Contacts of the helix formed by residues 466 - 493 (chain A) in PDB entry 4MG5
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 466 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A THR* 1.3 74.2 - - - +
467A LYS* 1.3 60.7 + - - +
469A LEU* 3.6 16.2 - - + +
470A GLU* 3.3 18.9 + - - +
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Residues in contact with LYS 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A THR* 3.0 11.8 + - - +
466A LEU* 1.3 75.8 - - - +
468A SER* 1.3 59.0 + - - +
469A LEU 2.9 4.3 - - - -
470A GLU* 2.9 24.0 + - - +
471A GLU* 3.1 17.0 + - - +
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Residues in contact with SER 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ASP* 6.0 2.0 - - - -
461A PHE* 4.6 16.2 - - - +
464A SER* 3.6 31.6 - - - -
465A THR* 3.4 6.8 + - - -
467A LYS* 1.3 77.9 - - - +
469A LEU* 1.3 64.6 + - - +
471A GLU* 3.5 15.2 - - - +
472A LYS* 3.4 19.2 + - - +
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Residues in contact with LEU 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A SER 5.7 4.3 - - - +
465A THR 3.0 20.6 - - - +
466A LEU* 3.6 16.8 - - + +
467A LYS 2.9 0.8 - - - -
468A SER* 1.3 82.2 - - - +
470A GLU* 1.3 64.0 + - - +
471A GLU 3.1 1.6 - - - -
472A LYS* 3.4 8.8 + - + +
473A ASP* 3.1 21.8 + - - +
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Residues in contact with GLU 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A LEU 3.3 9.7 + - - +
467A LYS* 2.9 12.0 + - - +
469A LEU* 1.3 77.4 - - - +
471A GLU* 1.3 68.3 + - - +
473A ASP* 3.3 9.6 + - - +
474A HIS* 3.2 20.4 + - - +
477A ARG* 4.9 2.4 + - - -
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Residues in contact with GLU 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ASP 4.7 2.0 - - - +
370A LEU* 3.8 14.0 - - + +
371A THR* 3.4 30.1 + - + +
374A ASP* 3.1 31.4 - - - +
461A PHE* 5.1 3.6 - - + -
467A LYS 3.1 15.5 + - - +
468A SER* 3.5 15.5 - - - +
469A LEU 3.1 0.2 - - - -
470A GLU* 1.3 77.7 - - - +
472A LYS* 1.3 66.8 + - - +
473A ASP 3.0 2.2 + - - -
474A HIS* 3.0 15.9 + - - +
475A ILE* 3.4 16.9 + - + +
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Residues in contact with LYS 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A VAL* 4.2 14.2 - - + +
459A TYR* 6.3 0.4 - - + -
461A PHE* 4.1 24.3 - - + -
468A SER 3.4 11.2 + - - +
469A LEU* 3.4 13.4 + - + +
471A GLU* 1.3 78.5 - - - +
473A ASP* 1.3 60.1 + - - +
475A ILE* 3.7 4.9 + - - +
476A HIS* 2.8 34.9 + - + +
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Residues in contact with ASP 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A LEU 3.1 14.1 + - - +
470A GLU* 3.4 14.1 - - - +
471A GLU 3.0 1.0 - - - -
472A LYS* 1.3 76.7 - - - +
474A HIS* 1.3 65.9 + - - +
476A HIS* 3.3 19.4 + - - +
477A ARG* 2.7 51.0 + - - +
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Residues in contact with HIS 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A SER* 3.6 22.7 - - - -
307A ALA* 5.1 0.4 - - + -
308A LEU* 3.9 28.8 - - + +
366A GLY* 4.1 5.2 + - - -
369A ASP* 3.4 27.1 + - + +
370A LEU* 4.1 20.9 - - + -
470A GLU 3.2 11.1 + - - +
471A GLU* 3.0 10.1 + - - +
473A ASP* 1.3 75.1 - - - +
475A ILE* 1.3 67.0 + - - +
477A ARG* 3.1 26.7 + - - +
478A VAL* 3.2 28.4 + - + +
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Residues in contact with ILE 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A LEU* 3.9 33.4 - - + -
374A ASP* 5.9 0.4 - - + -
378A LEU* 4.2 7.4 - - + -
454A LEU* 3.5 41.3 - - + +
458A VAL* 4.0 10.3 - - + -
461A PHE* 3.7 35.9 - - + -
471A GLU* 3.4 12.3 + - + +
472A LYS 3.8 6.3 - - - +
473A ASP 3.3 0.6 - - - -
474A HIS* 1.3 77.2 - - - +
476A HIS* 1.3 57.5 + - - +
478A VAL* 3.3 9.1 + - - +
479A LEU* 2.9 35.2 + - + +
