Contacts of the helix formed by residues 516 - 546 (chain A) in PDB entry 6M0X
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 GLU 516 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515A ASN* 1.3 78.2 - - - +
517A ASP* 1.3 63.8 + - - +
518A ASP* 3.4 5.4 - - + +
519A GLU* 3.1 10.6 + - + +
520A LYS* 2.9 22.5 + - - +
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Residues in contact with ASP 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A ASN 5.5 0.4 - - - -
516A GLU* 1.3 73.4 - - - +
518A ASP* 1.3 66.4 + - - +
519A GLU 3.0 1.8 - - - -
520A LYS* 3.9 22.4 - - + +
521A LYS* 2.8 35.5 + - + +
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Residues in contact with ASP 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A GLU* 3.4 3.8 - - + +
517A ASP* 1.3 77.3 - - - +
519A GLU* 1.3 58.6 + - - +
521A LYS* 3.6 10.0 + - - +
522A ALA* 3.0 22.9 + - - +
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Residues in contact with GLU 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A ASN* 3.7 24.9 - - + +
516A GLU* 3.1 13.2 + - + +
517A ASP 3.0 0.2 - - - -
518A ASP* 1.3 77.0 - - - +
520A LYS* 1.3 57.4 + - - +
522A ALA* 2.5 38.7 + - + +
523A ILE* 2.9 12.7 + - + +
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Residues in contact with LYS 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A ASN* 3.5 30.3 - - + +
516A GLU 2.9 18.0 + - - +
517A ASP* 3.1 23.7 + - - +
519A GLU* 1.3 70.7 - - - +
521A LYS* 1.3 66.3 - - + +
522A ALA 2.8 1.1 - - - -
523A ILE* 2.9 23.8 + - + +
524A GLN* 3.4 19.0 + - - +
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Residues in contact with LYS 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A ASP* 2.8 22.9 + - + +
518A ASP* 3.8 9.4 - - - +
520A LYS* 1.3 77.7 - - - +
522A ALA* 1.3 60.9 + - - +
523A ILE 3.2 0.7 + - - -
524A GLN* 3.4 20.8 - - + +
525A LYS* 3.3 25.1 + - - +
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Residues in contact with ALA 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A ASP 3.0 12.5 + - - +
519A GLU* 2.5 25.0 + - + +
521A LYS* 1.3 80.5 - - - +
523A ILE* 1.3 56.0 + - + -
525A LYS* 4.4 5.2 - - - +
526A ILE* 3.1 30.6 - - + +
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Residues in contact with ILE 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A GLU* 4.4 11.0 - - - +
515A ASN* 4.2 22.4 - - + +
519A GLU 2.9 14.0 + - - +
520A LYS* 2.9 15.1 + - + +
522A ALA* 1.3 77.5 - - - +
524A GLN* 1.3 61.7 + - - +
525A LYS 3.3 1.6 - - - -
526A ILE* 3.2 7.9 + - - +
527A GLN* 2.9 53.0 + - + +
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Residues in contact with GLN 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A LYS* 4.9 12.3 - - + +
520A LYS* 3.4 10.6 + - - +
521A LYS* 3.4 37.8 + - + +
523A ILE* 1.3 73.0 - - + +
525A LYS* 1.3 60.6 + - - +
527A GLN* 3.7 13.0 - - - +
528A LYS* 2.7 35.0 + - - +
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Residues in contact with LYS 525 (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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521A LYS 3.3 17.1 + - - +
522A ALA* 4.5 6.5 - - - +
524A GLN* 1.3 79.6 - - - +
526A ILE* 1.3 62.9 + - + +
528A LYS* 3.6 11.2 + - + +
529A ALA* 3.0 27.0 + - + +
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Residues in contact with ILE 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A ALA* 3.1 23.1 - - + +
523A ILE* 3.2 6.7 + - - +
524A GLN 3.1 0.2 - - - -
525A LYS* 1.3 79.9 - - + +
527A GLN* 1.3 62.2 + - + +
528A LYS 3.1 1.3 - - - -
529A ALA* 3.0 9.6 + - + +
530A ASN* 2.9 40.4 + - - +
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Residues in contact with GLN 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A LYS* 3.1 37.9 + - - +
523A ILE* 2.9 41.1 + - + +
524A GLN* 4.0 8.2 - - - +
