Contacts of the helix formed by residues 532 - 558 (chain A) in PDB entry 4DKT
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 ASN 532 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A TYR* 4.3 0.5 + - - -
524A GLN* 6.1 1.0 - - - +
528A ASN 3.3 12.2 + - - +
529A ILE* 3.0 19.4 + - - +
530A LEU 3.2 1.3 - - - -
531A SER* 1.3 76.6 - - - +
533A LYS* 1.3 64.2 + - - +
534A THR* 3.2 17.9 + - - +
535A LEU* 3.5 32.1 + - + +
536A ARG* 3.4 21.1 + - - +
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Residues in contact with LYS 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A SER 3.5 11.1 + - - +
532A ASN* 1.3 73.0 + - - +
534A THR* 1.3 65.6 + - - +
536A ARG* 3.1 13.4 + - - +
537A GLU* 2.9 32.7 + - - +
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Residues in contact with THR 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A ASN* 3.2 10.8 + - - +
533A LYS* 1.3 74.8 - - - +
535A LEU* 1.3 67.6 + - - +
537A GLU* 3.0 13.6 + - - +
538A HIS* 2.9 55.1 + - + +
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Residues in contact with LEU 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A TYR* 3.4 9.4 - - - +
524A GLN* 6.1 0.7 - - - +
529A ILE* 4.0 32.8 - - + +
532A ASN* 3.5 32.8 + - - +
534A THR* 1.3 80.6 - - - +
536A ARG* 1.3 55.6 + - - +
538A HIS* 3.2 7.6 + - + +
539A ASN* 2.7 57.5 + - - +
570A LEU* 5.0 4.5 - - + -
571A PHE 3.5 14.1 - - - +
572A LYS* 5.0 5.2 - - + -
582A PHE* 4.1 35.4 - - + -
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Residues in contact with ARG 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A TYR* 3.3 42.7 + - + +
502A GLN* 4.8 8.3 + - - +
530A LEU* 2.3 42.8 + - - +
531A SER 5.1 0.4 - - - -
532A ASN 3.4 12.0 + - - +
533A LYS* 3.1 17.4 + - - +
534A THR 3.0 0.8 - - - -
535A LEU* 1.3 78.3 - - - +
537A GLU* 1.3 60.0 + - + +
539A ASN* 3.8 0.7 - - - +
540A SER* 2.9 30.9 + - - +
708A EDO 3.9 24.3 + - - +
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Residues in contact with GLU 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A LYS* 2.9 23.6 + - - +
534A THR* 3.0 12.5 + - - +
536A ARG* 1.3 74.1 - - - +
538A HIS* 1.3 71.6 + - + +
540A SER* 2.9 18.1 + - - -
541A PHE* 2.9 14.4 + - - +
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Residues in contact with HIS 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A THR* 2.9 39.9 + - + +
535A LEU* 3.3 11.6 - - - +
537A GLU* 1.3 85.9 - - + +
539A ASN* 1.3 60.7 + - - +
541A PHE* 3.2 4.2 + - - +
542A VAL* 2.9 32.5 + - + +
571A PHE 4.6 4.7 - - - +
572A LYS* 4.2 6.4 - - + +
573A LEU* 3.3 62.5 + - + +
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Residues in contact with ASN 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A PRO* 3.7 21.5 - - + +
498A TYR* 3.6 24.9 + - + -
535A LEU* 2.7 54.5 + - - +
536A ARG 4.2 0.7 - - - +
538A HIS* 1.3 72.0 - - - +
540A SER* 1.3 59.6 + - - +
542A VAL* 3.9 6.1 - - - +
543A GLU* 2.9 28.5 + - - +
570A LEU* 3.7 8.8 - - - +
571A PHE* 2.7 36.7 + - - +
708A EDO 3.7 5.8 + - - +
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Residues in contact with SER 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A ARG* 2.9 15.5 + - - +
537A GLU* 2.9 13.0 + - - -
539A ASN* 1.3 77.2 - - - +
541A PHE* 1.3 57.7 + - - +
543A GLU* 3.2 11.5 + - - +
544A ARG* 2.9 31.3 + - - +
708A EDO 3.8 18.5 + - - -
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Residues in contact with PHE 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A TYR* 5.0 5.8 - + - -
