Contacts of the helix formed by residues 547 - 570 (chain A) in PDB entry 1XR2
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 PRO 547 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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545A ASP 4.7 1.1 - - - +
546A ILE* 1.3 93.1 - - + +
548A GLU* 1.3 66.4 + - - +
549A ARG* 4.3 9.2 - - + +
550A GLU* 3.2 39.9 + - + +
551A ILE* 3.4 10.4 + - - +
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Residues in contact with GLU 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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537A MET* 3.7 10.2 - - - +
542A TYR* 2.7 39.6 + - + +
546A ILE 3.6 2.1 + - - +
547A PRO* 1.3 71.7 - - - +
549A ARG* 1.3 65.8 + - - +
551A ILE* 3.0 10.0 + - - +
552A ALA* 2.9 24.0 + - - +
584A LYS* 3.3 13.6 + - - -
598A TRP* 3.7 31.5 + - + -
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Residues in contact with ARG 549 (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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547A PRO* 4.3 9.4 - - + +
548A GLU* 1.3 77.7 - - - +
550A GLU* 1.3 51.6 + - - +
552A ALA* 3.2 1.7 + - - +
553A TYR* 2.8 53.3 + - + +
598A TRP* 4.0 40.5 - - + +
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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
----------------------------------------------------------
371A VAL* 5.0 12.6 - - - +
374A VAL* 5.8 5.8 - - + -
375A ARG* 6.1 3.6 - - - +
546A ILE* 4.4 18.8 - - + +
547A PRO* 3.2 37.3 + - + +
549A ARG* 1.3 75.4 - - - +
551A ILE* 1.3 66.5 + - - +
553A TYR* 3.1 11.2 + - + +
554A GLN* 2.9 46.4 + - + +
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Residues in contact with ILE 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A ILE* 4.1 24.5 - - + -
504A VAL* 5.0 2.7 - - + -
537A MET* 4.0 10.8 - - + -
542A TYR* 4.1 20.0 - - + -
543A ARG* 3.6 28.5 - - + +
546A ILE* 3.5 34.3 - - + +
547A PRO 3.4 6.7 + - - +
548A GLU* 3.0 9.0 + - - +
550A GLU* 1.3 74.8 - - - +
552A ALA* 1.3 63.4 + - - +
554A GLN* 3.2 12.4 + - - +
555A ILE* 3.0 45.3 + - + +
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Residues in contact with ALA 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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533A PRO* 3.5 10.8 - - + +
534A VAL* 5.0 2.5 - - + -
537A MET* 3.4 28.6 - - + -
548A GLU 2.9 7.6 + - - +
549A ARG 3.4 8.1 - - - +
551A ILE* 1.3 78.6 - - - +
553A TYR* 1.3 58.6 + - + +
555A ILE* 3.4 5.5 + - - -
556A ALA* 2.9 28.5 + - - +
598A TRP* 3.8 17.7 - - + -
602A ALA* 4.1 12.3 - - + -
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Residues in contact with TYR 553 (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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374A VAL* 5.2 14.8 - - + +
382A PHE* 4.3 22.0 - + - -
549A ARG* 2.8 34.3 + - + +
550A GLU* 3.5 8.1 - - + +
552A ALA* 1.3 73.6 - - - +
554A GLN* 1.3 54.6 - - - +
556A ALA* 3.1 6.1 + - - +
557A LEU* 2.7 36.5 + - - +
598A TRP* 3.7 35.8 - - + +
601A ASN* 3.3 30.4 + - + +
602A ALA* 3.8 18.4 - - + -
605A LEU* 3.7 13.2 - - + +
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Residues in contact with GLN 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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370A ALA* 5.2 2.2 - - + +
371A VAL* 4.4 13.1 - - - +
374A VAL* 4.3 19.0 - - + +
502A GLY 4.4 0.7 - - - +
503A THR* 3.5 24.9 + - + +
504A VAL* 3.0 44.5 + - + +
546A ILE* 4.6 12.2 - - - +
550A GLU* 2.9 37.8 + - + +
551A ILE* 3.5 13.0 - - - +
553A TYR* 1.3 74.7 - - - +
555A ILE* 1.3 63.7 + - - +
557A LEU* 3.3 8.7 + - - +
558A ALA* 3.1 21.1 + - - +
