Contacts of the helix formed by residues 534 - 560 (chain A) in PDB entry 4N2F
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 534 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A LYS 3.6 10.4 + - - +
531A ILE 3.2 13.7 + - - +
532A LEU 3.2 0.6 - - - -
533A SER* 1.3 76.9 - - - +
535A GLU* 1.3 63.0 + - - +
536A SER* 3.1 12.2 + - - -
537A LEU* 3.0 38.7 + - + +
538A VAL* 3.1 25.7 + - - +
574A LYS* 6.1 3.4 - - - +
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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
----------------------------------------------------------
532A LEU 5.8 0.2 - - - -
533A SER 3.2 12.4 + - - +
534A ASN* 1.3 73.3 + - - +
536A SER* 1.3 63.5 + - - +
538A VAL* 3.2 11.6 + - - +
539A GLN* 3.2 26.4 + - + +
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Residues in contact with SER 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A ASN* 3.1 10.6 + - - -
535A GLU* 1.3 78.9 - - - +
537A LEU* 1.3 59.0 + - - +
539A GLN* 3.2 9.5 + - - +
540A GLU* 2.9 41.7 + - - +
574A LYS* 6.1 0.7 - - - -
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Residues in contact with LEU 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A TYR* 3.6 14.1 - - - +
531A ILE* 4.2 25.6 - - + +
534A ASN* 3.0 34.5 + - + +
536A SER* 1.3 75.5 + - - +
538A VAL* 1.3 65.3 + - - +
540A GLU* 3.3 18.2 + - - +
541A ASN* 3.0 34.4 + - - +
572A LEU* 5.0 1.8 - - + -
573A PHE 3.4 24.9 - - - +
574A LYS* 3.8 17.9 - - + +
584A PHE* 4.0 25.4 - - + -
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Residues in contact with VAL 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A TYR* 3.6 29.8 - - + +
502A ARG* 4.4 17.9 - - - +
531A ILE 4.9 0.7 - - - +
532A LEU 4.3 14.4 - - - +
534A ASN 3.1 16.9 + - - +
535A GLU* 3.2 10.7 + - - +
537A LEU* 1.3 76.4 - - - +
539A GLN* 1.3 64.9 + - - +
541A ASN* 3.2 2.9 + - - +
542A LEU* 2.9 46.0 + - + +
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Residues in contact with GLN 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A GLU* 3.2 14.4 + - + +
536A SER* 3.6 9.4 - - - +
538A VAL* 1.3 83.3 - - - +
540A GLU* 1.3 64.7 + - + +
542A LEU* 3.4 25.9 + - - +
543A TYR* 3.1 22.3 + - - +
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Residues in contact with GLU 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A SER* 2.9 29.1 + - - +
537A LEU* 3.6 16.0 - - - +
538A VAL 3.3 0.2 - - - -
539A GLN* 1.3 77.0 - - + +
541A ASN* 1.3 57.6 + - - +
543A TYR* 3.3 7.6 + - - +
544A PHE* 2.9 43.1 + - + -
574A LYS* 3.0 30.8 + - - +
575A MET* 2.9 53.8 + - + +
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Residues in contact with ASN 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A THR* 2.8 39.4 + - - +
498A TYR* 3.6 20.0 + - + -
537A LEU* 3.0 35.7 + - - +
538A VAL 3.9 1.3 - - - +
540A GLU* 1.3 78.3 - - - +
542A LEU* 1.3 59.5 + - - +
544A PHE* 3.8 7.1 - - - -
545A GLN 2.9 16.6 + - - -
572A LEU* 3.6 17.3 - - - +
573A PHE* 3.0 43.0 + - - +
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Residues in contact with LEU 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A SER* 6.0 3.1 - - - +
538A VAL* 2.9 30.1 + - + +
539A GLN* 3.7 33.7 - - - +
541A ASN* 1.3 75.5 - - - +
543A TYR* 1.3 63.4 + - - +
545A GLN* 3.2 9.9 + - + +
546A ARG* 3.1 25.0 + - - +
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Residues in contact with TYR 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A TYR* 3.9 12.0 + - - -
466A TRP* 4.6 4.3 - - + +
539A GLN 3.1 10.8 + - - +
540A GLU* 3.4 7.4 - - - +
542A LEU* 1.3 79.7 - - - +
544A PHE* 1.3 84.3 + + - +
546A ARG* 3.0 24.6 + - + +
547A CYS* 3.1 32.8 + - - -
