Contacts of the helix formed by residues 547 - 572 (chain A) in PDB entry 4IM3
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 ARG 547 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A HIS 4.0 0.8 + - - -
544A PRO 2.9 19.9 + - - +
545A LYS* 3.8 9.6 - - - +
546A ASP* 1.3 80.9 - - - +
548A ASN* 1.3 59.3 + - - +
550A GLU* 3.1 54.3 + - + +
551A LYS* 2.9 33.6 + - + +
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Residues in contact with ASN 548 (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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542A THR* 3.8 26.5 - - - +
543A HIS 5.2 0.8 + - - -
546A ASP* 3.6 27.5 - - - +
547A ARG* 1.3 78.6 - - - +
549A VAL* 1.3 59.6 + - + +
551A LYS* 3.3 12.8 + - - +
552A LEU* 2.9 33.8 + - - +
600A HIS* 3.0 25.6 + - - +
604A GLU* 4.6 11.5 + - - +
605A CYS* 3.7 24.7 - - - +
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Residues in contact with VAL 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A CYS* 3.8 23.1 - - - +
429A ALA* 4.2 11.7 - - + +
430A SER* 4.0 35.9 - - - +
433A LEU* 5.0 13.9 - - + -
547A ARG 3.3 0.2 - - - -
548A ASN* 1.3 75.6 - - + +
550A GLU* 1.3 65.8 + - + +
552A LEU* 3.0 9.3 + - - +
553A GLN* 2.6 39.9 + - + +
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Residues in contact with GLU 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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544A PRO 4.9 3.0 - - - +
547A ARG* 3.1 67.5 + - + +
549A VAL* 1.3 79.8 + - + +
551A LYS* 1.3 64.9 + - - +
553A GLN* 3.7 8.7 - - + +
554A VAL* 3.0 32.0 + - + +
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Residues in contact with LYS 551 (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 ASP* 3.1 28.0 + - - +
547A ARG* 2.9 23.7 + - + +
548A ASN* 3.4 20.9 + - - +
550A GLU* 1.3 76.7 - - - +
552A LEU* 1.3 61.5 + - - +
554A VAL* 3.7 8.5 + - - +
555A LEU* 3.6 25.0 + - - +
600A HIS* 4.1 19.3 - - + +
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Residues in contact with LEU 552 (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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422A VAL* 4.8 7.3 - - + +
425A ALA* 4.7 4.9 - - + +
426A CYS* 4.3 19.3 - - + +
429A ALA* 3.8 28.9 - - + -
548A ASN 2.9 18.2 + - - +
549A VAL* 3.3 9.4 - - - +
551A LYS* 1.3 76.6 - - - +
553A GLN* 1.3 58.4 + - - +
555A LEU* 3.2 9.5 + - + +
556A LEU* 2.8 28.6 + - - +
597A ALA* 3.7 40.4 - - + +
600A HIS* 4.3 15.0 - - + -
601A PHE* 4.6 9.0 - - + -
605A CYS* 4.3 11.7 - - - -
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Residues in contact with GLN 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A CYS* 3.9 14.6 - - - -
549A VAL* 2.6 26.3 + - + +
550A GLU* 3.2 10.7 + - + +
552A LEU* 1.3 70.4 - - - +
554A VAL* 1.3 60.0 + - - +
556A LEU* 3.7 23.8 - - - +
557A ASN* 2.8 62.1 + - - +
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Residues in contact with VAL 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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550A GLU* 3.0 21.4 + - + +
551A LYS* 3.7 9.0 - - - +
553A GLN* 1.3 78.6 - - - +
555A LEU* 1.3 66.4 + - + +
557A ASN* 3.4 7.6 + - - +
558A CYS* 3.2 32.8 + - - -
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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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422A VAL* 5.9 0.2 - - + -
551A LYS 3.6 14.8 + - - +
552A LEU* 3.2 11.8 + - + +
554A VAL* 1.3 82.2 - - + +
556A LEU* 1.3 64.9 + - - +
558A CYS* 3.4 7.1 + - - +
559A MET* 3.1 30.3 + - - +
593A HIS* 3.8 37.7 - - + +
596A LYS* 4.1 26.0 - - + +
597A ALA* 3.8 37.0 - - + +
600A HIS* 5.8 3.4 - - + -
