Contacts of the helix formed by residues 546 - 575 (chain F) in PDB entry 2CEA
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 546 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547E GLU* 2.9 22.4 - - - -
550E ALA* 3.8 4.6 - - - +
551E SER* 3.5 31.5 - - - -
554E ASP* 2.6 24.3 + - - -
543F ARG* 4.2 1.6 - - - -
545F TYR* 1.3 81.3 - - - +
547F GLU* 1.3 56.3 + - - +
548F GLU* 3.4 3.5 + - - +
549F VAL* 3.2 20.5 + - - +
550F ALA* 3.1 22.5 + - - +
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Residues in contact with GLU 547 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547E GLU* 2.5 28.0 + - + +
543F ARG* 3.7 22.6 + - - +
546F SER* 1.3 70.5 - - - +
548F GLU* 1.3 62.8 + - - +
549F VAL 3.2 0.2 - - - -
550F ALA* 3.7 7.2 - - - +
551F SER* 3.1 30.5 + - - -
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Residues in contact with GLU 548 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547E GLU* 4.0 1.4 + - - -
551E SER* 3.1 31.1 + - - +
555E GLU* 4.9 9.0 - - - +
546F SER* 3.2 9.0 + - - +
547F GLU* 1.3 78.1 - - - +
549F VAL* 1.3 64.6 + - + +
551F SER* 3.2 7.8 - - - -
552F LYS* 3.2 42.2 + - - +
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Residues in contact with VAL 549 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554E ASP* 3.5 26.5 - - + +
521F LEU* 3.7 26.5 - - + -
526F TRP* 3.9 26.2 - - + -
545F TYR* 4.1 5.8 - - + -
546F SER* 3.2 22.1 + - - +
548F GLU* 1.3 77.2 - - + +
550F ALA* 1.3 66.6 + - - +
551F SER 2.9 1.6 - - - -
552F LYS* 3.0 11.4 + - + +
553F ILE* 2.8 30.7 + - + +
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Residues in contact with ALA 550 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509F ARG* 6.4 0.2 - - - +
543F ARG* 3.8 25.6 - - - +
545F TYR* 3.8 16.1 - - + +
546F SER 3.1 17.8 + - - +
547F GLU* 3.8 13.2 - - - +
549F VAL* 1.3 75.8 - - - +
551F SER* 1.3 57.0 + - - +
553F ILE* 3.3 6.2 + - - +
554F ASP* 3.0 39.2 + - - +
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Residues in contact with SER 551 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547F GLU* 3.1 23.4 + - - -
548F GLU* 3.2 13.7 - - - -
550F ALA* 1.3 76.5 - - - +
552F LYS* 1.3 64.7 - - - +
554F ASP* 3.6 7.2 + - - +
555F GLU* 3.2 34.1 + - - +
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Residues in contact with LYS 552 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A LYS* 5.4 8.7 - - - +
555B GLU* 5.4 9.6 - - - +
555E GLU* 6.0 4.6 + - - +
558E LYS* 5.0 15.2 - - - +
520F GLU* 5.3 14.6 - - + -
521F LEU* 4.3 22.2 - - + -
548F GLU* 3.2 34.2 + - - +
549F VAL* 3.0 14.4 + - + +
551F SER* 1.3 77.3 - - - +
553F ILE* 1.3 65.8 + - - +
555F GLU* 3.1 17.4 + - - +
556F GLU* 2.9 28.0 + - + +
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Residues in contact with ILE 553 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509F ARG* 3.8 23.3 - - - +
512F VAL* 4.3 2.7 - - + -
513F CYS* 3.8 27.8 - - - -
521F LEU* 4.0 22.2 - - + -
526F TRP* 4.0 14.8 - - + -
545F TYR* 3.7 33.2 - - + +
549F VAL* 2.8 23.7 + - + +
550F ALA* 3.5 7.9 - - - +
552F LYS* 1.3 76.4 - - - +
554F ASP* 1.3 63.1 + - - +
556F GLU* 3.3 1.2 + - - +
557F VAL* 3.0 39.6 + - + +