575A MET* 3.6 26.7 - - + -
579A HIS* 4.2 11.2 + - + +
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Residues in contact with PHE 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A TRP* 3.7 26.6 - + + -
494A THR* 4.4 2.0 - - + -
540A GLU* 2.9 34.5 + - + +
541A ASN* 3.8 10.8 - - - +
542A LEU 3.3 0.4 - - - -
543A TYR* 1.3 100.6 - + - +
545A GLN* 1.3 56.7 + - - +
547A CYS* 3.1 7.9 + - - +
548A LEU* 2.9 33.7 + - - +
573A PHE* 3.6 32.5 - - + -
574A LYS 4.2 0.4 - - - -
575A MET* 3.6 36.8 - - + -
579A HIS 4.3 2.9 - - - -
581A ALA* 3.5 35.4 - - + -
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Residues in contact with GLN 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A ALA 4.6 1.0 + - - -
493A SER* 3.2 15.2 + - - +
494A THR* 2.8 42.7 + - - +
495A SER* 3.0 21.1 + - - -
541A ASN 2.9 8.7 + - - +
542A LEU* 3.6 12.3 - - + +
543A TYR 3.2 0.2 - - - -
544A PHE* 1.3 74.3 - - - +
546A ARG* 1.3 60.0 + - - +
548A LEU* 3.3 16.2 + - - +
549A ASP* 2.8 68.1 + - - +
552A ARG* 5.4 1.6 - - - +
568A ASP* 5.2 3.6 + - - -
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Residues in contact with ARG 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A LEU 3.1 17.2 + - - +
543A TYR* 3.0 19.3 + - + +
545A GLN* 1.3 75.8 - - - +
547A CYS* 1.3 58.3 + - - +
549A ASP* 3.3 10.6 + - - +
550A TRP* 2.9 30.6 + - - +
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Residues in contact with CYS 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A TYR* 3.9 14.0 - - + -
466A TRP* 3.6 47.3 - - + -
543A TYR* 3.1 44.2 + - - -
544A PHE* 3.1 10.8 + - - +
546A ARG* 1.3 75.3 - - - +
548A LEU* 1.3 62.2 + - - +
550A TRP* 3.4 6.4 + - - +
551A ASN* 3.0 30.0 + - - -
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Residues in contact with LEU 548 (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 15.7 - - + -
475A PHE* 3.5 36.6 - - + -
491A MET* 3.5 13.5 - - + +
492A ALA* 3.4 34.5 - - + +
494A THR* 4.2 13.7 - - + +
544A PHE 2.9 20.1 + - - +
545A GLN* 3.6 29.6 - - - +
547A CYS* 1.3 76.8 - - - +
549A ASP* 1.3 56.7 + - - +
551A ASN* 3.1 9.9 + - - +
552A ARG* 2.8 23.8 + - - +
573A PHE* 4.4 8.3 - - + -
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Residues in contact with ASP 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A GLN* 2.8 52.0 + - - +
546A ARG* 3.8 11.8 - - - +
547A CYS 3.3 0.2 - - - -
548A LEU* 1.3 72.7 - - - +
550A TRP* 1.3 66.2 + - - +
552A ARG* 3.4 21.7 + - + +
553A ASP* 3.0 32.4 + - - +
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Residues in contact with TRP 550 (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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435A PHE* 3.5 26.4 - + + -
462A LEU 4.8 0.4 - - - -
463A TYR* 3.7 37.2 - - + -
546A ARG* 2.9 17.3 + - - +
547A CYS* 3.6 8.3 - - - +
548A LEU 3.3 0.4 - - - -
549A ASP* 1.3 76.7 - - - +
551A ASN* 1.3 63.8 + - - +
553A ASP* 3.4 9.0 + - + +
554A ILE* 3.3 44.6 + - + +
705A MPD 3.4 44.2 - - + -
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Residues in contact with ASN 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A LEU* 3.3 14.1 - - + +
463A TYR* 2.7 55.2 + - - +
466A TRP* 3.7 8.3 - - - +
475A PHE* 3.5 25.9 - - + -
491A MET* 4.5 1.3 - - + -
547A CYS 3.0 22.0 + - - -
548A LEU* 3.1 9.1 + - - +
550A TRP* 1.3 77.8 - - - +
552A ARG* 1.3 65.6 + - - +
554A ILE* 3.1 5.1 + - - +
555A LEU* 2.9 31.4 + - + +
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Residues in contact with ARG 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A LEU* 5.6 0.4 - - - -
491A MET* 4.1 25.4 - - + +
545A GLN* 5.4 1.8 - - - +
548A LEU 2.8 12.7 + - - +
