Contacts of the helix formed by residues 512 - 536 (chain A) in PDB entry 3K5M
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 ASP 512 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A VAL* 3.9 15.2 - - + +
438A LEU* 3.8 6.8 - - + +
503A LEU 3.1 11.3 + - - +
510A PHE 3.4 1.8 + - - +
511A PHE* 1.3 77.2 - - - +
513A PRO* 1.3 66.3 - - - +
514A ARG* 2.6 72.8 + - - +
515A LEU* 2.7 48.0 + - + +
516A ALA 3.3 4.7 + - - -
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Residues in contact with PRO 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A VAL* 3.8 12.8 - - + -
395A PRO 4.0 4.7 - - - +
397A HIS* 3.5 42.0 - - + +
398A ALA 5.0 1.3 - - - +
399A SER* 3.8 11.7 - - - +
455A LEU* 4.0 15.3 - - + -
511A PHE* 3.6 21.0 - - + -
512A ASP* 1.3 91.4 - - - +
514A ARG* 1.3 55.2 + - + +
516A ALA* 4.6 1.6 - - + +
517A SER* 2.9 36.1 + - - +
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Residues in contact with ARG 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A VAL* 5.2 8.0 - - - +
438A LEU* 3.8 24.0 - - + +
442A MET* 4.1 25.6 - - - +
454A PHE 4.3 2.0 - - - +
455A LEU* 3.7 39.0 - - + +
456A ASP* 5.0 1.3 - - - -
457A ALA* 4.2 17.3 - - + +
459A PHE* 4.0 2.4 - - - -
512A ASP* 2.6 42.2 + - - +
513A PRO* 1.3 74.1 - - + +
515A LEU* 1.3 61.1 + - - +
518A SER* 3.0 29.1 + - - -
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Residues in contact with LEU 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ILE* 3.5 20.5 - - + +
434A ASP* 3.5 35.9 - - - +
435A PRO* 3.8 15.7 - - + -
438A LEU* 4.1 8.5 - - + -
459A PHE* 3.6 17.3 - - + -
503A LEU* 4.0 26.9 - - + -
510A PHE 3.2 27.1 - - - +
512A ASP* 2.7 29.4 + - + +
514A ARG* 1.3 74.5 - - - +
516A ALA* 1.3 61.3 + - - +
518A SER* 3.4 5.2 + - - -
519A ILE* 3.4 11.6 + - - +
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Residues in contact with ALA 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A SER* 3.2 22.7 - - - +
500A TYR* 4.4 20.8 - - + +
503A LEU* 4.6 4.1 + - - +
504A GLY* 3.8 28.7 - - - +
512A ASP 3.3 4.7 + - - +
513A PRO* 4.2 0.9 - - + +
515A LEU* 1.3 74.5 - - - +
517A SER* 1.3 66.3 + - - +
519A ILE* 3.0 15.6 + - - +
520A THR* 3.1 19.1 + - - +
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Residues in contact with SER 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ALA 4.6 1.7 + - - -
399A SER* 2.9 23.6 + - - -
400A PRO* 3.6 9.0 - - - +
454A PHE* 4.5 2.0 - - - -
455A LEU* 3.6 29.1 - - - +
513A PRO 2.9 16.4 + - - -
514A ARG 4.4 0.2 - - - -
516A ALA* 1.3 77.2 - - - +
518A SER* 1.3 57.8 + - - +
520A THR* 3.7 8.1 - - - -
521A MET* 2.9 46.1 + - - +
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Residues in contact with SER 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A PHE* 5.7 0.2 - - - +
433A ILE* 3.6 27.8 - - - +
453A GLY* 3.5 2.2 - - - -
454A PHE* 3.0 33.8 + - - +
457A ALA* 3.8 2.1 - - - +
459A PHE* 3.2 17.7 - - - -
514A ARG 3.0 23.8 + - - -
515A LEU 3.7 3.1 - - - -
516A ALA 3.2 0.6 - - - -
517A SER* 1.3 77.7 - - - +
519A ILE* 1.3 59.6 + - - +
522A ARG* 3.4 21.7 + - - +
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Residues in contact with ILE 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A TYR* 3.7 40.8 - - + +
427A ILE* 3.5 23.6 - - + +
428A ILE* 3.5 29.6 - - + -
433A ILE* 3.6 26.9 - - + -
500A TYR* 4.1 24.2 - - + -
503A LEU* 4.8 6.5 - - + -
515A LEU 3.4 13.2 + - - +
516A ALA* 3.0 6.3 + - - +
518A SER* 1.3 78.5 - - - +
520A THR* 1.3 64.5 + - - +
522A ARG* 3.4 2.4 + - - +
523A GLY 3.1 15.6 + - - -
