Contacts of the helix formed by residues 543 - 569 (chain A) in PDB entry 1E3H
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 543 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A TYR* 3.4 33.4 - - + +
542A ILE* 1.3 88.8 - - + +
544A ALA* 1.3 66.8 + - - +
545A SER* 4.0 10.8 - - - +
546A VAL* 2.9 29.2 + - + +
547A LEU* 3.1 10.4 + - - +
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Residues in contact with ALA 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A ILE 3.5 2.9 + - - -
543A PRO* 1.3 71.4 - - - +
545A SER* 1.3 57.4 - - - +
547A LEU* 3.3 8.8 + - - +
548A ALA* 3.0 30.4 + - - +
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Residues in contact with SER 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A PRO* 4.0 11.3 - - - +
544A ALA* 1.3 79.8 - - - +
546A VAL* 1.3 62.5 + - - +
548A ALA* 3.8 7.2 - - - +
549A ALA* 3.0 28.2 + - - +
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Residues in contact with VAL 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A LEU* 4.4 13.2 - - + -
503A TYR* 3.7 45.3 - - + -
542A ILE* 3.8 17.0 - - + -
543A PRO* 2.9 29.4 + - + +
545A SER* 1.3 79.0 + - - +
547A LEU* 1.3 59.9 + - - +
549A ALA* 3.2 5.8 + - - +
550A ALA* 2.9 28.4 + - - +
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Residues in contact with LEU 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ALA* 4.3 19.3 - - + +
229A LEU* 4.1 24.9 - - + -
519A MSE 5.1 5.8 - - + -
521A PHE* 6.3 2.7 - - + -
535A LEU* 4.9 18.2 - - + -
542A ILE* 3.6 26.8 - - + +
543A PRO 3.1 5.9 + - - +
544A ALA* 3.7 10.1 - - - +
546A VAL* 1.3 77.7 - - - +
548A ALA* 1.3 64.0 + - - +
550A ALA* 3.2 7.7 + - + +
551A LEU* 2.9 42.7 + - + +
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Residues in contact with ALA 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A GLU* 5.7 1.3 - - - +
223A GLU* 6.0 2.0 - - - +
226A ALA* 6.2 2.0 - - - -
544A ALA 3.0 16.0 + - - +
545A SER* 3.8 8.3 - - - +
547A LEU* 1.3 78.4 - - - +
549A ALA* 1.3 57.1 + - - +
551A LEU* 3.4 8.8 + - - +
552A LYS* 2.9 30.8 + - - +
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Residues in contact with ALA 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A SER 3.0 19.9 + - - +
546A VAL* 3.5 7.6 - - - +
548A ALA* 1.3 74.1 - - - +
550A ALA* 1.3 58.9 + - - +
552A LYS* 3.3 8.1 + - - +
553A GLN* 2.9 31.8 + - - +
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Residues in contact with ALA 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A MSE 4.9 0.9 - - - +
492A LEU* 4.7 8.3 - - + -
505A ALA* 4.2 25.0 - - + +
519A MSE 6.3 1.3 - - - -
521A PHE* 3.6 28.5 - - + -
542A ILE* 5.8 1.3 - - + -
546A VAL 2.9 17.2 + - - +
547A LEU* 3.6 9.4 - - + +
549A ALA* 1.3 77.4 - - - +
551A LEU* 1.3 57.9 + - + +
553A GLN* 3.3 4.3 + - - +
554A ALA* 2.9 28.6 + - - +
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Residues in contact with LEU 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A GLU* 3.7 44.5 - - + +
225A VAL* 5.3 6.5 - - + -
226A ALA* 4.6 8.5 - - + +
229A LEU* 6.1 1.1 - - + -
521A PHE* 4.1 22.7 - - + -
523A VAL* 4.4 14.6 - - + -
533A LEU* 4.7 11.4 - - + -
535A LEU* 6.5 0.9 - - + -
547A LEU* 2.9 46.2 + - + +
548A ALA* 3.8 6.7 - - - +
550A ALA* 1.3 74.0 - - - +
552A LYS* 1.3 60.4 + - - +
554A ALA* 3.4 5.0 + - - +
555A ARG* 2.8 28.8 + - - +
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Residues in contact with LYS 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A GLU* 4.7 3.8 - - - +
548A ALA 2.9 19.8 + - - +
549A ALA* 3.7 8.7 - - - +
551A LEU* 1.3 72.8 - - - +
553A GLN* 1.3 65.6 + - - +
555A ARG* 3.3 15.6 + - + +
556A ASP* 3.0 47.9 + - - +
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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