466A TRP* 4.6 13.5 - + + -
537A GLU 2.9 11.1 + - - +
538A HIS* 3.5 6.5 - - - +
540A SER* 1.3 74.0 - - - +
542A VAL* 1.3 70.3 + - + +
544A ARG* 2.8 27.1 + - + +
545A CYS* 3.0 37.9 + - - -
573A LEU* 3.7 36.8 - - + -
577A SER* 4.7 6.7 - - - -
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Residues in contact with VAL 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A TRP* 3.5 27.1 - - + -
494A PRO* 4.1 4.3 - - + -
538A HIS 2.9 21.1 + - - +
539A ASN* 3.9 6.5 - - - +
541A PHE* 1.3 78.4 - - + +
543A GLU* 1.3 63.8 + - - +
545A CYS* 3.0 8.2 + - - +
546A ILE* 2.9 44.6 + - + +
571A PHE* 3.7 36.6 - - + -
573A LEU* 4.0 21.3 - - + -
579A ALA* 4.1 0.4 - - + -
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Residues in contact with GLU 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A PRO* 4.7 11.8 - - + +
495A ARG* 2.9 53.7 + - - +
539A ASN 2.9 21.2 + - - +
540A SER* 3.2 10.8 + - - +
541A PHE 3.1 0.2 - - - -
542A VAL* 1.3 76.8 - - - +
544A ARG* 1.3 66.5 + - + +
546A ILE* 4.0 4.3 - - - +
547A ASP* 2.9 46.7 + - - +
708A EDO 3.7 14.4 + - - +
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Residues in contact with ARG 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A SER 2.9 20.8 + - - +
541A PHE* 2.8 20.9 + - + +
543A GLU* 1.3 79.5 - - - +
545A CYS* 1.3 57.0 + - - +
547A ASP* 3.2 8.0 + - - +
548A TRP* 2.9 28.4 + - - +
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Residues in contact with CYS 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A TYR* 4.3 13.9 - - + -
466A TRP* 3.6 39.7 - - + +
541A PHE* 3.0 52.4 + - - -
542A VAL 3.0 6.3 + - - +
544A ARG* 1.3 73.4 - - - +
546A ILE* 1.3 66.8 + - - +
548A TRP* 3.1 10.4 + - - +
549A ASN* 3.1 27.8 + - - -
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Residues in contact with ILE 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A TRP* 3.6 22.9 - - + -
475A PHE* 4.4 11.4 - - + -
491A LEU* 4.3 23.7 - - + +
492A ALA* 3.5 39.7 - - + +
494A PRO* 4.1 12.3 - - + -
542A VAL* 2.9 32.9 + - + +
543A GLU* 4.0 3.4 - - - +
545A CYS* 1.3 74.8 - - - +
547A ASP* 1.3 60.7 + - - +
549A ASN* 3.3 11.0 + - - +
550A ARG* 2.9 24.0 + - + +
571A PHE* 4.3 2.0 - - + -
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Residues in contact with ASP 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A GLU* 2.9 45.8 + - - +
544A ARG* 3.5 7.0 - - - +
546A ILE* 1.3 78.5 - - - +
548A TRP* 1.3 65.9 + - - +
550A ARG* 2.8 34.1 + - + +
551A GLU* 3.0 20.5 + - + +
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Residues in contact with TRP 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A CYS* 3.8 22.4 - - - -
463A TYR* 4.1 24.5 - + + -
544A ARG 2.9 12.8 + - - +
545A CYS* 3.3 12.1 - - - +
547A ASP* 1.3 74.5 - - - +
549A ASN* 1.3 59.0 + - - +
551A GLU* 3.4 7.6 + - + +
552A LEU* 3.0 45.9 + - + +
709A EDO 4.0 7.9 + - - -
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Residues in contact with ASN 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A LEU* 3.1 17.2 - - + +
463A TYR* 2.7 54.1 + - - +
466A TRP* 3.9 4.2 - - - +
475A PHE* 3.5 30.6 - - + -
491A LEU* 5.7 0.9 - - + -
545A CYS 3.1 24.7 + - - -
546A ILE* 3.5 8.0 - - - +
548A TRP* 1.3 78.0 - - - +
550A ARG* 1.3 57.4 + - - +
552A LEU* 3.3 7.5 - - - +
553A LEU* 2.9 36.4 + - + +
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Residues in contact with ARG 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A LEU* 6.1 0.2 - - - -
491A LEU* 3.8 29.0 - - + +
546A ILE 2.9 13.5 + - - +
547A ASP* 2.8 28.6 + - - +