526A ILE* 1.3 76.3 - - + +
528A LYS* 1.3 59.6 + - - +
530A ASN* 3.5 1.4 + - - +
531A LYS* 3.3 17.7 + - - +
7B A 4.3 4.1 - - - -
8B G 3.3 70.4 + - - +
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Residues in contact with LYS 528 (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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341A LYS* 4.0 32.1 - - + +
342A SER* 3.7 28.5 + - - +
524A GLN 2.7 23.1 + - - +
525A LYS* 3.8 9.4 - - + +
527A GLN* 1.3 72.1 - - - +
529A ALA* 1.3 59.6 + - - +
530A ASN 3.2 0.4 - - - -
531A LYS* 3.3 4.1 + - - +
532A ASP* 2.7 56.0 + - - +
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Residues in contact with ALA 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A LYS* 3.0 17.2 + - + +
526A ILE* 3.0 12.4 + - + +
528A LYS* 1.3 78.3 - - - +
530A ASN* 1.3 64.0 + - - +
532A ASP* 3.6 9.6 - - - +
533A GLU* 3.4 24.9 + - - +
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Residues in contact with ASN 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A ILE* 2.9 28.2 + - - +
527A GLN* 3.6 7.4 - - - +
528A LYS 3.2 0.2 - - - -
529A ALA* 1.3 77.6 - - - +
531A LYS* 1.3 62.7 + - - +
532A ASP 3.3 0.5 + - - -
533A GLU* 3.4 16.0 - - - +
534A LYS* 3.1 21.1 - - - +
567A ARG* 3.2 19.3 + - - +
8B G 3.1 38.3 + - - +
9B A 3.6 14.4 + - - +
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Residues in contact with LYS 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ASP* 5.1 12.3 - - - +
341A LYS* 4.6 11.9 - - + -
527A GLN 3.3 10.7 + - - +
528A LYS* 3.3 8.2 + - - +
530A ASN* 1.3 78.5 - - - +
532A ASP* 1.3 62.8 + - - +
534A LYS* 3.6 12.9 + - + +
535A ASP* 3.2 40.1 + - - +
7B A 4.2 34.6 + - - +
8B G 4.0 17.4 + - - +
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Residues in contact with ASP 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A SER* 4.8 4.9 + - - -
528A LYS* 2.7 56.3 + - - +
529A ALA* 3.6 10.5 - - - +
530A ASN 3.1 0.6 - - - -
531A LYS* 1.3 79.1 - - - +
533A GLU* 1.3 57.3 + - - +
535A ASP* 3.5 10.3 + - - +
536A ALA* 2.9 26.8 + - - +
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Residues in contact with GLU 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A ALA 3.4 11.2 + - - +
530A ASN* 3.4 21.3 - - - +
532A ASP* 1.3 77.9 - - - +
534A LYS* 1.3 61.4 + - - +
536A ALA* 3.6 9.7 - - + +
537A ALA* 2.7 30.8 + - - +
567A ARG* 3.2 28.6 + - + +
570A HIS* 4.8 10.6 - - + +
571A GLN* 2.7 33.9 + - - +
655A THR 5.3 1.0 - - - +
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Residues in contact with LYS 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A ASN 3.1 21.3 - - - +
531A LYS* 3.7 16.6 - - + +
532A ASP 3.3 0.2 - - - -
533A GLU* 1.3 73.7 - - - +
535A ASP* 1.3 63.4 + - - +
537A ALA* 3.1 6.0 + - - +
538A MET* 2.8 38.4 + - + +
563A ALA* 5.8 3.4 - - - +
564A THR* 6.3 3.4 - - - -
567A ARG* 4.1 35.9 - - + +
8B G 2.5 34.1 + - - +
9B A 4.6 8.5 + - - +
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Residues in contact with ASP 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A LYS* 3.2 37.2 + - - +
532A ASP* 3.7 10.8 - - - +
534A LYS* 1.3 78.1 - - - +
536A ALA* 1.3 54.6 + - - +
538A MET* 3.8 7.3 - - - +
539A LEU* 2.7 40.1 + - + +
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Residues in contact with ALA 536 (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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532A ASP 2.9 19.3 + - - +
533A GLU* 3.6 11.7 - - + +
534A LYS 3.2 0.2 - - - -
535A ASP* 1.3 76.0 - - - +
537A ALA* 1.3 57.4 + - - +
539A LEU* 3.9 8.6 - - - +
540A LYS* 3.1 28.1 + - - +
570A HIS* 4.7 14.6 - - + +
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Residues in contact with ALA 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A GLU 2.7 21.5 + - - +
534A LYS* 3.5 4.5 - - - +
536A ALA* 1.3 72.7 - - - +