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Residues in contact with THR 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A SER* 5.7 0.2 - - - -
400A PRO* 2.9 42.6 + - - +
401A GLY 3.9 8.1 - - - +
424A TYR* 3.8 24.9 + - + +
500A TYR* 3.6 34.5 - - + +
516A ALA 3.1 10.4 + - - +
517A SER 3.7 1.2 + - - -
519A ILE* 1.3 74.8 - - - +
521A MET* 1.3 66.3 + - - +
523A GLY* 3.0 3.2 + - - +
524A HIS* 3.0 29.6 + - - -
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Residues in contact with MET 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A PRO* 3.7 26.9 - - + -
454A PHE* 3.6 48.5 - - + -
455A LEU* 3.7 18.4 - - + -
517A SER* 2.9 40.6 + - - +
520A THR* 1.3 71.3 + - - +
522A ARG* 1.3 64.6 + - - +
524A HIS* 3.1 23.6 + - - +
525A GLN* 3.2 12.1 + - - +
528A ARG* 5.2 0.3 + - - -
805T G 4.1 15.3 - - + +
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Residues in contact with ARG 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ILE* 4.1 6.5 - - + -
431A PHE* 3.4 57.1 - - + +
452A GLU* 3.2 28.7 + - - +
453A GLY* 4.2 3.0 + - - -
454A PHE* 3.5 31.4 - - + -
518A SER 3.4 18.8 + - - +
519A ILE 3.4 5.3 + - - +
520A THR 3.2 0.2 - - - -
521A MET* 1.3 75.0 - - - +
523A GLY* 1.3 60.3 + - - +
525A GLN* 2.7 49.0 + - - +
526A ILE* 2.8 38.0 + - + +
584A GLN* 6.0 1.4 - - - +
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Residues in contact with GLY 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A TYR* 5.0 0.7 - - - -
423A LEU* 4.7 9.0 - - - -
424A TYR* 5.0 4.0 - - - -
427A ILE* 3.8 17.7 - - - +
519A ILE 3.1 8.0 + - - -
520A THR* 3.0 10.0 + - - -
522A ARG* 1.3 77.6 - - - +
524A HIS* 1.3 64.0 + - - +
526A ILE* 3.3 5.0 + - - +
527A MET* 3.0 31.5 + - - +
546A THR 5.3 1.3 - - - -
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Residues in contact with HIS 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A PRO* 4.0 26.2 - - + -
401A GLY 2.5 29.3 + - - -
402A GLY* 3.7 3.2 + - - -
403A TYR* 3.5 36.9 + + + -
520A THR 3.0 20.4 + - - -
521A MET* 3.1 16.2 + - + +
523A GLY* 1.3 78.5 - - - +
525A GLN* 1.3 56.5 + - - +
527A MET* 3.3 1.7 + - - +
528A ARG* 3.0 46.8 + - - +
805T G 5.8 0.2 - - - -
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Residues in contact with GLN 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A PHE* 5.3 0.9 - - - -
454A PHE* 4.9 7.4 - - + -
521A MET 3.2 7.9 + - - +
522A ARG* 2.7 47.6 + - - +
524A HIS* 1.3 80.3 - - - +
526A ILE* 1.3 63.5 + - - +
528A ARG* 3.3 29.6 + - - +
529A GLN* 3.0 25.9 + - + +
577A TRP* 5.6 8.5 - - + -
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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
----------------------------------------------------------
420A TYR* 3.6 32.1 - - + -
423A LEU* 4.3 6.7 - - + -
427A ILE* 3.8 23.3 - - + -
431A PHE* 4.3 10.5 - - + -
522A ARG* 2.8 24.1 + - + +
523A GLY* 3.8 4.7 - - - +
525A GLN* 1.3 76.4 - - + +
527A MET* 1.3 55.6 + - + +
530A THR* 2.5 36.9 + - - -
577A TRP* 3.5 35.3 - - + -
590A LEU* 3.8 30.1 - - + -
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Residues in contact with MET 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A TYR* 3.5 45.1 - - + -
420A TYR* 4.1 18.4 - - - -
423A LEU* 5.0 2.7 - - + -
523A GLY 3.0 19.7 + - - +
524A HIS 3.7 0.7 - - - +
526A ILE* 1.3 74.2 - - - +
528A ARG* 1.3 63.5 + - - +
530A THR* 3.4 3.6 + - - -
531A LYS* 3.1 21.8 + - - +
544A GLY* 4.9 0.9 - - - -
545A ASP 4.6 1.1 - - - +
546A THR 3.3 27.6 - - - +
547A ASP* 3.9 13.5 - - - -
548A SER 3.6 29.8 - - - +
549A THR* 3.7 16.2 + - - +
