Contacts of the helix formed by residues 555 - 579 (chain A) in PDB entry 3K23
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A PRO* 3.4 10.1 + - - -
554A ASP* 1.3 75.4 - - - +
556A THR* 1.3 66.3 + - - +
557A TRP* 3.6 10.3 + - - +
558A ARG* 3.4 24.4 + - - +
559A ILE* 3.3 25.3 + - - +
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Residues in contact with THR 556 (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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555A SER* 1.3 74.6 - - - +
557A TRP* 1.3 65.9 + - - +
559A ILE* 3.8 2.9 - - - +
560A MET* 2.9 36.8 + - - +
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Residues in contact with TRP 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A SER* 3.4 8.8 + - - +
556A THR* 1.3 79.3 - - - +
558A ARG* 1.3 87.7 + - + +
560A MET* 3.5 4.9 + - - +
561A THR* 2.7 62.8 + - + -
746A SER* 3.4 29.5 + - - -
747A ILE* 3.9 13.0 - - + +
748A GLU* 4.1 8.1 - - + +
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Residues in contact with ARG 558 (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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548A TYR* 5.0 14.6 - - + -
551A SER* 3.2 37.1 - - - -
552A VAL* 4.5 3.4 - - - +
553A PRO 5.3 8.5 - - - +
555A SER* 3.4 14.6 + - - +
557A TRP* 1.3 103.5 - - + +
559A ILE* 1.3 54.9 + - + +
561A THR* 4.0 5.4 - - + -
562A THR* 2.6 54.4 + - + +
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Residues in contact with ILE 559 (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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1A JZN 6.1 0.2 - - - -
548A TYR* 3.1 24.0 - - + +
554A ASP* 3.2 28.0 - - + +
555A SER 3.3 19.4 + - - +
556A THR* 3.3 4.8 + - - +
558A ARG* 1.3 76.1 - - + +
560A MET* 1.3 63.1 + - + +
562A THR* 2.6 20.6 + - - +
563A LEU* 2.9 27.7 + - + +
627A LEU* 5.6 5.4 - - + -
629A ILE* 4.3 26.0 - - + -
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Residues in contact with MET 560 (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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1A JZN 3.7 52.2 - - + +
556A THR* 2.9 29.5 + - - +
557A TRP* 3.8 2.5 - - - +
559A ILE* 1.3 77.4 - - + +
561A THR* 1.3 54.5 + - - +
563A LEU* 3.2 7.7 + - + +
564A ASN* 2.7 40.4 + - - +
638A GLY 4.3 6.1 - - - +
735A TYR* 4.1 21.5 - - + +
739A THR* 4.7 7.6 - - - -
747A ILE* 3.4 22.7 - - + -
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Residues in contact with THR 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A TRP* 2.7 53.5 + - + -
558A ARG* 3.6 9.9 - - + +
560A MET* 1.3 73.3 - - - +
562A THR* 1.3 58.8 + - + +
564A ASN* 3.1 14.7 + - - +
565A MET* 2.8 37.9 + - + +
747A ILE* 3.7 2.1 - - - +
748A GLU* 3.3 34.1 + - + -
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Residues in contact with THR 562 (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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546A ALA* 4.7 22.3 - - - +
547A GLY 5.0 2.5 - - - +
548A TYR* 3.9 26.6 - - + -
558A ARG* 2.6 36.8 + - + +
559A ILE* 2.6 27.2 + - - +
561A THR* 1.3 74.7 - - + +
563A LEU* 1.3 51.0 + - - +
565A MET* 3.0 9.8 + - + +
566A LEU* 2.7 38.1 + - - +
569A ARG* 5.6 0.2 + - - -
627A LEU* 5.0 5.4 - - - +
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Residues in contact with LEU 563 (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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1A JZN 2.5 69.4 + - + +
559A ILE* 2.9 32.6 + - + +
560A MET* 3.5 6.1 - - + +
562A THR* 1.3 75.3 + - - +
564A ASN* 1.3 55.6 + - - +
566A LEU* 3.7 5.6 - - + +
567A GLY* 2.8 24.8 + - - -
623A PHE* 3.5 39.7 - - + -
627A LEU* 3.7 24.2 - - + -
629A ILE* 4.8 6.3 - - + -
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Residues in contact with ASN 564 (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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1A JZN 3.0 34.4 + - - +
