Contacts of the helix formed by residues 444 - 468 (chain A) in PDB entry 4N78
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 THR 444 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A TYR* 1.3 76.3 - - - +
445A SER* 1.3 65.0 + - - +
446A GLU* 3.7 6.9 + - - +
447A GLU* 2.8 42.3 + - - +
448A LYS* 3.0 22.6 + - - +
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Residues in contact with SER 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A THR* 1.3 74.2 - - - +
446A GLU* 1.3 66.7 + - - +
448A LYS* 3.3 3.2 + - - +
449A PHE* 3.0 34.9 + - - -
651A HIS* 2.9 41.8 + - - -
655A THR* 4.9 2.3 - - - +
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Residues in contact with GLU 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ILE* 4.8 10.4 - - + +
444A THR* 3.2 6.7 + - - +
445A SER* 1.3 78.5 + - - +
447A GLU* 1.3 61.3 + - + +
449A PHE* 3.3 24.9 + - - +
450A ALA* 2.9 29.8 + - - +
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Residues in contact with GLU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A PRO* 5.4 7.1 - - - +
345A ILE* 4.3 26.9 - - + +
411A VAL* 5.7 1.1 - - - +
415A LYS* 2.8 32.0 + - - -
442A ASN 3.9 0.3 - - - +
443A TYR* 3.4 16.7 - - + -
444A THR* 2.8 49.4 + - - +
446A GLU* 1.3 77.0 - - + +
448A LYS* 1.3 58.6 + - - +
450A ALA* 3.3 6.1 + - - +
451A LEU* 3.0 36.1 + - + +
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Residues in contact with LYS 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ARG 5.2 5.3 + - - +
443A TYR* 3.6 28.4 + - + -
444A THR 3.0 19.2 + - - +
445A SER* 3.3 6.3 + - - +
447A GLU* 1.3 74.2 - - - +
449A PHE* 1.3 66.6 + - - +
451A LEU* 3.7 1.1 + - - -
452A VAL* 3.3 28.4 + - - +
647A ILE* 3.8 31.5 + - + +
648A LEU* 3.8 20.9 - - + +
651A HIS* 3.2 48.9 + - + +
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Residues in contact with PHE 449 (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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445A SER* 3.0 27.4 + - - -
446A GLU* 3.7 28.0 - - - +
448A LYS* 1.3 76.1 - - - +
450A ALA* 1.3 63.7 + - - +
452A VAL* 3.5 3.0 + - - +
453A GLU* 3.1 28.1 + - - +
651A HIS* 3.2 27.1 - + - -
652A ILE* 4.3 13.9 - - + -
655A THR* 3.3 27.4 - - + -
657A GLU* 3.5 32.8 - - + -
659A SER* 5.9 0.2 - - - -
660A MET* 3.4 29.2 - - + +
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Residues in contact with ALA 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ILE* 4.6 15.5 - - + -
349A MET* 3.8 28.0 - - + +
407A HIS* 6.1 0.7 - - - +
446A GLU 2.9 17.5 + - - +
447A GLU* 3.3 7.4 + - - +
449A PHE* 1.3 74.9 - - - +
451A LEU* 1.3 66.2 + - + +
453A GLU* 3.1 17.2 + - - +
454A VAL* 3.0 26.1 + - - +
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Residues in contact with LEU 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ILE* 6.2 2.0 - - + -
407A HIS* 4.8 11.2 - - + +
408A VAL* 4.4 33.7 - - + +
411A VAL* 4.5 17.3 - - + -
412A TYR* 6.2 2.0 - - + +
443A TYR* 3.5 38.8 - - + +
447A GLU* 3.0 19.2 + - + +
448A LYS 4.0 4.3 - - - +
450A ALA* 1.3 78.0 - - + +
452A VAL* 1.3 57.4 + - - +
454A VAL* 3.3 5.4 + - - +
455A ILE* 2.9 37.9 + - + +
644A MET* 4.7 5.6 - - + -
648A LEU* 4.3 22.7 - - + -
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Residues in contact with VAL 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A LYS 3.3 17.5 + - - +
449A PHE* 3.8 4.7 - - - +
450A ALA 3.3 0.4 - - - -
451A LEU* 1.3 73.0 - - - +
453A GLU* 1.3 60.8 + - - +
455A ILE* 3.7 6.9 - - + +
456A ALA* 2.8 29.2 + - + +
648A LEU* 3.7 38.8 - - + +
652A ILE* 3.9 17.7 - - + -
660A MET* 4.8 1.8 - - - -
663A TYR* 3.8 35.7 - - + +
666A TYR* 5.3 0.2 - - + -
667A SER* 4.1 15.9 - - - +