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Residues in contact with HIS 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A ASN* 5.9 0.2 - - - -
458A VAL* 4.1 15.5 - - + +
459A TYR* 3.0 43.1 - + - -
472A LYS* 2.8 31.3 + - + +
473A ASP* 3.3 14.1 + - - +
474A HIS 3.1 1.0 - - - -
475A ILE* 1.3 77.4 - - - +
477A ARG* 1.3 57.1 + - + +
479A LEU* 3.4 15.9 + - + +
480A ASP* 2.9 38.5 + - - +
434B ARG* 3.6 29.7 + - - +
506B GLN* 5.7 3.1 - - - +
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Residues in contact with ARG 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU* 3.6 36.9 - - + +
470A GLU 4.9 1.8 + - - -
473A ASP* 2.7 39.8 + - - +
474A HIS* 3.1 25.8 + - - +
476A HIS* 1.3 75.2 - - + +
478A VAL* 1.3 65.9 + - - +
480A ASP* 3.3 12.2 + - - +
481A LYS* 3.0 21.3 + - - +
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Residues in contact with VAL 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ALA* 4.6 6.7 - - + -
308A LEU* 4.1 7.9 - - + -
315A MET* 5.2 7.6 - - + -
364A VAL* 5.9 0.2 - - + -
365A PRO* 3.4 23.6 - - + +
366A GLY* 4.5 4.9 - - - -
454A LEU* 3.4 25.1 - - + -
474A HIS* 3.2 41.6 + - + +
475A ILE* 3.6 8.5 - - - +
477A ARG* 1.3 73.3 - - - +
479A LEU* 1.3 64.4 + - - +
481A LYS* 3.0 18.2 + - - +
482A ILE* 3.0 18.9 + - + +
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Residues in contact with LEU 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A ILE* 3.9 38.1 - - + +
454A LEU* 3.8 24.9 - - + +
455A ASN* 4.3 22.7 - - + +
458A VAL* 5.1 1.6 - - + -
475A ILE* 2.9 33.5 + - + +
476A HIS* 3.6 23.6 - - + +
478A VAL* 1.3 75.6 - - - +
480A ASP* 1.3 63.8 + - - +
482A ILE* 3.0 17.4 + - + +
483A THR* 3.0 17.0 + - - -
509B LEU* 4.4 13.5 - - + -
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Residues in contact with ASP 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A HIS* 2.9 25.8 + - - +
477A ARG* 3.5 13.1 - - - +
478A VAL 3.2 0.2 - - - -
479A LEU* 1.3 77.7 - - - +
481A LYS* 1.3 62.3 + - - +
483A THR* 3.3 10.2 + - - -
484A ASP* 3.0 29.5 + - - +
502B GLN* 3.7 30.8 + - - +
506B GLN* 2.9 37.4 + - - +
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Residues in contact with LYS 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ALA 5.4 4.9 - - - +
308A LEU* 5.5 7.6 - - + +
310A LEU 6.0 1.8 - - - +
315A MET* 4.2 18.8 - - + -
477A ARG 3.0 11.7 + - - +
478A VAL* 3.0 15.6 + - - +
480A ASP* 1.3 77.8 - - - +
482A ILE* 1.3 56.3 + - - +
484A ASP* 3.3 13.6 + - - +
485A THR* 2.8 29.8 + - - -
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Residues in contact with ILE 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A MET* 4.6 19.7 - - + -
319A LEU* 5.3 2.0 - - + -
364A VAL* 5.8 1.3 - - + -
447A CYS* 3.8 26.9 - - + +
450A SER* 3.9 25.6 - - - -
451A ILE* 3.6 34.8 - - + +
454A LEU* 4.0 24.2 - - + -
478A VAL* 3.0 13.0 + - + +
479A LEU* 3.0 9.5 + - - +
481A LYS* 1.3 73.8 - - - +
483A THR* 1.3 61.1 + - - +
485A THR* 3.2 7.8 + - - -
486A LEU* 2.9 27.4 + - - +
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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
----------------------------------------------------------
451A ILE* 5.3 4.4 - - - +
479A LEU 3.0 13.3 + - - -
480A ASP* 3.3 13.2 + - - -
482A ILE* 1.3 74.3 - - - +
484A ASP* 1.3 65.1 + - - +
486A LEU* 3.2 11.9 + - - +
487A ILE* 3.0 22.2 + - - +
504A LEU* 3.9 14.0 - - + +
508A LEU* 5.5 0.9 - - - +
501B HIS* 3.4 40.8 - - + +
502B GLN* 4.2 3.6 - - - -
505B ALA* 3.3 24.1 - - + +
509B LEU* 5.7 2.6 - - - +
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Residues in contact with ASP 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ALA* 5.3 2.5 - - + -
480A ASP 3.0 13.0 + - - +
481A LYS* 3.4 13.7 - - - +
483A THR* 1.3 75.2 - - - +
485A THR* 1.3 57.9 + - - +
487A ILE* 3.4 3.1 + - - +
488A HIS* 2.9 30.5 + - - +