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Residues in contact with LEU 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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419A THR* 3.8 17.0 - - + +
422A VAL* 3.6 27.3 - - + +
423A CYS* 3.5 44.4 - - - +
426A CYS* 4.7 8.5 - - + -
552A LEU 2.8 16.1 + - - +
553A GLN* 3.2 34.1 + - - +
555A LEU* 1.3 76.3 - - - +
557A ASN* 1.3 50.7 + - - +
559A MET* 3.1 7.2 + - + +
560A THR* 2.6 46.0 + - - +
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Residues in contact with ASN 557 (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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553A GLN* 2.8 44.9 + - - +
554A VAL* 3.7 7.5 - - - +
555A LEU 3.3 0.2 - - - -
556A LEU* 1.3 73.7 - - - +
558A CYS* 1.3 65.2 + - - +
560A THR* 3.9 7.1 + - - -
561A GLU* 3.1 27.4 + - - +
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Residues in contact with CYS 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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554A VAL* 3.2 25.7 + - - -
555A LEU* 3.7 9.2 - - - +
556A LEU 3.4 0.2 - - - -
557A ASN* 1.3 78.8 - - - +
559A MET* 1.3 62.3 + - - +
561A GLU* 3.6 5.0 + - - +
562A ILE* 3.3 30.1 + - + +
593A HIS* 3.9 28.5 - - + +
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Residues in contact with MET 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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418A ILE* 4.2 20.2 - - + +
419A THR* 3.9 16.5 + - + +
422A VAL* 4.2 14.6 - - + -
555A LEU* 3.1 18.8 - - - +
556A LEU* 3.1 11.6 + - - +
558A CYS* 1.3 75.1 - - - +
560A THR* 1.3 61.0 + - - +
562A ILE* 3.5 5.9 + - - +
563A TYR* 3.0 26.2 + - - +
590A LEU* 3.5 33.5 - - + +
593A HIS* 3.5 29.4 - - + +
594A ALA* 3.6 31.6 - - + -
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Residues in contact with THR 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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101A PRO* 5.0 6.2 - - + +
419A THR* 3.8 16.2 - - + +
556A LEU* 2.6 36.5 + - - +
557A ASN* 3.9 9.4 + - - -
558A CYS 3.3 0.2 - - - -
559A MET* 1.3 71.3 - - - +
561A GLU* 1.3 61.2 + - - +
563A TYR* 3.3 11.5 + - + +
564A TYR* 3.0 55.9 + - + +
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Residues in contact with GLU 561 (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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557A ASN 3.1 18.4 + - - +
558A CYS* 3.8 6.3 - - - +
560A THR* 1.3 77.0 - - - +
562A ILE* 1.3 58.1 + - + +
564A TYR* 3.3 15.6 + - - +
565A GLN* 2.9 29.5 + - - +
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Residues in contact with ILE 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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558A CYS* 3.3 20.3 + - + +
559A MET* 3.7 9.2 - - - +
560A THR 3.3 0.2 - - - -
561A GLU* 1.3 74.6 - - + +
563A TYR* 1.3 57.3 + - - +
565A GLN* 3.1 6.7 + - + +
566A PHE* 2.7 66.5 + - + -
586A ASP* 3.8 39.7 - - + +
589A LYS* 4.2 15.9 - - + -
590A LEU* 4.2 13.2 - - + +
593A HIS* 4.5 7.6 - - + +
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Residues in contact with TYR 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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99A GLU* 3.2 38.3 + - - +
101A PRO* 3.9 24.0 - - + -
412A ALA* 3.9 8.1 - - - -
415A ALA* 3.7 18.2 - - + -
416A LYS* 3.6 40.7 - - + +
419A THR* 4.1 11.7 - - - +
559A MET 3.0 14.3 + - - +
560A THR* 3.4 11.4 - - + +
561A GLU 3.3 0.2 - - - -
562A ILE* 1.3 76.7 - - - +
564A TYR* 1.3 90.8 + + - +
566A PHE* 3.2 2.3 + - - +
567A LYS* 2.8 43.6 + - + +
590A LEU* 5.5 0.4 - - + +
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Residues in contact with TYR 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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99A GLU 5.9 0.7 - - - -