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Residues in contact with GLU 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A MET* 3.6 12.7 - - + +
353A ARG* 3.0 44.0 + - - +
449A PHE* 3.1 19.6 + - - +
450A ALA* 3.1 18.4 + - - +
452A VAL* 1.3 75.8 - - - +
454A VAL* 1.3 57.8 + - - +
456A ALA* 3.1 3.6 + - - +
457A MET* 2.8 38.4 + - + +
660A MET* 3.6 24.1 - - + +
663A TYR* 4.0 18.0 + - + -
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Residues in contact with VAL 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A MET* 3.6 24.2 - - + -
352A ILE* 4.1 9.6 - - + -
404A TRP* 3.6 32.3 - - + +
407A HIS* 3.9 18.8 - - + +
408A VAL* 3.5 23.8 - - + -
450A ALA 3.0 14.8 + - - +
451A LEU* 3.7 5.8 - - - +
453A GLU* 1.3 74.5 - - - +
455A ILE* 1.3 53.0 + - - +
457A MET* 3.1 9.5 + - + +
458A ILE* 2.8 39.6 + - + +
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Residues in contact with ILE 455 (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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408A VAL* 4.3 15.5 - - + -
451A LEU* 2.9 23.0 + - + +
452A VAL* 3.7 8.5 - - + +
454A VAL* 1.3 75.3 - - - +
456A ALA* 1.3 58.2 + - - +
458A ILE* 3.5 8.8 + - - +
459A LYS* 3.0 42.7 + - + +
618A LEU* 4.0 14.4 - - + -
621A LEU* 4.3 9.0 - - + -
648A LEU* 4.0 19.3 - - + -
666A TYR 3.9 25.4 - - - +
667A SER* 4.7 2.0 - - - -
670A LEU* 3.8 28.9 - - + -
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Residues in contact with ALA 456 (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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452A VAL 2.8 20.8 + - - +
453A GLU 3.5 1.1 - - - +
455A ILE* 1.3 71.2 - - - +
457A MET* 1.3 61.6 + - - +
460A GLY* 2.8 27.5 + - - -
663A TYR* 3.4 29.2 - - + -
666A TYR* 3.5 40.2 - - + -
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Residues in contact with MET 457 (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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349A MET* 3.9 15.7 - - + -
352A ILE* 3.6 26.2 - - + -
353A ARG* 4.2 16.4 - - + -
356A HIS* 3.4 49.4 + - + +
404A TRP* 3.4 20.6 - - + -
453A GLU* 2.8 35.8 + - + +
454A VAL* 3.7 7.9 - - - +
456A ALA* 1.3 73.6 - - - +
458A ILE* 1.3 66.6 + - - +
460A GLY* 4.0 0.6 - - - -
461A LEU* 3.1 18.5 + - - +
663A TYR* 5.4 7.2 - - + -
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Residues in contact with ILE 458 (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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401A LEU* 3.5 8.7 - - + +
404A TRP* 3.5 30.5 - - + +
405A SER* 3.3 45.3 - - - +
408A VAL* 4.4 3.6 - - + -
454A VAL* 2.8 27.7 + - + +
455A ILE* 3.6 4.3 - - - +
457A MET* 1.3 77.8 - - - +
459A LYS* 1.3 62.3 + - + +
460A GLY 3.2 0.3 + - - -
461A LEU 3.2 0.2 + - - -
462A GLN* 2.9 27.4 + - - +
616A CYS* 3.9 26.9 - - + +
618A LEU* 4.2 21.1 - - + -
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Residues in contact with LYS 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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455A ILE* 3.0 27.2 + - + +
458A ILE* 1.3 83.2 - - + +
460A GLY* 1.3 62.0 + - - +
462A GLN* 3.5 20.9 + - - +
463A VAL* 3.2 28.3 + - + +
616A CYS 5.5 3.1 + - - +
618A LEU* 4.5 5.7 - - + +
666A TYR* 3.6 44.6 - - + +
669A ASP* 2.8 34.3 + - + +
670A LEU* 4.1 8.1 - - - -
673A ASP* 2.6 36.5 + - - -
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Residues in contact with GLY 460 (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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356A HIS* 6.0 1.3 - - - -
360A ILE* 5.7 0.9 - - - -
456A ALA 2.8 19.0 + - - -
457A MET* 4.0 1.3 - - - -
459A LYS* 1.3 77.5 - - - +
461A LEU* 1.3 61.5 + - - +
463A VAL* 3.2 16.4 + - - +
464A LEU* 3.4 17.0 + - - +
666A TYR* 4.1 15.9 - - - -