549A ASN* 1.3 78.3 - - - +
551A GLU* 1.3 67.5 + - - +
553A LEU* 3.5 4.8 + - - +
554A LYS* 2.9 34.9 + - + +
561A GLU* 2.5 43.4 + - - -
564A ILE* 3.8 26.2 + - + +
566A ASP* 2.9 41.4 + - - -
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Residues in contact with GLU 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A ASP* 3.0 17.4 + - + +
548A TRP* 3.9 8.5 - - + +
550A ARG* 1.3 82.1 - - - +
552A LEU* 1.3 67.2 + - - +
554A LYS* 3.1 38.6 + - - +
555A ARG* 2.9 27.7 + - - +
561A GLU* 5.0 0.3 - - - +
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Residues in contact with LEU 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A VAL* 5.4 0.2 - - + -
461A LYS 3.7 23.6 - - - +
462A LEU* 4.1 19.1 - - + -
548A TRP* 3.0 39.6 + - + +
549A ASN* 3.3 17.0 - - - +
551A GLU* 1.3 75.2 - - - +
553A LEU* 1.3 59.1 + - - +
555A ARG* 3.0 39.0 + - - +
556A GLU* 2.9 37.3 + - + +
709A EDO 4.3 9.2 - - - +
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Residues in contact with LEU 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A LEU* 4.2 13.0 - - + -
460A VAL* 5.5 2.0 - - + -
462A LEU* 3.7 31.0 - - + -
476A LEU* 3.9 22.7 - - + -
478A PHE* 5.6 0.4 - - + -
489A LEU* 3.6 33.0 - - + -
491A LEU* 4.5 10.1 - - + -
549A ASN* 2.9 25.9 + - + +
550A ARG* 3.8 4.3 - - - +
552A LEU* 1.3 70.3 - - - +
554A LYS* 1.3 61.7 + - + +
556A GLU* 4.6 2.7 - - + +
557A LEU* 2.9 60.0 + - + +
559A LEU* 4.1 3.3 - - + +
564A ILE* 6.4 0.2 - - + -
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Residues in contact with LYS 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A ARG* 2.9 24.5 + - - +
551A GLU* 3.1 43.5 + - - +
553A LEU* 1.3 74.3 - - - +
555A ARG* 1.3 57.2 + - - +
558A GLY* 3.0 23.6 + - - -
559A LEU* 3.1 34.2 + - + +
560A ALA* 4.8 3.8 - - - -
561A GLU* 2.9 31.3 + - + +
564A ILE* 4.0 26.2 - - + -
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Residues in contact with ARG 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A VAL* 3.4 19.1 - - - +
419A ARG* 3.8 28.8 + - - +
551A GLU* 2.9 12.9 + - - +
552A LEU* 3.5 39.1 - - - +
554A LYS* 1.3 79.9 - - - +
556A GLU* 1.3 85.5 + - - +
558A GLY* 3.5 1.2 + - - -
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Residues in contact with GLU 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A VAL* 3.0 18.6 - - - +
419A ARG* 5.7 2.8 + - - -
427A ARG* 3.1 36.9 + - - +
460A VAL* 3.8 37.5 - - + +
552A LEU* 2.9 22.0 + - + +
553A LEU* 4.7 1.8 - - + +
555A ARG* 1.3 113.1 + - - +
557A LEU* 1.3 63.0 + - + +
558A GLY 3.5 0.4 - - - -
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Residues in contact with LEU 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A SER* 4.0 16.4 - - - +
416A VAL* 2.8 37.1 - - + +
417A THR 4.2 0.3 - - - +
418A VAL* 3.5 9.2 - - - +
427A ARG* 4.1 24.9 - - + -
429A LEU* 4.3 9.4 - - + -
460A VAL* 5.0 0.7 - - + -
478A PHE* 4.0 24.5 - - + -
487A PHE* 6.2 0.7 - - + -
553A LEU* 2.9 42.0 + - + +
556A GLU* 1.3 89.4 - - + +
558A GLY* 1.3 63.0 + - - +
559A LEU* 3.5 22.1 + - + +
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Residues in contact with GLY 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A THR 4.4 8.6 - - - +
418A VAL* 3.7 13.7 - - - +
419A ARG 5.6 0.4 - - - -
485A LYS* 2.7 28.8 + - - -
554A LYS 3.0 11.9 + - - -
555A ARG 3.5 5.6 + - - -
556A GLU 3.5 3.2 - - - -
557A LEU* 1.3 78.2 - - - +
559A LEU* 1.3 53.3 + - - +
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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