLY* 1.3 73.1 - - - +
471E LEU* 1.3 60.2 + - + +
472E ASN 2.9 5.2 - - - -
473E GLN* 2.9 7.3 + - + +
474E VAL* 2.2 69.0 + - + +
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Residues in contact with LEU 471 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E PRO* 5.3 2.7 - - + -
136E PHE* 3.2 24.2 - - + +
137E ASP* 5.0 3.8 - - - +
284E LYS* 4.2 23.8 - - + -
285E TYR* 3.2 39.7 - - + +
288E PHE* 4.5 16.2 - - + -
467E LEU 2.8 17.1 + - - +
468E THR* 3.5 5.6 + - - +
470E HIS* 1.3 75.3 - - + +
472E ASN* 1.3 56.3 + - - +
475E PRO* 3.8 21.2 - - + +
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Residues in contact with ASN 472 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E PHE* 3.3 28.9 - - + -
215E GLN* 5.9 2.6 - - - +
217E LYS* 6.2 0.2 - - - -
468E THR* 3.5 17.2 + - + +
469E GLY* 3.8 5.7 - - - +
470E HIS 2.9 0.4 - - - -
471E LEU* 1.3 77.9 - - - +
473E GLN* 1.3 55.3 + - - +
474E VAL 3.6 1.1 - - - -
475E PRO* 4.1 0.6 - - - -
476E GLU* 2.4 74.4 + - - +
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Residues in contact with GLN 473 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469E GLY 2.9 19.9 + - - +
470E HIS* 2.9 10.3 + - + +
472E ASN* 1.3 79.6 - - - +
474E VAL* 1.3 63.7 + - - +
476E GLU* 3.4 30.6 - - - +
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Residues in contact with VAL 474 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470E HIS* 2.2 58.4 + - + +
473E GLN* 1.3 73.5 - - - +
475E PRO* 1.3 74.4 - - + +
476E GLU* 2.8 15.9 - - - +
----------------------------------------------------------
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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