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Residues in contact with ASP 554 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509F ARG* 3.2 29.2 + - - +
550F ALA* 3.0 25.6 + - - +
551F SER* 3.9 7.3 - - - +
553F ILE* 1.3 76.6 - - - +
555F GLU* 1.3 63.6 + - + +
557F VAL* 4.0 4.5 - - - +
558F LYS* 3.0 25.5 + - - +
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Residues in contact with GLU 555 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B GLU* 4.6 12.9 - - - +
551F SER* 3.2 25.3 + - - +
552F LYS* 3.1 20.4 + - - +
554F ASP* 1.3 76.8 - - + +
556F GLU* 1.3 59.8 + - + +
558F LYS* 3.3 6.1 + - - +
559F LYS* 2.9 31.9 + - - +
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Residues in contact with GLU 556 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B LYS* 4.8 2.6 + - - -
512F VAL* 4.2 17.3 - - + -
518F SER* 3.1 29.8 + - - +
519F GLU* 3.3 34.6 - - - +
520F GLU* 4.0 14.4 - - + +
521F LEU* 3.9 9.0 - - + -
552F LYS* 2.9 18.4 + - + +
553F ILE 3.8 2.9 - - - +
555F GLU* 1.3 76.2 - - + +
557F VAL* 1.3 67.6 + - - +
559F LYS* 3.0 23.3 + - - +
560F ILE* 3.0 32.5 + - - +
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Residues in contact with VAL 557 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505F THR* 4.3 11.4 - - + +
508F ALA* 3.7 26.2 - - + +
509F ARG* 3.9 42.6 - - + +
512F VAL* 4.1 10.3 - - + -
553F ILE* 3.0 27.2 + - + +
554F ASP* 4.0 5.8 - - - +
556F GLU* 1.3 76.0 - - - +
558F LYS* 1.3 63.7 + - - +
560F ILE* 3.3 3.2 + - - +
561F VAL* 3.2 26.0 + - + +
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Residues in contact with LYS 558 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554F ASP 3.0 18.5 + - - +
555F GLU* 3.7 5.6 - - - +
557F VAL* 1.3 74.6 - - - +
559F LYS* 1.3 64.9 + - - +
561F VAL* 4.7 3.4 - - - +
562F THR* 2.5 45.5 + - - +
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Residues in contact with LYS 559 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B GLU* 4.0 28.1 - - - +
520B GLU* 3.3 32.8 + - - +
556B GLU* 5.3 2.8 + - - -
559B LYS* 3.2 30.3 - - - +
519F GLU* 4.3 17.5 + - - +
555F GLU* 2.9 17.1 + - - +
556F GLU* 3.0 23.0 + - - +
558F LYS* 1.3 77.2 - - - +
560F ILE* 1.3 65.4 + - + +
562F THR* 3.8 2.9 - - - -
563F ASN* 2.9 44.7 + - - +
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Residues in contact with ILE 560 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469F ARG* 4.7 16.2 - - - +
473F LEU* 4.0 19.0 - - + +
476F LEU* 3.9 25.6 - - + -
508F ALA* 4.1 10.8 - - + +
511F MET* 4.5 15.5 - - + -
512F VAL* 3.6 31.4 - - + -
517F MET 5.2 2.7 - - - +
518F SER* 5.6 0.9 - - - -
519F GLU* 5.7 4.3 - - - +
556F GLU* 3.0 21.2 + - - +
557F VAL* 3.8 6.3 - - - +
558F LYS 3.3 0.2 - - - -
559F LYS* 1.3 78.3 - - + +
561F VAL* 1.3 58.7 + - - +
563F ASN* 3.5 6.0 - - - +
564F CYS* 3.0 34.3 + - - -
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Residues in contact with VAL 561 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476F LEU* 4.3 5.2 - - + -
480F LEU* 3.7 24.5 - - + +
501F ILE* 5.9 1.3 - - + +
504F ALA* 4.1 18.4 - - + +
505F THR* 4.4 10.8 - - - +
508F ALA* 3.6 22.7 - - + -
557F VAL* 3.2 18.0 + - + +
