Contacts of the helix formed by residues 535 - 562 (chain A) in PDB entry 4XK8
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 GLY 535 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A ASP* 4.0 11.4 - - - -
485A GLN* 3.8 7.4 - - - -
486A PRO* 3.1 18.1 - - - +
533A PRO 4.2 0.8 - - - -
534A LEU* 1.3 73.8 - - - +
536A THR* 1.3 66.3 + - - -
537A ALA* 3.3 3.4 - - - -
538A ASP* 3.1 20.0 + - - +
539A PHE 3.1 9.7 + - - -
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Residues in contact with THR 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A PHE* 3.6 27.6 - - + +
478A SER* 3.5 17.6 + - - +
479A ASP* 2.8 27.7 + - - -
483A GLN* 3.9 0.5 - - - -
484A LEU* 3.1 47.9 + - + +
485A GLN* 4.1 0.9 + - - -
535A GLY* 1.3 71.2 - - - -
537A ALA* 1.3 62.3 + - - +
539A PHE* 3.2 3.3 + - - +
540A LEU* 2.9 33.2 + - + +
647A ILE* 5.1 0.9 - - + -
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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
----------------------------------------------------------
461A TYR* 4.2 0.3 + - - -
479A ASP* 5.0 1.8 + - - +
535A GLY 3.3 0.6 - - - -
536A THR* 1.3 78.8 - - - +
538A ASP* 1.3 60.0 + - - +
540A LEU* 3.3 7.8 + - - +
541A VAL* 2.9 32.3 + - - +
642A PHE* 3.6 15.5 - - + -
643A ALA* 4.3 13.6 + - + +
646A SER* 3.3 28.4 - - - +
647A ILE* 4.1 19.6 - - + +
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Residues in contact with ASP 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A PRO* 4.6 2.5 - - + -
533A PRO 3.8 0.9 - - - +
534A LEU* 3.6 24.8 - - + +
535A GLY* 3.1 29.9 + - - +
537A ALA* 1.3 77.9 - - - +
539A PHE* 1.3 66.0 + - - +
541A VAL* 3.6 6.5 - - - -
542A HIS* 2.6 40.9 + - + +
615A HIS* 4.0 14.6 + - - -
619A LYS* 3.1 34.6 + - - +
642A PHE* 4.2 5.1 - - - -
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Residues in contact with PHE 539 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A HIS 5.6 1.3 - - - -
460A LEU* 4.7 7.0 - - + -
484A LEU* 3.3 47.6 - - + +
485A GLN 4.3 13.9 - - - -
486A PRO* 4.1 13.7 - - + +
535A GLY 3.1 8.5 + - - +
536A THR 3.3 9.0 - - - +
538A ASP* 1.3 75.6 - - - +
540A LEU* 1.3 76.3 + - + +
542A HIS* 3.7 3.0 - - - +
543A HIS* 2.7 69.1 + + + -
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Residues in contact with LEU 540 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A SER* 4.7 2.7 - - - +
460A LEU* 3.6 32.8 - - + -
461A TYR* 3.2 33.9 - - + +
464A ASN* 4.2 15.7 - - - +
477A PHE* 4.3 1.8 - - + +
484A LEU* 4.2 9.6 - - + -
536A THR* 2.9 25.8 + - + +
537A ALA* 3.3 7.6 - - - +
538A ASP 3.2 0.2 - - - -
539A PHE* 1.3 87.7 - - + +
541A VAL* 1.3 58.3 + - - +
543A HIS* 3.2 5.9 + - - +
544A ILE* 2.9 29.5 + - - +
647A ILE* 4.0 28.5 - - + +
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Residues in contact with VAL 541 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A TYR* 3.3 16.4 - - - +
537A ALA 2.9 21.8 + - - +
538A ASP* 3.3 17.5 - - - +
540A LEU* 1.3 73.7 - - - +
542A HIS* 1.3 61.8 + - - +
544A ILE* 3.1 9.5 + - + +
545A HIS* 2.9 35.1 + - + +
611A VAL* 5.7 4.7 - - + -
615A HIS* 3.4 41.5 - - + +
642A PHE* 4.4 8.7 - - + -
646A SER 5.2 1.6 - - - +
652A TRP* 4.1 24.0 - - + -
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Residues in contact with HIS 542 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A LEU* 5.2 10.5 - - + +
538A ASP* 2.6 42.1 + - + +
539A PHE* 3.7 5.6 - - - +
541A VAL* 1.3 77.4 - - - +
543A HIS* 1.3 63.6 + - + +
545A HIS* 3.2 18.4 + + + +
546A ALA* 2.9 26.0 + - - +
615A HIS* 3.9 19.9 + + - -
----------------------------------------------------------
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Residues in contact with HIS 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A LEU* 4.4 17.2 - - + +
456A HIS 5.1 5.2 - - - +
457A SER* 3.9 17.6 - - - -
460A LEU* 6.4 0.4 - - + -
539A PHE* 2.7 76.2 + + + +
540A LEU* 3.8 4.5 - - - +
542A HIS* 1.3 77.5 - - + +
544A ILE* 1.3 60.0 + - - +
546A ALA* 3.5 8.3 + - + +
547A PHE* 2.9 29.3 + - - +