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Residues in contact with ARG 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A TYR* 3.9 19.3 - - + -
521A MET 5.2 0.4 + - - -
524A HIS* 3.0 39.0 + - - +
525A GLN* 3.4 38.0 - - - +
527A MET* 1.3 72.3 - - - +
529A GLN* 1.3 67.3 + - - +
531A LYS* 3.2 8.7 + - - +
532A ALA* 3.1 20.8 + - - +
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Residues in contact with GLN 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A GLN* 3.0 17.7 + - + +
526A ILE 3.9 3.1 - - - +
528A ARG* 1.3 77.3 - - - +
530A THR* 1.3 58.0 + - - +
532A ALA* 3.2 14.2 + - - +
533A LEU* 2.8 61.8 + - + +
576A TRP* 3.4 41.4 - - + -
577A TRP* 4.0 10.5 - - + -
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Residues in contact with THR 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LEU* 6.0 0.2 - - + -
420A TYR* 2.5 42.1 + - + +
526A ILE 2.5 21.2 + - - -
527A MET* 3.6 7.4 - - - -
528A ARG 3.2 0.2 - - - -
529A GLN* 1.3 77.7 - - - +
531A LYS* 1.3 61.1 + - - +
533A LEU* 3.3 10.2 + - - +
534A ILE* 3.1 27.9 + - + +
549A THR* 3.7 22.9 - - - +
573A VAL* 4.6 6.7 - - + -
577A TRP* 4.3 0.9 - - - -
592A LEU* 4.4 16.2 - - + -
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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
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403A TYR* 4.0 17.6 + - - +
405A MET* 3.8 29.6 - - - +
527A MET 3.1 13.4 + - - +
528A ARG* 3.5 10.1 - - - +
530A THR* 1.3 79.1 - - - +
532A ALA* 1.3 62.9 + - - +
534A ILE* 3.5 2.0 + - - +
535A GLU* 3.1 53.9 + - - +
541A VAL* 3.7 32.1 + - + -
549A THR* 5.0 4.0 + - - +
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Residues in contact with ALA 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A ARG 3.1 13.0 + - - +
529A GLN* 3.2 21.1 + - - +
531A LYS* 1.3 78.1 - - - +
533A LEU* 1.3 62.5 + - - +
535A GLU* 3.5 12.8 + - - +
536A ALA* 3.1 24.0 + - - +
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Residues in contact with LEU 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A GLN* 2.8 59.5 + - + +
530A THR* 3.3 8.0 + - - +
532A ALA* 1.3 77.8 - - - +
534A ILE* 1.3 61.4 + - - +
536A ALA* 3.4 9.1 - - + +
537A GLN* 3.4 25.6 + - - +
572A HIS* 4.9 13.2 + - + +
573A VAL* 4.4 27.6 - - + -
576A TRP* 3.8 46.2 - - + +
577A TRP* 4.9 2.2 - - - +
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Residues in contact with ILE 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LEU* 3.6 23.1 - - + -
530A THR* 3.1 25.1 + - + +
531A LYS 3.9 3.4 - - - +
532A ALA 3.3 0.2 - - - -
533A LEU* 1.3 75.0 - - - +
535A GLU* 1.3 58.8 + - - +
537A GLN* 2.8 26.5 + - - +
538A GLY 3.5 3.3 + - - -
539A TYR* 3.5 11.1 + - + +
541A VAL* 3.7 20.9 - - + -
549A THR* 4.8 3.8 - - + -
551A VAL* 3.7 26.0 - - + -
569A LEU* 3.3 41.5 - - + -
573A VAL* 4.9 9.2 - - + -
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Residues in contact with GLU 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ARG* 5.6 2.6 + - - -
531A LYS* 3.1 49.0 + - - +
532A ALA* 3.9 11.1 - - - +
534A ILE* 1.3 75.4 - - - +
536A ALA* 1.3 57.1 + - - +
538A GLY* 2.9 19.6 + - - -
539A TYR 3.3 19.6 + - - +
540A ASP* 5.1 0.7 - - - -
541A VAL* 4.1 14.1 + - + +
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Residues in contact with ALA 536 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A ALA 3.1 17.6 + - - +
533A LEU* 3.4 11.4 - - + +
535A GLU* 1.3 75.8 - - - +
537A GLN* 1.3 68.1 + - - +
538A GLY 3.1 1.2 + - - -
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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