----------------------------------------------------------
345A VAL* 3.3 9.4 + - - +
346A THR* 3.8 21.8 - - + +
490A MSE 4.9 3.2 - - - -
505A ALA* 3.3 42.0 + - - +
506A LEU 4.1 0.6 - - - -
507A THR* 2.6 32.1 + - - +
549A ALA 2.9 17.2 + - - +
550A ALA 3.4 6.1 - - - +
552A LYS* 1.3 75.9 - - - +
554A ALA* 1.3 62.3 + - - +
556A ASP* 3.0 21.0 + - + +
557A ALA* 3.1 12.6 + - - +
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Residues in contact with ALA 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A ILE* 3.6 12.3 - - + +
490A MSE 3.6 35.6 - - + -
521A PHE* 4.1 8.3 - - + -
523A VAL* 4.5 13.0 - - + -
550A ALA 2.9 17.0 + - - +
551A LEU* 3.6 6.1 - - - +
553A GLN* 1.3 77.6 - - - +
555A ARG* 1.3 56.3 + - - +
557A ALA* 3.3 4.3 + - - +
558A ARG* 3.0 28.3 + - - +
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Residues in contact with ARG 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A GLU* 3.5 33.0 + - - +
527A LYS 4.0 18.0 + - - -
551A LEU 2.8 18.1 + - - +
552A LYS* 3.4 15.3 - - - +
553A GLN 3.2 0.2 - - - -
554A ALA* 1.3 74.9 - - - +
556A ASP* 1.3 76.1 + - - +
558A ARG* 3.2 22.7 + - - +
559A LEU* 3.0 51.5 + - + +
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Residues in contact with ASP 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A LYS* 3.0 40.2 + - - +
553A GLN* 3.0 12.2 + - + +
555A ARG* 1.3 89.5 + - - +
557A ALA* 1.3 63.2 + - - +
559A LEU* 3.3 10.5 + - - +
560A HIS* 3.1 22.2 + - - +
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Residues in contact with ALA 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ILE* 3.8 16.6 - - + -
488A ILE* 3.9 13.2 - - + -
507A THR* 3.8 28.7 - - + -
553A GLN 3.1 9.7 + - - +
554A ALA* 3.5 9.6 - - - +
555A ARG 3.2 0.2 - - - -
556A ASP* 1.3 76.9 - - - +
558A ARG* 1.3 62.0 + - - +
560A HIS* 3.2 4.0 + - - +
561A ILE* 3.1 30.1 + - - +
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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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222A GLU* 2.5 31.7 + - - -
486A ALA* 3.4 27.8 - - + +
487A GLY* 4.5 1.6 - - - +
488A ILE* 4.7 8.9 - - + +
523A VAL* 4.1 14.0 - - + +
524A ALA 4.5 2.0 - - - -
525A GLY* 3.2 27.0 - - - +
526A THR 2.5 33.4 + - - -
527A LYS* 4.6 4.6 + - - +
528A GLU 5.0 0.2 - - - -
529A PHE* 3.4 20.9 + - - +
530A VAL* 4.0 10.9 - - - +
554A ALA 3.0 13.3 + - - +
555A ARG* 3.2 24.2 + - - +
557A ALA* 1.3 78.2 - - - +
559A LEU* 1.3 60.0 + - - +
561A ILE* 3.3 10.9 + - - +
562A LEU* 3.0 31.2 + - - +
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Residues in contact with LEU 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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526A THR 4.7 2.0 - - - +
527A LYS* 3.7 45.5 - - + +
555A ARG* 3.0 57.2 + - + +
556A ASP* 3.7 8.3 - - - +
557A ALA 3.3 0.2 - - - -
558A ARG* 1.3 75.9 - - + +
560A HIS* 1.3 66.2 + - - +
562A LEU* 3.3 10.6 + - + +
563A ASP* 3.2 26.4 + - - +
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Residues in contact with HIS 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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348A ILE* 3.7 27.1 - - + +
351A LEU* 4.0 20.0 - - + +
556A ASP 3.1 12.1 + - - +
557A ALA* 3.2 8.9 + - - +
559A LEU* 1.3 76.0 - - - +
561A ILE* 1.3 57.8 + - - +
563A ASP* 2.9 34.9 + - + +
564A VAL* 3.2 18.0 + - + +
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Residues in contact with ILE 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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348A ILE* 4.4 8.3 - - + -
351A LEU* 4.0 25.6 - - + -
367A PHE* 4.1 13.9 - - + -
369A ARG* 4.8 11.4 - - - +
468A CYS* 4.0 14.6 - - - -
486A ALA* 4.0 3.8 - - + -
487A GLY 3.8 12.6 - - - +