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Residues in contact with ILE 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A SER* 3.6 23.1 - - - +
458A PHE* 3.8 21.1 - - + +
461A TYR* 3.6 24.7 - - + +
540A LEU 2.9 19.4 + - - +
541A VAL* 3.1 11.2 + - + +
543A HIS* 1.3 77.8 - - - +
545A HIS* 1.3 56.8 + - - +
547A PHE* 3.2 9.6 + - + +
548A THR* 2.9 41.1 + - + +
611A VAL* 3.9 28.5 - - + -
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Residues in contact with HIS 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A VAL* 2.9 21.3 + - + -
542A HIS* 3.2 22.4 + + + +
544A ILE* 1.3 76.5 - - - +
546A ALA* 1.3 63.0 + - - +
548A THR* 3.0 6.7 + - - -
549A ILE* 2.9 38.5 + - + +
611A VAL* 3.9 21.8 - - + +
612A VAL* 3.6 45.5 - - + +
615A HIS* 3.0 33.7 - + + +
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Residues in contact with ALA 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A LEU* 4.1 13.7 - - + -
542A HIS 2.9 12.5 + - - +
543A HIS* 3.6 14.8 - - + +
545A HIS* 1.3 75.1 - - - +
547A PHE* 1.3 57.2 + - - +
549A ILE* 3.9 5.2 - - - +
550A HIS* 2.8 47.3 + - + +
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Residues in contact with PHE 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A CYS* 3.4 20.6 - - - -
453A LEU* 3.9 15.8 - - + +
454A GLY* 3.3 30.7 - - - -
457A SER* 3.8 12.8 - - - +
458A PHE* 5.6 5.8 - - + -
543A HIS 2.9 15.2 + - - +
544A ILE* 3.3 13.9 - - + +
546A ALA* 1.3 76.5 - - - +
548A THR* 1.3 73.4 + - + +
550A HIS* 3.1 3.8 + - - +
551A VAL* 2.9 40.8 + - + +
604A TRP* 3.7 29.2 - + - -
607A ASN* 6.0 0.2 - - - -
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Residues in contact with THR 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A ILE* 2.9 32.3 + - + +
545A HIS* 3.0 14.6 + - - -
547A PHE* 1.3 84.3 - - + +
549A ILE* 1.3 64.9 + - - +
551A VAL* 3.3 2.6 + - - +
552A THR* 2.8 30.7 + - - -
604A TRP* 3.8 22.6 - - + -
607A ASN* 4.5 7.4 - - - +
608A SER* 3.3 32.7 + - - -
611A VAL* 4.4 6.8 - - + +
612A VAL* 5.8 0.5 - - - +
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Residues in contact with ILE 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A HIS* 2.9 26.9 + - + +
546A ALA* 4.0 5.2 - - - +
548A THR* 1.3 84.3 + - - +
550A HIS* 1.3 62.0 + - + +
552A THR* 3.3 7.6 + - - -
553A VAL* 2.9 45.4 + - + +
608A SER* 5.0 7.6 - - - -
612A VAL* 6.3 4.0 - - + -
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Residues in contact with HIS 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A LEU* 3.9 15.7 - - + +
449A VAL* 3.8 28.0 - - + +
450A CYS* 3.3 18.1 - - - -
453A LEU* 3.7 20.1 - - + +
546A ALA* 2.8 36.3 + - + +
547A PHE 3.5 4.0 - - - +
549A ILE* 1.3 81.7 - - + +
551A VAL* 1.3 55.9 + - - +
553A VAL* 3.5 8.9 + - + +
554A LEU* 2.9 22.9 + - - +
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Residues in contact with VAL 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A CYS* 3.6 18.8 - - + -
547A PHE* 2.9 49.6 + - + +
548A THR 3.7 0.7 - - - +
549A ILE 3.3 0.2 - - - -
550A HIS* 1.3 72.4 - - - +
552A THR* 1.3 66.7 + - - +
554A LEU* 2.9 10.4 + - + +
555A ILE* 2.9 31.9 + - + +
604A TRP* 3.4 43.1 - - + +
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Residues in contact with THR 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ILE* 6.4 1.3 - - + -
408A VAL* 5.1 0.9 - - + -
548A THR 2.8 20.8 + - - -
549A ILE* 3.5 10.1 - - - -
551A VAL* 1.3 76.1 - - - +
553A VAL* 1.3 64.1 + - + +
555A ILE* 3.4 10.5 + - - +
556A LEU* 3.0 46.2 + - + +
601A GLY 3.9 21.8 - - - +
604A TRP* 3.7 19.5 + - - +
605A MET* 4.2 14.2 - - + +
608A SER* 4.4 3.0 + - - +
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Residues in contact with VAL 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A LEU* 3.7 19.7 - - + -
549A ILE* 2.9 35.3 + - + +
550A HIS* 3.6 8.5 - - + +
552A THR* 1.3 75.7 - - + +
554A LEU* 1.3 57.6 + - - +
556A LEU* 4.8 4.5 - - - -
557A LEU* 2.9 40.5 + - + +
----------------------------------------------------------
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Residues in contact with LEU 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ILE* 3.7 28.2 - - + +