549A ASP* 3.2 27.8 + - - +
551A ASN* 1.3 77.5 - - - +
553A ASP* 1.3 61.3 + - - +
555A LEU* 3.4 6.1 + - - +
556A LYS* 2.9 45.9 + - + +
563A GLU* 2.8 39.7 + - - -
566A ILE* 3.7 27.9 + - + +
568A ASP* 2.8 41.2 + - - -
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Residues in contact with ASP 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A ASP* 3.0 17.2 + - - +
550A TRP* 3.7 10.5 - - + +
551A ASN 3.2 0.2 - - - -
552A ARG* 1.3 84.5 - - - +
554A ILE* 1.3 62.0 + - + +
556A LYS* 3.5 15.0 + - - +
557A LYS* 3.0 29.9 + - - +
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Residues in contact with ILE 554 (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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460A VAL* 4.0 16.6 - - + -
461A GLU 4.0 7.2 - - - +
462A LEU* 3.7 23.3 - - + -
550A TRP* 3.3 50.2 + - + +
551A ASN* 3.1 8.1 + - - +
553A ASP* 1.3 75.6 - - + +
555A LEU* 1.3 61.3 + - - +
557A LYS* 4.4 15.3 - - + +
558A GLU* 2.8 37.3 + - + +
705A MPD 4.9 10.8 - - + -
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Residues in contact with LEU 555 (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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430A LEU* 4.0 13.0 - - + -
462A LEU* 3.9 31.0 - - + -
475A PHE* 4.7 0.7 - - + -
476A MET* 4.1 18.4 - - + -
478A PHE* 4.9 0.9 - - + -
489A LEU* 4.1 17.9 - - + -
491A MET* 3.9 28.3 - - - -
551A ASN* 2.9 25.5 + - + +
552A ARG* 3.7 3.8 - - - +
554A ILE* 1.3 76.6 - - - +
556A LYS* 1.3 57.8 + - - +
558A GLU* 5.2 0.7 - - - -
559A LEU* 2.9 60.5 + - + +
561A LEU* 4.1 2.9 - - + +
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Residues in contact with LYS 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A ARG* 2.9 30.2 + - + +
553A ASP* 3.9 13.6 + - - +
555A LEU* 1.3 75.3 - - + +
557A LYS* 1.3 58.2 + - - +
560A GLY* 3.0 24.6 + - - -
561A LEU* 3.0 37.4 + - + +
562A THR* 4.5 1.3 - - - +
563A GLU* 2.8 46.6 + - - +
566A ILE* 3.8 20.6 - - + -
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Residues in contact with LYS 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A VAL* 3.4 18.0 - - - +
420A ASN* 5.2 3.0 + - - +
553A ASP 3.0 18.0 + - - +
554A ILE* 3.7 15.8 - - + +
556A LYS* 1.3 79.0 - - - +
558A GLU* 1.3 85.1 + - + +
559A LEU 3.7 0.2 + - - -
560A GLY* 3.8 0.9 + - - -
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Residues in contact with GLU 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A VAL* 3.2 14.6 - - - +
428A ARG* 3.0 53.2 + - - +
430A LEU* 6.2 0.2 - - + -
460A VAL* 3.9 31.2 - - + -
554A ILE* 2.8 30.6 + - + +
555A LEU* 4.8 0.7 - - - +
557A LYS* 1.3 100.4 + - + +
559A LEU* 1.3 61.1 + - + +
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Residues in contact with LEU 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A SER* 3.6 26.9 - - - +
417A VAL* 3.5 28.7 - - + +
418A THR 4.0 1.4 - - - +
419A VAL* 3.7 9.0 - - - +
428A ARG* 4.1 18.2 - - + -
430A LEU* 4.5 10.3 - - + -
460A VAL* 5.3 0.4 - - + -
478A PHE* 3.7 33.7 - - + -
487A PHE* 5.9 0.4 - - + -
555A LEU* 2.9 39.1 + - + +
558A GLU* 1.3 86.0 - - + +
560A GLY* 1.3 65.8 + - - +
561A LEU* 3.4 17.6 - - + +
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Residues in contact with GLY 560 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A THR 3.9 15.3 - - - +
419A VAL* 3.8 7.4 - - - +
420A ASN 5.7 0.7 - - - -
556A LYS 3.0 10.9 + - - -
557A LYS 3.8 4.9 + - - -
558A GLU 3.5 2.4 - - - -
559A LEU* 1.3 80.1 - - - +
561A LEU* 1.3 62.7 + - - +
562A THR* 4.4 2.8 + - - +
565A ASP* 4.5 1.7 - - - +
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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