Contacts of the helix formed by residues 555 - 579 (chain K) in PDB entry 4P6X
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 SER 555 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548K TYR* 4.4 1.2 + - - -
553K PRO 3.9 1.7 + - - -
554K ASP* 1.3 76.8 - - - +
556K THR* 1.3 65.1 + - - +
557K TRP* 3.6 10.3 + - - +
558K ARG* 3.0 28.4 + - - +
559K ILE* 3.1 24.2 + - - +
636K LEU* 4.5 8.7 - - - -
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Residues in contact with THR 556 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555K SER* 1.3 71.4 - - - +
557K TRP* 1.3 57.8 + - - +
559K ILE* 3.7 0.3 - - - +
560K MET* 3.0 62.3 + - + +
636K LEU* 3.4 13.8 - - - +
637K PRO* 3.3 36.8 - - + +
638K CYS* 4.3 14.8 - - + +
639K MET* 4.4 13.2 - - + +
745K MET* 5.0 13.5 - - - -
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Residues in contact with TRP 557 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555K SER* 3.1 8.1 - - - +
556K THR* 1.3 80.7 - - - +
558K ARG* 1.3 94.7 + - + +
560K MET* 4.2 0.5 - - - +
561K THR* 2.9 56.9 + - + -
745K MET* 3.0 38.3 + - + -
746K SER* 2.7 23.0 + - - -
747K ILE* 3.7 19.2 - - + +
748K GLU* 3.6 26.7 - - - -
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Residues in contact with ARG 558 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548K TYR* 2.9 44.8 + - + -
549K ASP* 2.7 29.3 + - - +
552K VAL* 3.0 46.6 + - - +
553K PRO 3.0 16.0 + - - -
554K ASP* 3.6 1.0 + - - +
555K SER* 3.0 20.9 + - - +
557K TRP* 1.3 97.4 - - + +
559K ILE* 1.3 55.8 + - - +
561K THR* 3.9 2.0 - - - +
562K THR* 2.7 42.0 + - - +
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Residues in contact with ILE 559 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548K TYR* 3.6 29.8 - - + +
554K ASP* 4.3 6.1 - - + -
555K SER 3.1 14.2 + - - +
556K THR 3.7 2.7 - - - +
558K ARG* 1.3 76.6 - - - +
560K MET* 1.3 58.9 + - - +
562K THR* 3.1 5.4 + - - -
563K LEU* 2.9 43.5 + - + +
627K LEU* 4.5 8.7 - - + +
629K ILE* 3.9 17.0 - - + -
633K ARG* 4.3 19.3 - - + +
636K LEU* 3.8 19.7 - - + -
639K MET* 3.6 29.8 - - + -
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Residues in contact with MET 560 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556K THR* 3.0 41.4 + - + +
557K TRP 4.2 0.2 - - - +
559K ILE* 1.3 77.0 - - - +
561K THR* 1.3 61.7 + - - +
563K LEU* 3.3 13.1 + - + +
564K ASN* 3.1 28.4 + - - -
638K CYS* 4.0 17.0 - - + +
639K MET* 4.1 20.2 - - - -
642K GLN* 3.2 41.5 - - + +
739K THR* 4.7 0.2 - - - -
747K ILE* 3.6 36.3 - - + -
900K HCY 3.9 15.6 - - - +
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Residues in contact with THR 561 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557K TRP* 2.9 49.0 + - + -
558K ARG* 3.9 4.7 - - - +
560K MET* 1.3 75.6 - - - +
562K THR* 1.3 64.9 + - - +
564K ASN* 3.3 4.2 + - - +
565K MET* 3.2 29.0 + - + +
747K ILE* 3.3 10.6 - - - +
748K GLU* 3.0 44.6 + - + +
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Residues in contact with THR 562 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546K ALA* 3.7 26.4 - - + +
547K GLY 5.1 0.4 - - - -
548K TYR* 3.6 23.3 - - + -
558K ARG* 2.7 27.1 + - - +
559K ILE 3.4 4.3 - - - -
561K THR* 1.3 76.5 - - - +
563K LEU* 1.3 58.4 + - - +
565K MET* 3.3 10.4 + - + +
566K LEU* 2.9 26.2 + - - +
627K LEU* 3.7 21.1 - - + -
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Residues in contact with LEU 563 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559K ILE* 2.9 32.4 + - + +
560K MET* 3.5 15.3 - - + +
561K THR 3.2 0.2 - - - -
562K THR* 1.3 76.8 - - - +
564K ASN* 1.3 51.2 + - - +
566K LEU* 3.2 10.3 + - + +
