Contacts of the helix formed by residues 548 - 577 (chain C) in PDB entry 5MKF
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 PHE 548 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C SER* 5.1 3.1 - - - -
436C PHE* 3.4 34.5 - + + -
438C VAL* 3.5 29.8 - - + -
460C LEU* 3.4 28.0 - - + -
462C LEU* 3.8 23.6 - - + -
532C VAL* 5.2 1.1 - - + -
536C LEU* 3.7 25.8 - - + -
545C PHE* 5.0 3.2 - - + -
546C PRO* 3.2 15.1 + - + +
547C ASN* 1.3 74.6 - - - +
549C GLU* 1.3 64.3 + - - +
550C HIS 3.4 0.4 - - - -
551C LEU* 2.8 41.3 + - + +
552C ALA* 3.1 14.7 + - + -
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Residues in contact with GLU 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C GLY* 5.6 1.4 - - - -
377C SER* 5.0 9.0 + - - -
425C ASP* 5.2 6.1 - - + +
438C VAL* 5.1 12.1 - - + +
440C ARG* 2.9 51.7 + - + -
545C PHE* 5.7 5.4 - - + -
547C ASN* 2.5 11.5 + - - +
548C PHE* 1.3 76.4 - - - +
550C HIS* 1.3 81.3 + - - +
552C ALA* 2.7 24.6 + - - +
553C TYR* 2.9 22.4 + - - +
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Residues in contact with HIS 550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C ASN 4.8 4.9 - - - +
376C GLY* 5.3 0.4 - - - -
377C SER* 3.4 32.8 - - - +
547C ASN* 3.4 20.5 + - - +
548C PHE 3.4 0.4 - - - -
549C GLU* 1.3 89.8 + - - +
551C LEU* 1.3 67.8 + - + +
553C TYR* 2.8 39.4 + + + +
554C TRP* 3.9 27.6 + + - -
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Residues in contact with LEU 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460C LEU* 5.2 1.6 - - - +
529C THR* 4.3 19.4 - - - +
532C VAL* 3.5 48.4 - - + +
535C LEU* 4.9 5.6 - - + -
536C LEU* 3.6 25.4 - - + -
547C ASN* 4.8 10.8 - - + +
548C PHE* 2.8 40.0 + - + +
550C HIS* 1.3 88.1 - - + +
552C ALA* 1.3 57.3 + - - +
554C TRP* 4.4 3.9 + - - +
555C GLN* 4.9 1.4 + - - +
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Residues in contact with ALA 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C VAL* 4.9 12.3 - - + -
458C GLN* 5.2 6.1 - - + +
460C LEU* 3.8 16.4 - - + -
548C PHE* 3.1 26.8 + - + -
549C GLU* 2.7 11.1 + - - +
551C LEU* 1.3 74.1 - - - +
553C TYR* 1.3 67.7 + - - +
554C TRP 3.0 3.1 - - - -
555C GLN* 2.7 25.6 + - + +
556C ILE* 3.7 6.1 + - - +
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Residues in contact with TYR 553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C SER* 5.6 6.5 - - - -
378C SER 5.7 5.4 - - - -
549C GLU* 2.9 18.0 + - - +
550C HIS* 2.8 38.6 + + + +
552C ALA* 1.3 76.9 - - - +
554C TRP* 1.3 88.3 + + - +
556C ILE* 3.7 7.2 + - - +
557C GLN* 3.0 59.3 + - + +
1006C PX6 4.4 22.8 + - - +
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Residues in contact with TRP 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524C ILE* 4.7 26.9 - - + +
528C ARG* 3.7 45.1 - - + +
529C THR* 4.1 26.0 - - + -
550C HIS* 3.9 31.5 - + - -
551C LEU* 4.9 2.9 - - - +
552C ALA 3.0 1.0 - - - -
553C TYR* 1.3 92.4 - + - +
555C GLN* 1.3 54.5 + - - +
557C GLN* 3.0 27.2 + - + +
558C PHE* 2.3 43.2 + - + +
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Residues in contact with GLN 555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C MET* 4.3 14.8 - - - +
458C GLN* 4.5 18.4 - - + +
459C PRO 4.6 0.7 - - - +
460C LEU* 3.1 36.8 - - + +