560A MET 2.7 18.2 + - - +
561A THR* 3.2 5.6 - - - +
563A LEU* 1.3 74.8 - - - +
565A MET* 1.3 62.7 + - - +
567A GLY 3.2 0.2 + - - -
568A GLY 3.0 17.3 + - - -
747A ILE* 3.2 19.8 - - - +
748A GLU 2.8 25.9 + - - +
749A PHE* 3.0 37.2 - - + -
750A PRO* 3.4 20.8 - - + +
753A LEU* 3.5 4.4 - - - +
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Residues in contact with MET 565 (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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561A THR* 2.8 25.8 + - + +
562A THR* 3.5 9.9 - - + +
564A ASN* 1.3 74.3 - - - +
566A LEU* 1.3 61.6 + - - +
568A GLY* 3.3 9.0 + - - -
569A ARG* 3.4 24.2 + - - +
748A GLU* 3.3 49.8 - - + +
749A PHE 3.6 7.6 - - - +
750A PRO* 4.0 23.6 - - - +
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Residues in contact with LEU 566 (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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1A JZN 3.6 18.6 - - + +
544A LEU* 4.2 8.1 - - + -
545A TYR 4.6 3.1 - - - +
546A ALA* 4.1 24.5 - - + +
562A THR 2.7 20.2 + - - +
563A LEU* 3.7 15.5 - - + +
565A MET* 1.3 69.6 - - - +
567A GLY* 1.3 63.6 - - - +
568A GLY 3.1 2.0 + - - -
569A ARG* 3.2 36.7 + - - +
570A GLN* 2.8 54.5 + - + +
623A PHE* 4.6 7.4 - - + +
624A ALA* 4.5 13.5 - - + -
627A LEU* 4.6 0.2 - - + -
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Residues in contact with GLY 567 (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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1A JZN 4.0 11.6 - - - -
563A LEU 2.8 21.3 + - - -
564A ASN 3.6 2.5 - - - -
566A LEU* 1.3 73.1 - - - +
568A GLY* 1.3 58.7 + - - +
571A VAL* 3.0 28.1 + - - +
604A MET* 3.0 28.0 - - - +
753A LEU* 3.8 6.7 - - - -
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Residues in contact with GLY 568 (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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564A ASN 3.0 10.3 + - - -
565A MET 3.3 4.7 + - - -
566A LEU 3.1 0.8 - - - -
567A GLY* 1.3 76.9 - - - +
569A ARG* 1.3 56.6 + - - +
570A GLN 3.2 0.2 + - - -
571A VAL* 3.3 4.4 + - - +
572A ILE* 2.8 37.3 + - - +
750A PRO* 3.9 13.7 - - - -
752A MET* 4.3 5.3 - - - +
753A LEU* 3.8 16.3 - - - +
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Residues in contact with ARG 569 (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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544A LEU* 3.5 41.8 - - + +
545A TYR 2.7 34.5 + - - +
546A ALA* 3.8 12.3 + - - +
562A THR 5.6 0.2 + - - -
565A MET* 3.4 14.2 + - - +
566A LEU* 3.2 30.9 + - - +
568A GLY* 1.3 75.8 - - - +
570A GLN* 1.3 52.7 + - - +
572A ILE* 3.4 16.9 - - + +
573A ALA* 2.7 32.1 + - - +
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Residues in contact with GLN 570 (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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1A JZN 3.0 81.6 + - - +
542A GLU 5.8 0.4 + - - -
544A LEU* 4.2 17.7 - - + +
566A LEU* 2.8 37.3 + - + +
568A GLY 3.1 0.6 - - - -
569A ARG* 1.3 73.1 - - - +
571A VAL* 1.3 54.7 + - - +
573A ALA* 3.2 7.6 - - - +
574A ALA* 2.6 36.3 + - - +
604A MET* 3.1 14.6 - - + -
611A ARG* 4.8 6.4 + - - +
623A PHE 4.5 2.8 - - - +
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Residues in contact with VAL 571 (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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567A GLY 3.0 23.2 + - - +
568A GLY 3.5 4.3 - - - +
570A GLN* 1.3 77.2 - - - +
572A ILE* 1.3 60.9 + - - +
574A ALA* 3.2 9.6 + - + +
575A VAL* 3.0 32.4 + - + +
596A LEU* 6.5 1.1 - - + -
600A TRP* 4.1 24.5 - - + +
604A MET* 3.8 9.6 - - + +
752A MET* 3.5 25.6 - - + -
753A LEU* 3.3 19.3 - - + -
756A ILE* 3.5 20.9 - - + -