567K GLY 2.7 30.8 + - - -
623K PHE* 3.5 55.0 - - + -
627K LEU* 3.5 28.0 - - + -
629K ILE* 5.1 0.2 - - + -
639K MET* 5.6 3.8 - - - -
646K MET* 6.1 0.2 - - + -
900K HCY 3.3 34.4 - - + +
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Residues in contact with ASN 564 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560K MET 3.1 20.4 + - - -
561K THR 3.7 2.0 - - - +
562K THR 3.3 0.2 - - - -
563K LEU* 1.3 74.3 - - - +
565K MET* 1.3 60.6 + - - +
567K GLY 3.2 0.2 + - - -
568K GLY 2.9 24.3 + - - -
747K ILE* 3.4 18.0 - - - +
748K GLU 3.3 17.8 + - - +
749K PHE* 3.2 43.1 - - + -
750K PRO* 3.4 13.3 - - + +
753K LEU* 3.2 10.3 - - - +
900K HCY 2.9 37.5 + - - +
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Residues in contact with MET 565 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546K ALA 6.1 0.9 - - - +
561K THR* 3.2 17.6 + - + +
562K THR* 3.5 10.1 - - + +
563K LEU 3.3 0.2 - - - -
564K ASN* 1.3 76.1 - - - +
566K LEU* 1.3 64.0 + - - +
568K GLY* 3.3 9.9 + - - -
569K ARG* 3.3 19.4 + - - +
748K GLU* 3.3 38.1 - - + +
749K PHE 3.4 4.9 - - - +
750K PRO* 3.4 40.3 - - + +
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Residues in contact with LEU 566 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544K LEU* 3.9 19.1 - - + -
545K TYR 4.0 9.0 - - - +
546K ALA* 4.3 13.7 + - + +
562K THR 2.9 13.9 + - - +
563K LEU* 3.3 11.9 - - + +
565K MET* 1.3 76.5 - - - +
567K GLY* 1.3 56.9 + - - +
569K ARG* 3.0 32.3 + - - +
570K GLN* 2.8 58.1 + - + +
623K PHE* 3.7 24.0 - - + +
624K ALA* 4.1 10.8 - - + -
900K HCY 4.1 9.0 - - + -
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Residues in contact with GLY 567 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563K LEU 2.7 18.1 + - - -
564K ASN 3.2 4.2 + - - -
566K LEU* 1.3 73.1 - - - +
568K GLY* 1.3 57.2 + - - +
570K GLN* 3.6 4.4 - - - +
571K VAL* 2.8 36.2 + - - +
753K LEU* 3.9 7.2 - - - -
900K HCY 3.9 29.2 - - - -
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Residues in contact with GLY 568 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564K ASN 2.9 14.0 + - - -
565K MET 3.3 4.5 + - - -
566K LEU 3.2 0.4 - - - -
567K GLY* 1.3 76.0 - - - +
569K ARG* 1.3 61.6 + - - +
571K VAL* 3.5 3.5 + - - +
572K ILE* 3.2 31.5 + - - +
750K PRO* 3.9 17.0 - - - -
752K MET* 4.5 8.3 - - - +
753K LEU* 3.6 10.9 - - - +
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Residues in contact with ARG 569 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544K LEU* 3.7 37.4 - - + +
545K TYR 2.4 33.1 + - - +
546K ALA* 4.5 4.4 + - - +
565K MET 3.3 13.2 + - - +
566K LEU* 3.0 21.6 + - - +
568K GLY* 1.3 74.2 - - - +
570K GLN* 1.3 60.4 + - - +
572K ILE* 3.4 14.9 + - + +
573K ALA* 3.0 26.9 + - - +
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Residues in contact with GLN 570 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543K VAL* 6.3 0.6 - - - +
544K LEU* 4.3 15.1 + - + +
566K LEU* 2.8 46.0 + - + +
567K GLY 3.6 7.6 - - - +
569K ARG* 1.3 75.2 - - - +
571K VAL* 1.3 52.9 + - - +
573K ALA* 3.1 8.3 + - - +
574K ALA* 2.7 34.1 + - - +
604K MET* 3.3 30.0 - - + +
607K ALA* 5.8 0.5 - - - +
611K ARG* 4.2 11.3 + - - +
623K PHE 4.0 6.5 + - - -
900K HCY 3.1 39.3 + - - +
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Residues in contact with VAL 571 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567K GLY 2.8 20.3 + - - +
568K GLY* 3.8 4.9 - - - +
570K GLN* 1.3 72.5 - - - +
572K ILE* 1.3 62.4 + - - +
574K ALA* 2.9 23.0 + - + +
575K VAL* 3.0 21.9 + - + +
596K LEU* 6.2 2.5 - - + -
600K TRP* 3.8 27.8 - - + -
604K MET* 4.0 9.4 - - - -
752K MET* 4.6 13.9 - - + -