538A MET* 1.3 60.5 + - - +
540A LYS* 3.7 1.4 - - - +
541A ALA 2.8 23.9 + - - -
563A ALA 5.7 0.2 - - - +
566A ILE* 3.3 27.1 - - + +
567A ARG* 3.9 11.4 - - - +
569A TRP* 4.8 1.2 - - - -
570A HIS* 3.7 32.5 - - + -
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Residues in contact with MET 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A LYS* 2.8 30.4 + - + +
535A ASP* 3.8 7.0 - - - +
537A ALA* 1.3 70.8 - - - +
539A LEU* 1.3 55.2 + - - +
541A ALA* 3.2 3.4 + - - +
542A ALA* 2.8 37.5 + - - +
550A GLU* 6.2 0.2 - - - -
551A LEU* 4.3 11.9 + - + +
556A PHE* 3.5 32.5 - - + -
563A ALA* 4.0 31.9 - - + +
566A ILE* 3.8 23.3 - - + -
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Residues in contact with LEU 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A ASP* 2.7 23.2 + - + +
536A ALA* 3.9 8.3 - - - +
538A MET* 1.3 71.9 - - - +
540A LYS* 1.3 58.9 + - - +
542A ALA* 3.2 5.8 + - - +
543A ASN* 3.0 69.9 + - - +
549A ALA* 4.3 23.1 - - + +
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Residues in contact with LYS 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A ALA 3.1 16.3 + - - +
537A ALA* 3.7 4.0 - - - +
539A LEU* 1.3 77.9 - - - +
541A ALA* 1.3 66.9 + - - +
543A ASN* 3.3 6.8 + - - +
544A GLN* 2.9 49.0 + - + +
569A TRP* 4.7 6.4 - - + -
570A HIS* 3.3 37.5 + - + +
573A GLY* 5.7 1.0 - - - -
574A GLU* 2.2 41.4 + - - +
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Residues in contact with ALA 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A ALA 2.8 21.5 + - - +
538A MET 3.7 4.0 - - - +
540A LYS* 1.3 73.5 - - - +
542A ALA* 1.3 57.5 + - - +
544A GLN* 3.5 3.3 + - - +
545A TYR* 2.9 33.3 + - - +
551A LEU* 4.0 7.4 - - + -
566A ILE* 3.7 22.0 - - + -
569A TRP* 4.5 2.8 - - + -
585A ILE* 3.5 34.4 - - + +
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Residues in contact with ALA 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A MET 2.8 21.9 + - - +
539A LEU 3.4 5.2 - - - +
540A LYS 3.1 0.2 - - - -
541A ALA* 1.3 72.6 - - - +
543A ASN* 1.3 57.1 + - - +
546A ASN* 2.7 32.1 + - - +
547A GLY 3.0 3.8 + - - -
548A LYS 3.1 6.0 - - - +
549A ALA 3.6 3.6 - - - -
550A GLU* 3.3 42.0 - - - +
551A LEU* 3.7 13.8 - - - +
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Residues in contact with ASN 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A LEU* 3.0 37.4 + - - +
540A LYS* 3.3 5.4 + - - +
542A ALA* 1.3 73.2 - - - +
544A GLN* 1.3 66.4 + - + +
545A TYR 4.6 0.2 - - - +
547A GLY* 3.1 27.6 + - - +
548A LYS 2.4 40.3 + - - -
549A ALA* 3.4 8.7 - - - +
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Residues in contact with GLN 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A LYS* 2.9 49.8 + - + +
541A ALA* 3.9 4.7 - - - +
543A ASN* 1.3 78.3 - - + +
545A TYR* 1.3 60.5 + - - +
569A TRP* 4.1 12.4 - - + -
574A GLU* 3.5 19.5 + - - +
584A SER* 6.1 0.3 - - - -
585A ILE* 4.2 13.9 + - + +
586A HIS* 3.0 19.0 + - + -
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Residues in contact with TYR 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A ALA 2.9 17.2 + - - +
542A ALA 4.0 0.4 - - - +
544A GLN* 1.3 80.5 - - - +
546A ASN* 1.3 76.3 + - - +
547A GLY 3.5 0.2 + - - -
551A LEU* 3.6 22.7 - - + -
552A PRO* 4.9 3.8 - - + -
555A VAL* 4.1 23.1 - - + +
585A ILE* 3.5 14.1 - - + -
586A HIS* 3.5 39.1 - + - -
589A ILE* 4.2 10.3 - - + -
590A ASN* 2.7 42.0 + - - -
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Residues in contact with ASN 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A ALA 2.7 15.1 + - - +
545A TYR* 1.3 86.3 - - + +
547A GLY* 1.3 54.8 + - - +
548A LYS* 3.0 21.2 + - + +
550A GLU 3.6 11.5 + - - +
551A LEU* 5.0 0.7 - - + -
552A PRO* 3.3 37.8 - - + +
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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