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Residues in contact with ILE 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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476A LEU* 4.7 8.7 - - + -
479A ILE* 5.4 0.9 - - + -
500A ILE* 4.0 18.8 - - + -
504A VAL* 4.0 20.6 - - + -
533A PRO* 4.0 15.3 - - + +
536A ILE* 3.9 36.3 - - + -
537A MET* 4.0 16.4 - - + -
551A ILE* 3.0 32.6 + - + +
552A ALA* 3.7 5.6 - - - +
554A GLN* 1.3 76.3 - - - +
556A ALA* 1.3 58.5 + - - +
558A ALA* 3.2 7.5 + - + +
559A ILE* 2.8 29.7 + - + +
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Residues in contact with ALA 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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533A PRO* 3.6 11.6 - - + +
552A ALA 2.9 14.8 + - - +
553A TYR* 3.3 10.1 - - - +
555A ILE* 1.3 74.9 - - - +
557A LEU* 1.3 65.7 + - - +
559A ILE* 3.2 1.0 + - - -
560A ASN* 2.8 24.6 + - - +
602A ALA 3.3 27.6 - - - +
605A LEU* 3.8 17.0 - - + -
606A ALA* 3.6 12.0 - - - +
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Residues in contact with LEU 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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373A ARG* 5.7 2.9 - - + +
374A VAL* 5.1 19.5 - - + -
381A SER* 6.1 0.9 - - - -
553A TYR 2.7 14.2 + - - +
554A GLN* 3.4 12.8 - - - +
556A ALA* 1.3 72.0 - - - +
558A ALA* 1.3 63.5 + - - +
560A ASN* 2.9 20.7 + - + +
561A GLU* 3.0 14.5 + - + +
605A LEU* 3.7 33.9 - - + -
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Residues in contact with ALA 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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476A LEU* 5.0 7.9 - - + -
504A VAL* 4.6 6.1 - - + -
505A THR* 4.4 7.2 - - - -
506A ARG* 3.9 41.8 - - + +
510A MET* 4.5 2.0 - - + +
554A GLN 3.1 10.0 + - - +
555A ILE* 3.3 13.0 - - + +
557A LEU* 1.3 82.1 - - - +
559A ILE* 1.3 61.6 + - + +
561A GLU* 3.3 15.0 + - - +
562A GLU* 3.5 7.3 + - - +
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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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472A PHE* 6.4 1.1 - - + -
476A LEU* 6.1 1.3 - - + -
510A MET* 4.8 9.2 - - + -
530A LEU* 4.2 23.6 - - + -
531A THR 2.9 31.9 - - - +
532A GLY 3.6 0.9 - - - -
533A PRO* 3.3 33.2 - - + -
536A ILE* 3.9 13.0 - - + -
555A ILE* 2.8 24.2 + - + +
556A ALA 3.7 4.5 - - - +
557A LEU 3.2 0.2 - - - -
558A ALA* 1.3 74.2 - - + +
560A ASN* 1.3 62.2 + - - +
562A GLU* 3.3 10.2 + - - +
563A VAL* 3.1 21.5 + - + +
576A ILE* 4.9 4.7 - - + -
606A ALA* 3.8 15.9 - - + +
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Residues in contact with ASN 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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556A ALA 2.8 13.4 + - - +
557A LEU* 2.9 15.5 + - + +
559A ILE* 1.3 74.2 - - - +
561A GLU* 1.3 65.3 + - - +
562A GLU 3.0 1.8 - - - -
563A VAL* 3.0 9.6 + - - +
564A LYS* 3.0 48.6 + - - +
605A LEU* 3.4 21.6 + - + +
606A ALA 3.2 20.2 + - - +
608A ASN* 3.2 27.1 + - - +
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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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506A ARG* 3.8 22.0 - - + +
557A LEU* 3.0 13.4 + - + +
558A ALA* 3.3 13.0 + - - +
560A ASN* 1.3 76.7 - - - +
562A GLU* 1.3 60.0 + - - +
564A LYS* 3.4 11.3 + - - +
565A ASP* 3.2 26.3 + - - +
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Residues in contact with GLU 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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506A ARG* 2.6 42.2 + - - +
509A PRO* 3.6 1.7 - - - +
510A MET* 2.9 38.0 + - + +
511A THR* 2.6 39.8 + - - +
512A LEU* 3.8 5.7 + - - -
530A LEU* 3.7 25.4 - - + -
558A ALA 3.5 2.4 + - - +
559A ILE* 3.3 11.6 + - - +
560A ASN 3.0 0.2 - - - -
561A GLU* 1.3 77.5 - - - +