461C LYS* 6.0 0.2 - - - +
529C THR* 5.6 1.0 - - - +
551C LEU 4.9 0.6 + - - -
552C ALA* 2.7 29.4 + - + +
554C TRP* 1.3 69.9 - - - +
556C ILE* 1.3 54.2 + - + +
558C PHE* 2.8 23.5 + - - -
559C ASN* 2.4 57.9 + - + +
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Residues in contact with ILE 556 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456C GLN* 4.8 17.9 - - + +
458C GLN* 3.1 43.7 - - + +
552C ALA 3.7 5.0 + - - +
553C TYR* 4.1 6.7 - - - +
554C TRP 3.3 0.2 - - - -
555C GLN* 1.3 75.3 - - - +
557C GLN* 1.3 54.4 + - - +
558C PHE 3.1 0.7 + - - -
559C ASN* 3.1 12.9 + - + +
560C ASN* 2.7 34.7 + - + +
1006C PX6 4.2 32.5 - - + +
622D GLN* 5.8 0.9 - - - +
653D ASN* 4.6 19.1 - - - +
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Residues in contact with GLN 557 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524C ILE* 5.4 1.6 - - + -
553C TYR* 3.0 58.2 + - + +
554C TRP* 3.0 33.3 + - + +
556C ILE* 1.3 78.3 - - - +
558C PHE* 1.3 53.4 + - - +
560C ASN* 2.6 20.6 + - - +
561C ILE* 3.1 15.1 - - - +
1006C PX6 3.1 54.4 + - - +
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Residues in contact with PHE 558 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C MET* 4.6 22.4 - - + -
242C MET* 6.5 0.9 - - + -
521C ALA* 3.8 30.3 - - + -
524C ILE* 4.0 27.1 - - + -
525C ASN* 4.3 21.5 - - + -
554C TRP* 2.3 31.1 + - + +
555C GLN* 2.8 25.9 + - - +
557C GLN* 1.3 70.1 - - - +
559C ASN* 1.3 58.9 + - - +
561C ILE* 3.0 6.6 + - + +
562C ALA* 2.6 53.8 + - + +
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Residues in contact with ASN 559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C MET* 4.9 14.9 - - - +
458C GLN* 5.2 9.5 + - - +
555C GLN* 2.4 48.0 + - + +
556C ILE* 3.1 10.2 + - + +
558C PHE* 1.3 72.7 - - - +
560C ASN* 1.3 65.9 + - - +
562C ALA* 3.1 6.4 - - - +
563C ALA* 3.0 17.7 + - - +
617D LEU* 3.2 24.2 + - - +
618D VAL* 5.0 6.3 + - - -
621D THR* 5.0 14.8 + - - +
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Residues in contact with ASN 560 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556C ILE 2.7 8.6 + - - +
557C GLN 2.6 19.5 + - - +
559C ASN* 1.3 75.7 - - - +
561C ILE* 1.3 67.9 + - - -
563C ALA* 2.5 29.8 + - - +
564C VAL* 2.6 25.8 + - + +
1006C PX6 3.2 50.5 - - - +
618D VAL* 4.9 5.8 - - + +
653D ASN* 4.7 3.5 - - - +
656D LEU* 3.3 33.4 - - + +
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Residues in contact with ILE 561 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517C LEU* 4.4 33.2 - - + +
520C VAL* 4.1 27.1 - - + -
521C ALA* 4.8 7.4 - - + +
524C ILE* 4.8 8.3 - - + -
557C GLN 3.1 18.4 - - - +
558C PHE* 3.0 23.0 + - + +
560C ASN* 1.3 84.6 + - - +
562C ALA* 1.3 60.9 + - - +
564C VAL* 4.0 9.0 - - + -
565C THR* 3.3 22.2 + - - +
1006C PX6 5.1 20.9 - - + -
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Residues in contact with ALA 562 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521C ALA* 5.1 5.2 - - - -
558C PHE* 2.6 45.5 + - + +
559C ASN* 3.1 13.0 - - - +
561C ILE* 1.3 74.5 - - - +
563C ALA* 1.3 58.1 + - - +
565C THR* 2.5 26.5 + - - -
566C VAL* 3.5 9.3 - - - +
617D LEU* 5.2 0.9 - - + -
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Residues in contact with ALA 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559C ASN 3.0 10.3 + - - +