446A LEU* 3.6 33.8 - - + +
447A ASN* 3.7 27.1 - - + +
450A CYS* 4.1 13.2 - - + -
550A HIS 2.9 14.4 + - - +
551A VAL* 3.1 16.8 - - + +
553A VAL* 1.3 75.7 - - - +
555A ILE* 1.3 67.0 + - + +
557A LEU* 4.3 0.2 - - - +
558A LYS* 2.9 33.8 + - + +
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Residues in contact with ILE 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A VAL* 2.9 21.2 + - + +
552A THR* 3.7 5.2 - - - +
554A LEU* 1.3 81.7 - - + +
556A LEU* 1.3 58.5 + - - +
558A LYS* 3.7 3.9 - - - +
559A GLY* 2.9 23.4 + - - -
597A HIS* 3.4 41.2 - - + +
600A LEU* 3.9 17.5 - - + +
601A GLY* 3.8 13.2 - - - +
604A TRP* 3.4 45.3 - - + +
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Residues in contact with LEU 556 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ILE* 4.7 8.5 - - + +
408A VAL* 4.2 23.3 - - + +
411A ALA* 3.6 31.9 - - + -
552A THR* 3.0 38.1 + - + +
553A VAL* 4.2 3.8 - - - +
555A ILE* 1.3 75.8 - - - +
557A LEU* 1.3 59.6 + - - +
559A GLY* 3.0 5.0 + - - +
560A VAL* 3.0 32.5 + - - +
597A HIS* 3.5 23.5 - - - +
598A VAL* 4.0 12.8 - - + -
601A GLY* 3.9 12.6 - - - -
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Residues in contact with LEU 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A ILE* 4.0 26.7 - - + -
443A ILE* 4.2 4.0 - - + -
446A LEU* 4.2 15.9 - - + -
553A VAL* 2.9 30.4 + - + +
554A LEU 4.3 0.4 - - - +
556A LEU* 1.3 70.3 - - - +
558A LYS* 1.3 67.1 + - - +
560A VAL* 3.2 15.1 + - + +
561A LEU* 2.9 54.0 + - + +
----------------------------------------------------------
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Residues in contact with LYS 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ILE* 3.7 38.2 - - + +
554A LEU* 2.9 25.0 + - + +
555A ILE* 3.7 5.2 - - - +
557A LEU* 1.3 75.4 - - - +
559A GLY* 1.3 62.2 + - - +
562A PHE* 3.1 40.1 + - + +
572A LYS* 6.1 0.8 - - - +
597A HIS* 3.0 33.3 + - + +
----------------------------------------------------------
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Residues in contact with GLY 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A ILE 2.9 10.9 + - - -
556A LEU 3.0 6.0 + - - -
558A LYS* 1.3 78.0 - - - +
560A VAL* 1.3 61.1 + - - +
562A PHE* 4.0 1.1 - - - -
563A ALA* 3.4 15.4 + - - -
594A ALA* 3.4 20.5 - - - +
597A HIS* 3.3 36.3 + - - -
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Residues in contact with VAL 560 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A ALA* 3.4 30.3 - - - +
414A ALA* 4.1 11.4 - - + -
415A ALA* 3.7 25.1 - - + +
418A MET* 3.4 26.5 - - + +
556A LEU 3.0 14.7 + - - +
557A LEU* 3.4 28.7 - - + +
559A GLY* 1.3 75.1 - - - +
561A LEU* 1.3 74.4 + - + +
563A ALA* 3.5 6.2 - - - +
----------------------------------------------------------
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Residues in contact with LEU 561 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A MET* 5.7 2.4 - - + +
432A LEU* 5.8 3.4 - - + -
435A VAL* 3.8 22.9 - - + -
436A LEU* 3.8 21.8 - - + +
439A ARG* 3.1 44.3 + - + -
442A ILE* 4.3 17.3 - - + -
443A ILE* 4.0 13.2 - - + -
557A LEU* 2.9 49.4 + - + +
558A LYS* 4.3 2.2 - - - +
560A VAL* 1.3 84.1 - - + +
562A PHE* 1.3 65.3 + - + +
563A ALA 3.4 1.2 + - - -
564A ARG* 4.9 1.9 + - - +
----------------------------------------------------------
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Residues in contact with PHE 562 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ARG* 3.5 36.1 - - + +
440A ASP* 3.7 26.9 - - - -
443A ILE* 3.7 31.2 - - + -
558A LYS* 3.1 34.9 + - + +
559A GLY* 4.0 2.5 - - - -
561A LEU* 1.3 77.6 - - + +
563A ALA* 1.3 61.2 + - - +
564A ARG 3.2 3.4 + - - -
565A SER 3.3 25.7 - - - +
566A SER* 3.8 15.7 - - - -
567A ARG* 5.5 2.5 - - + -
572A LYS* 2.9 31.8 + - - +
597A HIS* 6.2 1.8 - - + +
----------------------------------------------------------
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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