563A VAL* 1.3 65.0 + - - +
565A ASP* 3.1 3.6 + - - +
566A LEU* 3.0 27.4 + - + +
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Residues in contact with VAL 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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530A LEU* 3.6 19.7 - - + -
559A ILE* 3.1 16.2 + - + +
560A ASN* 3.0 16.1 + - - +
562A GLU* 1.3 77.0 - - - +
564A LYS* 1.3 61.3 + - + +
566A LEU* 3.4 11.7 + - - +
567A GLU* 3.1 26.7 + - + +
574A VAL* 4.5 12.7 - - + +
576A ILE* 4.5 9.4 - - + -
606A ALA 3.4 18.4 - - - +
607A ALA 5.5 0.2 - - - -
609A ALA* 3.8 29.2 - - + -
615A ILE* 4.9 4.0 - - + -
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Residues in contact with LYS 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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560A ASN* 3.0 36.7 + - - +
561A GLU* 3.7 11.2 - - - +
562A GLU 3.1 0.2 - - - -
563A VAL* 1.3 75.7 - - + +
565A ASP* 1.3 60.7 + - - +
567A GLU* 3.1 20.9 + - - +
568A GLU* 2.9 29.5 + - - +
608A ASN* 3.7 21.2 + - - +
609A ALA* 5.3 1.4 - - - +
610A ARG 5.8 0.4 - - - +
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Residues in contact with ASP 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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506A ARG* 2.8 38.9 + - - +
509A PRO* 4.1 8.1 - - - +
512A LEU* 3.6 27.6 - - + +
561A GLU 3.2 8.3 + - - +
562A GLU* 3.1 8.3 + - - +
564A LYS* 1.3 76.4 - - - +
566A LEU* 1.3 58.4 + - - +
568A GLU* 3.3 7.3 + - - +
569A ALA* 2.9 30.7 + - - +
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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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511A THR* 4.1 13.9 - - - +
512A LEU* 3.8 21.5 - - + -
515A ILE* 3.9 35.7 - - + -
528A GLY* 4.2 12.8 - - - -
530A LEU* 4.3 20.4 - - + -
562A GLU* 3.0 20.4 + - + +
563A VAL* 3.5 8.3 - - - +
565A ASP* 1.3 77.8 - - - +
567A GLU* 1.3 59.9 + - - +
569A ALA 3.3 0.3 + - - -
570A GLY 3.1 2.6 + - - -
571A ILE* 2.8 43.4 + - + +
574A VAL* 4.0 22.7 - - + -
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Residues in contact with GLU 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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563A VAL* 3.1 14.2 + - + +
564A LYS* 3.1 30.3 + - - +
566A LEU* 1.3 74.3 - - + +
568A GLU* 1.3 60.9 + - - +
570A GLY* 2.9 20.3 + - - -
571A ILE 4.0 9.1 - - - +
574A VAL* 5.5 0.2 - - + -
609A ALA* 3.2 11.0 - - - +
610A ARG* 2.9 32.1 + - - +
613A THR* 2.5 42.0 + - + +
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Residues in contact with GLU 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 LYS 2.9 16.0 + - - +
565A ASP* 3.8 8.1 - - - +
567A GLU* 1.3 76.8 - - - +
569A ALA* 1.3 60.0 + - - +
570A GLY* 3.3 0.9 + - - -
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Residues in contact with ALA 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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512A LEU* 3.9 14.4 - - + -
516A THR* 4.2 13.4 - - + +
565A ASP 2.9 18.6 + - - +
567A GLU 3.1 0.4 - - - -
568A GLU* 1.3 76.4 - - - +
570A GLY* 1.3 58.8 + - - +
571A ILE* 3.6 20.0 - - + +
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Residues in contact with GLY 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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398A ARG* 5.4 3.3 + - - -
519A GLN* 4.9 10.5 - - - +
567A GLU 2.9 13.5 + - - -
568A GLU 3.1 1.4 - - - -
569A ALA* 1.3 79.8 - - - +
571A ILE* 1.3 66.4 + - - +
572A LYS* 3.3 20.1 + - - +
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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
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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