488A ILE* 3.6 30.3 - - + -
557A ALA 3.1 17.5 + - - +
558A ARG* 3.6 7.9 - - - +
560A HIS* 1.3 77.1 - - - +
562A LEU* 1.3 61.7 + - - +
564A VAL* 3.2 3.7 + - + +
565A MSE 3.0 39.7 + - - +
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Residues in contact with LEU 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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484A PRO* 3.9 19.1 - - + +
485A VAL 3.9 6.7 - - - -
486A ALA* 3.4 27.8 - - + +
525A GLY 4.2 4.0 - - - +
526A THR* 3.9 7.6 - - - +
527A LYS* 3.6 50.5 - - + +
558A ARG* 3.0 19.4 + - - +
559A LEU* 3.6 16.4 - - + +
560A HIS 3.2 0.2 - - - -
561A ILE* 1.3 76.1 - - - +
563A ASP* 1.3 59.5 + - - +
565A MSE 3.4 15.3 + - + +
566A MSE 2.9 37.0 + - - +
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Residues in contact with ASP 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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527A LYS* 5.2 8.3 - - - -
559A LEU* 3.2 15.8 + - - +
560A HIS* 2.9 20.2 + - - +
562A LEU* 1.3 76.5 - - - +
564A VAL* 1.3 65.9 + - + +
566A MSE 3.2 15.3 + - - +
567A GLU* 3.3 19.9 + - - +
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Residues in contact with VAL 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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351A LEU* 3.7 40.4 - - + -
352A ALA* 4.8 1.6 - - - +
353A ALA* 4.2 24.6 - - + +
367A PHE* 6.2 2.5 - - + -
560A HIS* 3.2 27.3 + - + +
561A ILE* 3.2 6.5 + - + +
563A ASP* 1.3 75.8 - - + +
565A MSE 1.3 63.2 + - + +
567A GLU* 3.3 28.7 + - - +
568A ALA* 3.7 3.5 + - - +
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Residues in contact with MSE 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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353A ALA* 4.5 2.7 - - + -
367A PHE* 4.9 3.4 - - + -
468A CYS* 3.7 22.4 - - + +
471A THR* 3.5 28.7 - - + -
472A MSE 3.9 34.2 - - + +
484A PRO* 4.7 2.0 - - + -
485A VAL 3.3 21.8 - - - +
486A ALA* 3.7 24.7 - - - -
561A ILE* 3.0 25.4 + - + +
562A LEU* 3.6 15.0 - - + +
564A VAL* 1.3 77.4 - - + +
566A MSE 1.3 60.5 + - + +
568A ALA* 3.0 20.6 + - - +
569A ILE* 3.1 13.4 + - - +
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Residues in contact with MSE 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A THR* 5.9 0.4 - - - -
475A LEU* 5.2 3.4 - - + -
484A PRO* 3.7 41.7 - - + -
527A LYS* 4.3 16.6 - - - +
562A LEU* 2.9 28.2 + - - +
563A ASP* 3.2 8.0 + - - +
565A MSE 1.3 77.6 - - - +
567A GLU* 1.3 65.5 + - + +
568A ALA 3.2 0.2 - - - -
569A ILE* 3.3 29.3 - - - +
570A ASP* 3.0 51.0 + - - +
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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
----------------------------------------------------------
563A ASP* 3.3 15.4 + - - +
564A VAL* 3.6 20.3 - - - +
565A MSE 3.1 1.0 - - - -
566A MSE 1.3 78.4 - - - +
568A ALA* 1.3 61.9 + - - +
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Residues in contact with ALA 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ALA* 3.9 37.9 - - + +
354A GLU* 4.2 8.7 - - - -
355A VAL* 4.0 13.4 - - - +
472A MSE 4.1 8.1 - - - -
564A VAL 3.7 1.8 + - - +
565A MSE 3.0 10.2 + - - +
567A GLU* 1.3 82.3 - - - +
569A ILE* 1.3 62.8 + - + +
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Residues in contact with ILE 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A VAL* 3.7 21.3 - - + -
472A MSE 4.0 27.4 - - + -
475A LEU* 3.6 18.1 - - + +
476A ASN* 3.4 29.8 - - + +
565A MSE 3.1 10.7 + - - +
566A MSE 3.3 18.1 - - - +
567A GLU 3.5 0.4 - - - -
568A ALA* 1.3 80.4 - - + +
570A ASP* 1.3 63.7 + - - +
571A THR 3.4 16.2 - - - +
573A ASP* 3.4 28.9 - - - +
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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