558F LYS* 4.3 3.8 - - - +
560F ILE* 1.3 74.1 - - - +
562F THR* 1.3 61.8 + - - +
564F CYS* 3.2 6.1 + - - +
565F TYR* 2.8 29.5 + - + +
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Residues in contact with THR 562 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B GLU* 6.1 1.1 - - - +
558F LYS* 2.5 43.1 + - - +
559F LYS* 3.8 3.4 - - - -
561F VAL* 1.3 80.4 - - - +
563F ASN* 1.3 65.6 + - - +
565F TYR* 3.1 9.1 + - + +
566F GLU* 2.9 35.8 + - + +
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Residues in contact with ASN 563 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B GLU* 4.1 21.4 + - - +
559F LYS* 2.9 36.6 + - - +
560F ILE* 3.5 6.7 - - - +
562F THR* 1.3 77.5 - - - +
564F CYS* 1.3 60.1 + - - +
566F GLU* 3.2 8.5 + - - +
567F ARG* 3.0 27.5 + - - +
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Residues in contact with CYS 564 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473F LEU* 3.6 45.3 - - - -
476F LEU* 4.1 10.1 - - + -
477F THR* 3.7 22.4 + - - +
480F LEU* 4.1 12.7 - - + +
560F ILE* 3.0 25.8 + - - +
561F VAL* 3.6 5.2 - - - +
563F ASN* 1.3 76.3 - - - +
565F TYR* 1.3 66.8 + - - +
567F ARG* 3.3 7.7 + - - +
568F ALA* 3.1 20.6 + - - +
----------------------------------------------------------
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Residues in contact with TYR 565 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480F LEU* 3.9 29.4 - - + +
483F ARG* 3.3 40.8 + - + +
484F ALA* 3.8 15.9 - - + -
487F GLU* 2.6 38.0 + - - +
493F VAL* 4.7 1.0 - - - +
561F VAL* 2.8 15.2 + - + +
562F THR* 3.3 14.6 - - + +
564F CYS* 1.3 77.5 - - - +
566F GLU* 1.3 68.6 + - - +
568F ALA* 3.1 14.9 + - - +
569F LYS* 3.1 34.4 + - + +
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Residues in contact with GLU 566 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566C GLU* 5.8 0.6 - - - +
562F THR* 2.9 28.3 + - + +
563F ASN* 3.6 9.9 - - - +
565F TYR* 1.3 83.0 - - + +
567F ARG* 1.3 61.1 + - - +
569F LYS* 3.3 33.6 + - - +
570F GLU* 3.2 28.7 + - - +
573F ARG* 4.6 8.8 + - - -
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Residues in contact with ARG 567 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434F VAL* 3.0 30.4 - - - +
435F PRO* 3.8 11.3 - - - +
473F LEU* 4.0 8.3 + - - +
474F ASP* 2.9 27.9 + - - +
477F THR* 3.2 25.0 + - + +
563F ASN 3.0 12.9 + - - +
564F CYS* 3.5 12.8 - - - +
565F TYR 3.1 0.2 - - - -
566F GLU* 1.3 76.0 - - - +
568F ALA* 1.3 64.3 + - - +
570F GLU* 3.4 15.8 + - + +
571F ILE* 3.2 33.6 + - + +
----------------------------------------------------------
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Residues in contact with ALA 568 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430F VAL* 4.2 10.7 - - + +
477F THR* 3.9 27.5 - - + +
480F LEU 4.4 3.6 - - - +
481F GLY* 4.2 2.2 - - - -
484F ALA* 3.6 18.8 - - + -
564F CYS 3.1 10.7 + - - +
565F TYR* 3.1 11.8 + - - +
567F ARG* 1.3 75.6 - - - +
569F LYS* 1.3 58.9 + - - +
571F ILE* 3.2 4.2 + - - +
572F ILE* 2.9 32.4 + - - +
----------------------------------------------------------
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Residues in contact with LYS 569 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484F ALA* 3.9 17.9 - - + -