560C ASN* 2.5 14.0 + - - +
562C ALA* 1.3 70.7 - - - +
564C VAL* 1.3 57.3 + - - +
566C VAL* 2.7 25.5 + - - +
567C PHE* 3.0 10.6 + - - +
614D LEU* 4.4 7.1 - - + +
617D LEU* 3.5 41.7 - - + +
618D VAL* 4.0 19.5 - - + -
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Residues in contact with VAL 564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517C LEU* 4.5 11.7 - - + -
560C ASN* 2.6 33.5 + - + +
561C ILE* 4.1 9.4 - - + +
562C ALA 3.4 0.2 - - - -
563C ALA* 1.3 72.3 - - + +
565C THR* 1.3 65.2 + - - +
567C PHE* 3.1 14.8 - - + +
568C PHE* 3.0 41.3 - - + -
1006C PX6 4.7 28.7 - - + -
1007C PLM 5.3 10.1 - - + -
614D LEU* 4.5 9.9 - - + -
618D VAL* 5.9 0.9 - - + -
656D LEU* 5.0 12.6 - - + -
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Residues in contact with THR 565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C LEU* 5.5 2.0 - - - +
514C ILE* 4.7 12.4 - - - +
517C LEU* 3.6 32.5 - - + -
518C SER* 4.2 16.2 - - - +
561C ILE 3.3 15.5 - - - +
562C ALA* 2.5 23.8 + - - -
564C VAL* 1.3 77.5 - - - +
566C VAL* 1.3 69.5 + - - +
568C PHE* 2.8 23.9 + - - +
569C VAL* 3.0 17.9 + - - +
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Residues in contact with VAL 566 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C LEU* 4.3 29.2 - - + -
235C CYS* 6.4 0.7 - - - -
238C THR* 5.1 5.4 - - + -
562C ALA 3.5 16.8 - - - +
563C ALA 2.7 11.9 + - - +
565C THR* 1.3 80.4 + - - +
567C PHE* 1.3 65.2 + - - +
569C VAL* 3.0 21.4 + - + +
570C TRP* 3.0 39.7 - - + -
613D GLN* 4.7 6.7 - - + +
617D LEU* 4.2 23.8 - - + -
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Residues in contact with PHE 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563C ALA 3.0 6.9 + - - +
564C VAL* 3.1 13.7 - - + +
566C VAL* 1.3 78.9 - - - +
568C PHE* 1.3 102.6 + + - +
569C VAL 2.8 0.7 + - - -
570C TRP* 3.0 26.3 + - - +
571C ILE* 3.9 14.9 + - + +
1007C PLM 3.5 39.9 - - + -
607D ILE* 4.4 14.6 - - + -
610D ALA* 3.6 30.0 - - + +
611D TYR* 4.3 13.9 - + - -
614D LEU* 3.8 40.1 - - + +
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Residues in contact with PHE 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510C LEU* 5.4 17.0 - - + -
513C VAL* 5.2 14.6 - - + -
514C ILE* 5.1 16.4 - - + +
517C LEU* 4.8 10.1 - - + -
564C VAL* 3.0 46.0 - - + -
565C THR* 2.8 13.2 + - - +
567C PHE* 1.3 94.7 - + - +
569C VAL* 1.3 63.4 + - - +
571C ILE* 3.0 43.2 - - + +
572C LYS* 3.1 8.7 + - - +
1006C PX6 4.3 23.6 - - + -
1007C PLM 4.4 21.1 - - + -
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Residues in contact with VAL 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C TYR* 5.9 3.8 - - + -
230C PHE* 4.2 23.6 - - + -
231C LEU* 5.1 13.7 - - + -
234C LEU* 4.6 14.4 - - + -
514C ILE* 3.9 24.2 - - + -
565C THR* 3.2 18.8 - - - +
566C VAL* 3.2 19.5 - - + +
567C PHE 2.8 1.4 + - - -
568C PHE* 1.3 77.7 - - - +
570C TRP* 1.3 64.3 + - + +
572C LYS* 3.1 22.2 - - + +
573C LEU* 3.7 3.8 + - - +
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Residues in contact with TRP 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C LEU* 6.1 4.2 - - + +
235C CYS* 4.7 13.9 - - - -
566C VAL* 3.0 49.1 - - + -
567C PHE* 3.0 16.6 + - - +
569C VAL* 1.3 75.3 - - + +