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Residues in contact with ILE 572 (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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568A GLY 2.8 23.3 + - - +
569A ARG* 3.4 20.4 - - + +
570A GLN 3.2 0.2 - - - -
571A VAL* 1.3 71.9 - - - +
573A ALA* 1.3 70.1 + - - +
575A VAL* 3.3 11.1 + - - +
576A LYS* 3.5 9.9 + - - +
752A MET* 4.1 28.3 - - + -
748D LEU* 4.1 24.1 - - + +
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Residues in contact with ALA 573 (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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1A JZN 4.4 3.8 - - + -
541A PRO* 4.0 25.4 - - + +
544A LEU* 4.3 12.6 - - + -
569A ARG 2.7 17.6 + - - +
570A GLN* 3.2 13.5 - - - +
572A ILE* 1.3 72.8 - - - +
574A ALA* 1.3 64.4 + - - +
575A VAL 2.8 2.3 + - - -
576A LYS* 2.9 19.0 + - - +
577A TRP* 3.1 12.3 + - - +
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Residues in contact with ALA 574 (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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1A JZN 4.1 20.8 - - + +
570A GLN 2.6 19.2 + - - +
571A VAL* 3.3 12.8 - - + +
573A ALA* 1.3 72.6 - - - +
575A VAL* 1.3 51.1 + - - +
577A TRP* 3.3 14.1 - - - +
578A ALA* 2.7 34.8 + - - +
596A LEU* 4.0 8.0 - - + +
600A TRP* 6.0 4.5 - - + -
603A LEU* 4.5 16.6 - - + -
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Residues in contact with VAL 575 (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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571A VAL* 3.0 24.7 - - + +
572A ILE* 3.6 5.2 - - - +
573A ALA 2.8 4.6 + - - -
574A ALA* 1.3 70.5 - - - +
576A LYS* 1.3 55.6 + - - +
578A ALA* 3.0 2.8 + - - +
579A LYS* 2.8 35.8 + - - +
596A LEU* 4.0 17.3 - - + -
752A MET* 5.3 0.7 - - - -
745D LEU* 4.1 15.9 - - + -
748D LEU* 3.7 37.7 - - + +
749D LEU* 3.8 32.1 - - + -
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Residues in contact with LYS 576 (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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572A ILE 3.5 5.9 + - - +
573A ALA* 2.9 11.0 + - - +
575A VAL* 1.3 78.6 - - - +
577A TRP* 1.3 65.8 + - - +
579A LYS* 3.4 12.9 + - - +
580A ALA* 3.4 17.5 + - - +
748D LEU* 5.5 2.1 - - + +
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Residues in contact with TRP 577 (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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1A JZN 5.7 2.5 - - + -
536A LEU* 4.7 5.2 + - + +
539A ILE* 3.3 43.9 - - + +
540A GLU* 4.0 4.4 + - - -
541A PRO* 3.8 25.1 - - + -
573A ALA 3.1 10.5 + - - +
574A ALA* 3.3 23.6 - - - +
576A LYS* 1.3 76.9 - - - +
578A ALA* 1.3 69.3 + - - +
580A ALA* 2.8 21.2 + - - +
581A ILE* 3.3 32.9 + - + +
603A LEU* 3.6 27.4 - - + -
664A LEU* 5.3 0.4 - - - +
667A LYS* 3.7 35.4 - - + +
668A THR* 3.9 33.0 - - - -
671A LEU* 3.9 12.8 - - + -
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Residues in contact with ALA 578 (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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574A ALA 2.7 18.3 + - - +
575A VAL* 3.0 8.5 + - - +
577A TRP* 1.3 73.1 - - + +
579A LYS* 1.3 59.0 + - - +
580A ALA 2.8 7.1 + - - -
581A ILE* 2.8 33.4 + - - +
584A PHE* 3.4 31.8 - - + +
596A LEU* 3.6 22.9 - - + -
671A LEU* 4.2 5.6 - - + -
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Residues in contact with LYS 579 (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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575A VAL* 2.8 21.6 + - - +
576A LYS* 3.8 11.0 - - - +
577A TRP 3.1 0.4 + - - -
578A ALA* 1.3 71.8 - - - +
580A ALA* 1.3 54.5 + - - +
584A PHE* 4.0 9.2 - - + -
585A ARG* 2.7 57.7 + - - +
592A GLN* 4.6 4.3 - - - +
748D LEU 3.2 26.7 + - - -
749D LEU* 3.6 22.4 - - + +
751D LYS* 3.3 34.2 + - - +
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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