100A GLU* 4.1 24.5 + - - +
101A PRO* 4.4 6.6 - - - +
560A THR* 3.0 42.8 + - + +
561A GLU* 3.7 18.8 - - - +
563A TYR* 1.3 102.1 - + - +
565A GLN* 1.3 57.4 + - - +
567A LYS* 3.2 18.4 - - + +
568A LYS* 2.9 38.0 + - - +
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Residues in contact with GLN 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 GLU* 2.9 17.0 + - - +
562A ILE* 3.1 11.9 + - - +
564A TYR* 1.3 75.4 - - - +
566A PHE* 1.3 57.3 + - + +
568A LYS* 3.0 28.3 + - - +
569A ASP* 2.5 71.5 + - - +
582A ILE* 6.6 0.4 - - + -
586A ASP* 5.5 6.3 - - - +
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Residues in contact with PHE 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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408A LEU 4.7 1.0 - - - +
411A ASP* 4.1 11.9 - - + -
412A ALA* 3.8 17.8 - - + +
414A MET* 4.9 0.7 - - + -
415A ALA* 4.1 18.2 - - + -
562A ILE* 2.7 41.8 + - + +
563A TYR* 3.5 6.5 - - - +
565A GLN* 1.3 74.5 - - + +
567A LYS* 1.3 59.6 + - - +
569A ASP* 3.7 8.8 - - - +
570A LYS* 2.9 28.9 + - - +
583A HIS* 3.3 61.4 - + + -
586A ASP* 4.1 8.3 - - + -
587A LYS* 3.6 30.1 - - + -
590A LEU* 4.4 7.4 - - + -
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Residues in contact with LYS 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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95A TYR* 5.8 3.0 - - - -
99A GLU* 3.6 26.8 + - - +
412A ALA* 4.5 10.3 - - + +
563A TYR* 2.8 46.7 + - + +
564A TYR* 3.2 26.2 - - + +
566A PHE* 1.3 78.2 - - - +
568A LYS* 1.3 59.4 - - + +
570A LYS* 3.6 7.2 + - + +
571A ALA* 3.5 18.9 + - - +
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Residues in contact with LYS 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 TYR* 2.9 25.3 + - - +
565A GLN* 3.0 31.4 + - - +
567A LYS* 1.3 74.9 - - + +
569A ASP* 1.3 63.8 + - - +
570A LYS 3.1 0.2 - - - -
571A ALA* 3.2 16.0 + - - +
572A GLU* 3.3 13.2 + - - +
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Residues in contact with ASP 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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408A LEU* 3.2 13.5 - - + +
565A GLN* 2.5 57.4 + - - +
566A PHE* 3.3 11.4 + - - +
568A LYS* 1.3 72.4 - - - +
570A LYS* 1.3 54.7 + - - +
572A GLU* 2.6 29.4 - - - +
575A LEU* 4.0 29.5 - - + +
579A GLU 5.0 1.0 - - - +
583A HIS* 3.4 30.1 + - - +
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Residues in contact with LYS 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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408A LEU* 3.9 24.7 - - + +
409A ASP* 3.8 33.7 + - - +
412A ALA* 4.1 17.3 - - + +
413A SER* 6.0 1.0 - - - +
566A PHE 2.9 17.3 + - - +
567A LYS* 3.6 11.0 - - + +
568A LYS 3.1 0.4 - - - -
569A ASP* 1.3 76.9 - - - +
571A ALA* 1.3 68.0 + - - +
572A GLU 3.2 6.6 + - - +
573A ARG* 3.7 18.2 + - - +
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Residues in contact with ALA 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 LYS 3.5 8.7 + - - +
568A LYS* 3.2 10.8 + - - +
570A LYS* 1.3 80.3 - - - +
572A GLU* 1.3 59.6 + - - +
573A ARG* 3.5 14.8 + - - +
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Residues in contact with GLU 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A LEU* 3.6 1.2 - - - +
568A LYS 3.3 11.9 + - - +
569A ASP* 2.6 26.3 - - - +
570A LYS 3.2 1.4 - - - +
571A ALA* 1.3 77.0 - - - +
573A ARG* 1.3 63.3 + - - +
574A ARG* 3.1 25.1 + - - +
575A LEU* 3.4 19.8 - - + +
576A ALA 5.0 1.4 + - - -
579A GLU* 5.5 3.5 - - - +
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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
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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