753K LEU* 3.8 21.3 - - + -
756K ILE* 4.0 24.0 - - + -
745L LEU* 5.9 0.7 - - + -
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Residues in contact with ILE 572 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568K GLY 3.2 19.2 + - - +
569K ARG* 3.5 15.7 - - + +
571K VAL* 1.3 76.2 - - - +
573K ALA* 1.3 61.9 + - - +
575K VAL* 3.5 11.4 + - - +
576K LYS* 3.5 13.8 + - + +
752K MET* 3.4 38.1 - - + -
744L LEU* 5.4 4.3 - - + -
748L LEU* 4.4 16.7 - - + +
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Residues in contact with ALA 573 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541K PRO* 4.4 15.9 - - + +
544K LEU* 5.1 9.4 - - + -
569K ARG 3.0 15.3 + - - +
570K GLN* 3.1 10.7 + - - +
572K ILE* 1.3 75.4 - - - +
574K ALA* 1.3 65.1 + - - +
575K VAL 3.3 0.2 - - - -
576K LYS* 3.0 42.8 - - - +
577K TRP* 3.1 6.8 + - - +
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Residues in contact with ALA 574 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541K PRO* 5.6 1.8 - - - -
570K GLN 2.7 16.5 + - - +
571K VAL* 2.9 16.1 + - + +
573K ALA* 1.3 76.6 - - - +
575K VAL* 1.3 58.0 + - - +
577K TRP* 3.2 17.8 - - + +
578K ALA* 2.8 27.0 + - - +
596K LEU* 4.3 5.9 - - + +
603K LEU* 4.6 18.4 - - + -
604K MET* 4.4 15.0 - - + -
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Residues in contact with VAL 575 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571K VAL* 3.0 27.2 + - + +
572K ILE* 3.8 7.4 - - - +
573K ALA 3.3 0.2 - - - -
574K ALA* 1.3 73.9 - - - +
576K LYS* 1.3 66.7 + - - +
577K TRP 3.1 1.1 - - - -
578K ALA* 3.4 2.4 + - - +
579K LYS* 3.2 23.3 + - - +
596K LEU* 3.8 18.6 - - + -
752K MET* 5.0 4.3 - - + -
745L LEU* 3.4 24.0 - - + -
748L LEU* 4.0 27.4 - - + +
749L LEU* 3.6 30.0 - - + +
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Residues in contact with LYS 576 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539K ILE 3.5 19.0 + - - -
541K PRO* 3.1 36.9 - - - +
572K ILE* 3.5 6.3 + - + +
573K ALA* 3.0 32.3 + - - +
575K VAL* 1.3 79.4 - - - +
577K TRP* 1.3 62.9 + - - +
579K LYS* 3.3 22.4 - - + +
580K ALA* 3.7 9.7 + - - +
748L LEU 6.0 0.2 - - - -
753L ASP* 5.0 8.5 - - - +
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Residues in contact with TRP 577 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536K LEU* 5.0 4.6 + - - +
539K ILE* 3.5 41.0 - - + +
540K GLU* 3.7 4.2 + - - -
541K PRO* 3.9 14.4 - - + -
573K ALA 3.1 11.6 + - - +
574K ALA* 3.2 28.5 - - + +
576K LYS* 1.3 90.4 - - - +
578K ALA* 1.3 71.7 + - + +
580K ALA* 3.0 17.9 + - - +
581K ILE* 3.4 35.0 + - + +
603K LEU* 3.7 38.1 - - + -
664K LEU 5.4 0.2 - - - -
667K LYS* 3.3 37.3 - - + +
668K VAL* 4.1 16.8 - - + -
671K LEU* 4.0 10.1 - - + -
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Residues in contact with ALA 578 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574K ALA 2.8 19.1 + - - +
575K VAL 3.4 5.1 + - - +
577K TRP* 1.3 79.5 - - + +
579K LYS* 1.3 57.9 + - - +
581K ILE* 2.9 34.9 + - - +
584K PHE* 3.0 39.3 - - + +
596K LEU* 4.1 15.9 - - + -
671K LEU* 4.1 6.1 - - + -
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Residues in contact with LYS 579 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575K VAL* 3.2 12.7 + - - +
576K LYS* 3.3 20.4 - - - +
578K ALA* 1.3 78.4 - - - +
580K ALA* 1.3 58.4 + - + +
581K ILE 3.2 3.9 + - - +
584K PHE* 3.8 11.0 - - + -
585K ARG* 3.2 49.4 + - + +
592K GLN* 5.3 0.2 - - - +
748L LEU 2.7 27.3 + - - -
749L LEU* 2.9 32.7 + - + +
751L LYS 3.5 5.3 + - - -
753L ASP* 2.6 40.3 + - - +
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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