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Residues in contact with LEU 461 (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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356A HIS* 5.5 0.6 + - - -
359A PHE* 3.9 29.2 - - + -
360A ILE* 4.2 21.3 - - + +
363A LEU* 4.0 13.2 - - + -
397A GLY 4.2 3.4 - - - +
400A LEU* 4.1 12.8 - - + -
401A LEU* 3.6 28.7 - - + -
404A TRP* 4.0 16.2 - - + -
457A MET 3.1 18.3 + - - +
460A GLY* 1.3 71.9 - - - +
462A GLN* 1.3 60.5 + - - +
464A LEU* 3.0 9.8 + - + +
465A MET* 2.8 49.2 + - + +
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Residues in contact with GLN 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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401A LEU* 4.1 5.6 - - - +
458A ILE 2.9 15.9 + - - +
459A LYS* 3.5 24.8 + - - +
461A LEU* 1.3 77.2 - - - +
463A VAL* 1.3 57.6 + - + +
465A MET* 3.8 6.2 - - - +
466A GLY* 3.0 25.3 + - - -
612A LEU* 3.9 14.8 - - + +
613A GLN* 4.4 21.2 - - - +
616A CYS* 3.6 39.6 + - - +
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Residues in contact with VAL 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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459A LYS 3.2 15.7 + - - +
460A GLY* 3.2 10.9 + - - +
461A LEU 3.1 0.4 - - - -
462A GLN* 1.3 76.5 - - + +
464A LEU* 1.3 64.7 + - + +
466A GLY* 3.4 1.8 + - - -
467A ARG* 3.0 57.6 + - + +
666A TYR* 5.9 2.7 - - + -
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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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360A ILE* 3.6 40.2 - - + -
363A LEU* 4.2 16.2 - - + -
364A ALA* 6.1 3.4 - - + +
460A GLY 3.7 12.3 - - - +
461A LEU* 3.0 10.8 + - + +
463A VAL* 1.3 75.4 - - + +
465A MET* 1.3 65.6 + - - +
467A ARG* 3.2 33.0 + - - +
468A MET* 3.2 26.9 + - - +
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Residues in contact with MET 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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359A PHE* 4.2 3.8 - - - -
363A LEU* 4.0 13.2 - - - -
394A ALA* 3.6 26.2 - - - +
397A GLY* 3.7 21.1 - - - -
398A LEU* 3.9 8.5 - - + +
401A LEU* 4.1 8.1 - - + -
461A LEU* 2.8 48.4 + - + +
462A GLN 3.8 3.8 - - - +
464A LEU* 1.3 72.8 - - - +
466A GLY* 1.3 58.2 + - - +
468A MET* 2.9 19.6 + - - +
469A GLU 3.2 8.3 + - - -
472A PHE* 3.9 16.9 - - + -
608A PHE* 3.8 26.7 - - + -
612A LEU* 3.9 15.3 - - + -
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Residues in contact with GLY 466 (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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462A GLN 3.0 18.4 + - - -
463A VAL* 3.7 2.0 - - - -
465A MET* 1.3 77.2 - - - +
467A ARG* 1.3 61.7 + - - +
469A GLU* 3.1 27.4 + - - +
608A PHE* 5.0 0.2 - - - -
612A LEU* 3.8 13.4 - - - +
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Residues in contact with ARG 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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463A VAL* 3.0 40.7 + - + +
464A LEU* 3.2 33.9 + - - +
466A GLY* 1.3 74.6 - - - +
468A MET* 1.3 67.0 + - + +
469A GLU 3.3 0.6 + - - -
470A SER* 4.9 3.3 + - - -
471A VAL* 6.0 0.2 - - - +
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Residues in contact with MET 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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363A LEU* 4.5 17.5 - - + -
366A TYR* 3.2 29.2 - - - +
367A SER* 3.5 20.2 - - - +
390A LEU* 5.6 1.1 - - - -
464A LEU 3.2 13.7 + - - +
465A MET 2.9 10.8 + - - +
467A ARG* 1.3 86.4 - - + +
469A GLU* 1.3 56.9 + - - +
470A SER 3.4 2.2 - - - -
471A VAL* 3.2 36.6 + - + +
472A PHE* 2.8 52.4 + - + +
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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