487F GLU* 3.7 39.9 + - + +
488F VAL* 3.9 16.2 - - + -
565F TYR* 3.1 32.4 + - + +
566F GLU* 3.3 39.3 + - - +
567F ARG 3.3 0.2 - - - -
568F ALA* 1.3 73.8 - - - +
570F GLU* 1.3 65.7 + - - +
572F ILE* 3.6 4.4 + - - +
573F ARG* 3.1 48.6 + - - +
----------------------------------------------------------
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Residues in contact with GLU 570 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566F GLU* 3.2 18.9 + - - +
567F ARG* 3.5 19.7 - - + +
568F ALA 3.2 0.2 - - - -
569F LYS* 1.3 77.4 - - - +
571F ILE* 1.3 63.2 + - + +
573F ARG* 3.2 19.4 + - - +
574F LYS* 2.9 26.2 + - - +
----------------------------------------------------------
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Residues in contact with ILE 571 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429F VAL* 4.2 12.6 - - + -
430F VAL* 3.8 33.0 - - + +
433F VAL* 4.0 32.1 - - + -
434F VAL* 4.9 8.1 - - + +
477F THR* 4.4 7.9 - - + -
567F ARG* 3.2 23.8 + - + +
568F ALA* 3.2 6.8 + - - +
570F GLU* 1.3 74.7 - - + +
572F ILE* 1.3 67.8 + - - +
574F LYS* 3.0 7.6 + - + -
575F TYR* 2.9 40.1 + - + +
----------------------------------------------------------
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Residues in contact with ILE 572 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426F GLY* 3.9 28.0 - - - +
429F VAL* 4.9 9.0 - - + -
430F VAL* 4.0 13.5 - - + -
481F GLY 4.0 6.7 - - - +
484F ALA* 3.7 17.9 - - + -
485F ALA* 4.0 9.2 - - + +
488F VAL* 4.2 24.9 - - + -
489F VAL* 5.2 0.2 - - + -
568F ALA 2.9 21.6 + - - +
569F LYS 3.8 4.9 - - - +
571F ILE* 1.3 77.6 - - - +
573F ARG* 1.3 57.7 + - - +
575F TYR* 3.2 3.2 - - - -
576F ARG* 2.8 33.5 + - - +
579F LEU* 3.4 27.1 - - + -
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Residues in contact with ARG 573 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573C ARG* 3.3 59.3 - - - +
488F VAL* 3.8 30.4 - - + +
566F GLU* 4.6 10.5 + - - -
569F LYS* 3.1 48.5 + - - +
570F GLU* 3.6 18.8 - - - +
571F ILE 3.1 0.6 - - - -
572F ILE* 1.3 80.6 - - - +
574F LYS* 1.3 62.6 + - - +
576F ARG* 3.6 16.8 + - - +
----------------------------------------------------------
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Residues in contact with LYS 574 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570F GLU 2.9 16.8 + - - +
571F ILE* 3.6 6.7 - - + +
573F ARG* 1.3 77.7 - - - +
575F TYR* 1.3 93.2 + - + +
576F ARG 3.5 0.6 + - - -
578F GLN* 5.0 1.0 + - - -
----------------------------------------------------------
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Residues in contact with TYR 575 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429F VAL* 4.2 13.1 - - + +
433F VAL* 3.5 41.3 - - + +
571F ILE* 2.9 22.8 + - + +
572F ILE 3.2 4.4 - - - +
574F LYS* 1.3 116.6 + - + +
576F ARG* 1.3 61.4 + - - +
577F LYS 3.2 2.9 + - - -
578F GLN* 3.5 33.6 - - + +
579F LEU* 3.2 21.1 + - - +
605F PHE* 3.9 18.2 - + - -
----------------------------------------------------------
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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