571C ILE* 1.3 56.4 + - + +
572C LYS 2.7 4.9 + - - -
573C LEU* 2.5 63.1 + - + +
574C PHE 3.3 0.9 + - - -
1010C CHS 5.6 8.7 - - + +
606D ILE* 5.7 6.7 - - + +
609D LEU* 6.1 4.2 - - + +
610D ALA* 4.9 20.6 - - + -
613D GLN* 2.9 51.6 - - + -
614D LEU 5.4 1.3 - - - -
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Residues in contact with ILE 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507C TRP* 5.8 2.8 - - - -
510C LEU* 5.3 12.8 - - + -
567C PHE* 4.3 14.6 - - + +
568C PHE* 3.0 52.0 - - + +
570C TRP* 1.3 77.1 - - + +
572C LYS* 1.3 61.7 + - - +
574C PHE* 3.0 31.1 - - + +
575C LYS* 4.4 2.6 + - - +
1007C PLM 4.9 24.7 - - + +
607D ILE* 3.7 30.3 - - + -
610D ALA* 5.4 2.0 - - + -
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Residues in contact with LYS 572 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C TYR* 4.6 36.5 + - + -
511C ASP* 2.8 47.5 + - - +
514C ILE* 5.6 13.7 - - + -
568C PHE 3.1 10.3 + - - +
569C VAL* 3.1 18.8 - - + +
570C TRP 2.7 4.0 + - - -
571C ILE* 1.3 73.8 - - - +
573C LEU* 1.3 59.1 + - - +
574C PHE 2.8 10.3 + - - -
575C LYS* 3.4 13.1 + - - +
576C PHE* 3.0 45.7 - - + -
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Residues in contact with LEU 573 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C LEU* 6.2 3.1 - - + -
231C LEU* 5.3 13.9 - - + -
569C VAL 3.7 2.1 + - - +
570C TRP* 2.5 54.6 + - + +
572C LYS* 1.3 75.1 - - - +
574C PHE* 1.3 67.7 + - - +
575C LYS 3.1 0.2 - - - -
576C PHE* 2.9 25.7 + - + -
577C ILE* 3.6 21.0 + - + -
578C ASN* 4.5 3.1 + - - +
606D ILE* 5.8 8.5 - - + -
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Residues in contact with PHE 574 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507C TRP* 4.5 12.1 - + - -
570C TRP 3.3 3.2 + - - +
571C ILE* 3.0 33.0 - - + +
572C LYS 2.8 2.2 + - - -
573C LEU* 1.3 84.2 - - - +
575C LYS* 1.3 55.1 + - - -
578C ASN* 2.2 39.8 + - - +
587C SER* 4.9 15.0 - - - -
1007C PLM 3.1 46.7 - - + -
603D MET* 3.4 50.5 - - + -
606D ILE* 5.4 8.3 - - + -
607D ILE* 6.1 3.8 - - + -
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Residues in contact with LYS 575 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507C TRP* 3.1 52.7 - - + +
508C ASN* 4.4 1.0 - - - +
511C ASP* 3.6 24.7 + - - -
571C ILE 4.4 1.7 + - - -
572C LYS* 3.4 8.3 + - - +
574C PHE* 1.3 78.5 - - - +
576C PHE* 1.3 99.1 + - + +
578C ASN* 2.7 23.0 - - - +
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Residues in contact with PHE 576 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C GLU* 6.2 0.4 - - - -
224C LEU* 3.8 32.5 - - + -
227C TYR* 5.9 6.7 - + - -
572C LYS* 3.0 64.4 - - + -
573C LEU* 2.9 16.6 + - - +
575C LYS* 1.3 101.4 - - + +
577C ILE* 1.3 64.4 + - + +
578C ASN 3.1 14.8 + - - -
579C PHE* 4.0 6.4 + - - +
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Residues in contact with ILE 577 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C LEU* 3.5 40.2 - - + -
228C LEU* 4.2 23.1 - - + -
573C LEU* 3.6 19.9 + - + +
576C PHE* 1.3 81.5 - - + +
578C ASN* 1.3 57.8 + - - +
579C PHE* 3.4 6.2 + - - +
580C ASN* 5.2 3.8 + - - +
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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).
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