498B GLN* 3.9 13.9 + - - +
501B HIS* 2.8 35.8 + - + -
502B GLN* 3.1 25.1 + - - +
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Residues in contact with THR 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ALA* 3.7 18.0 - - + +
315A MET* 3.6 24.5 - - + +
316A VAL* 3.4 32.3 - - + -
447A CYS* 3.8 15.9 - - - -
481A LYS 2.8 15.4 + - - -
482A ILE* 3.3 11.7 - - - -
484A ASP* 1.3 73.4 - - - +
486A LEU* 1.3 65.2 + - - +
488A HIS* 3.3 8.0 + - + +
489A LEU* 3.0 23.2 + - + +
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Residues in contact with LEU 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A GLU* 4.0 24.7 - - + +
447A CYS* 3.6 25.8 - - + -
448A LEU* 4.6 6.7 - - + -
451A ILE* 4.0 25.4 - - + -
482A ILE 2.9 14.3 + - - +
483A THR* 3.2 10.1 + - - +
485A THR* 1.3 77.4 - - - +
487A ILE* 1.3 62.3 + - - +
489A LEU* 3.2 8.7 + - + +
490A MET* 3.1 31.3 + - + +
504A LEU* 3.7 28.3 - - + -
507A LEU* 4.3 17.7 - - + -
508A LEU* 4.5 7.6 - - + -
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Residues in contact with ILE 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A THR 3.0 17.4 + - - +
484A ASP 3.7 6.7 - - - +
486A LEU* 1.3 74.6 - - - +
488A HIS* 1.3 64.2 + - - +
490A MET* 3.0 7.0 + - - +
491A ALA* 2.8 24.2 + - + +
497A LEU* 6.2 0.9 - - + -
500A GLN* 3.4 48.6 - - + +
501A HIS* 4.3 5.4 - - + +
504A LEU* 4.0 20.0 - - + -
501B HIS* 3.6 42.2 - - + +
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Residues in contact with HIS 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ALA* 3.4 28.6 - - + +
313A ASP* 3.0 34.6 + - - -
316A VAL* 5.7 0.7 - - + -
484A ASP 2.9 14.5 + - - +
485A THR 3.3 9.6 - - - +
487A ILE* 1.3 77.8 - - - +
489A LEU* 1.3 74.0 + - + +
491A ALA* 3.4 5.9 + - - +
492A LYS* 3.0 47.1 + - + +
----------------------------------------------------------
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Residues in contact with LEU 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ASP* 5.8 1.1 - - - +
316A VAL* 4.1 19.7 - - + -
443A GLU* 3.6 51.6 - - + +
444A GLU* 4.0 15.0 - - + +
447A CYS* 4.3 12.8 - - - -
485A THR 3.0 18.3 + - - +
486A LEU* 3.5 9.2 - - - +
487A ILE 3.2 0.2 - - - -
488A HIS* 1.3 84.5 - - + +
490A MET* 1.3 64.5 + - + +
492A LYS* 3.3 7.2 + - + +
493A ALA* 3.0 23.3 + - - +
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Residues in contact with MET 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A GLU* 4.2 13.5 - - - +
486A LEU* 3.1 28.2 + - + +
487A ILE* 3.0 7.7 + - - +
489A LEU* 1.3 76.1 - - + +
491A ALA* 1.3 61.8 + - - +
493A ALA* 3.3 10.6 + - - -
495A LEU* 3.2 34.9 + - + +
500A GLN* 3.3 39.5 - - + +
503A ARG* 3.8 19.7 - - + -
504A LEU* 3.6 21.1 - - + +
507A LEU* 3.4 34.1 - - + -
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Residues in contact with ALA 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A ILE* 2.8 18.3 + - + +
488A HIS* 3.7 7.4 - - - +
490A MET* 1.3 74.7 - - - +
492A LYS* 1.3 60.6 + - + +
494A GLY* 2.9 21.8 + - - -
495A LEU 4.5 1.4 - - - +
500A GLN* 3.6 27.5 - - - +
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Residues in contact with LYS 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A HIS* 3.0 43.4 + - + +
489A LEU* 3.6 9.6 - - + +
491A ALA* 1.3 76.1 - - + +
493A ALA* 1.3 59.9 + - - +
494A GLY* 2.9 6.9 + - - -
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Residues in contact with ALA 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A LEU 3.0 15.5 + - - +
490A MET* 3.7 7.9 - - - +
491A ALA 3.2 0.6 - - - -
492A LYS* 1.3 73.8 - - - +
494A GLY* 1.3 60.6 + - - +
495A LEU* 3.5 16.7 + - + +
----------------------------------------------------------
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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