Contacts of the helix formed by residues 546 - 575 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A ARG* 4.2 1.3 - - - -
545A TYR* 1.3 79.9 - - - +
547A GLU* 1.3 59.9 + - - +
548A GLU* 3.5 5.7 + - - +
549A VAL* 3.1 19.2 + - - +
550A ALA* 2.9 23.9 + - - +
543B ARG* 5.4 1.3 - - - +
547B GLU* 3.4 21.8 - - - -
550B ALA* 3.8 7.0 - - - +
551B SER* 3.7 22.1 + - - -
554B ASP* 2.6 27.1 + - - +
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Residues in contact with GLU 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A ARG* 3.3 25.1 + - - +
546A SER* 1.3 70.4 - - - +
548A GLU* 1.3 65.1 + - - +
550A ALA* 3.2 10.5 + - - +
551A SER* 3.0 30.3 + - - -
547B GLU* 2.9 26.5 + - + +
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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
----------------------------------------------------------
546A SER* 3.2 2.6 - - - +
547A GLU* 1.3 79.7 - - - +
549A VAL* 1.3 62.7 + - + +
551A SER* 3.5 5.2 + - - -
552A LYS* 3.3 45.2 + - - +
547B GLU* 3.3 7.5 + - - +
551B SER* 3.0 29.5 + - - +
555B GLU* 5.1 11.0 - - - +
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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
----------------------------------------------------------
521A LEU* 3.7 23.8 - - + -
526A TRP* 3.7 27.1 - - + -
545A TYR* 4.2 5.6 - - + -
546A SER* 3.1 12.3 + - - +
548A GLU* 1.3 73.5 - - + +
550A ALA* 1.3 65.3 + - - +
551A SER 3.1 2.0 - - - -
552A LYS* 3.1 8.4 + - + +
553A ILE* 2.9 41.7 + - + +
554B ASP* 3.4 37.2 - - + +
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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
----------------------------------------------------------
543A ARG* 4.0 17.3 - - - +
545A TYR* 3.7 21.9 - - + +
546A SER 2.9 14.3 + - - +
547A GLU* 3.2 20.8 + - - +
549A VAL* 1.3 76.1 - - - +
551A SER* 1.3 61.7 + - - +
553A ILE* 3.5 5.4 + - - +
554A ASP* 3.2 30.0 + - - +
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Residues in contact with SER 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A GLU* 3.0 22.6 + - - -
548A GLU* 3.8 6.9 + - - -
549A VAL 3.1 0.2 - - - -
550A ALA* 1.3 76.8 - - - +
552A LYS* 1.3 66.0 + - - +
554A ASP* 3.4 9.5 + - - +
555A GLU* 3.2 30.8 + - - +
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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
----------------------------------------------------------
520A GLU* 6.1 6.7 - - + -
521A LEU* 3.9 22.9 - - + -
548A GLU* 3.3 34.9 + - - +
549A VAL* 3.1 11.9 + - + +
551A SER* 1.3 76.2 - - - +
553A ILE* 1.3 66.4 + - - +
555A GLU* 3.2 18.6 + - - +
556A GLU* 3.0 26.9 + - + +
555E GLU* 5.3 10.6 + - - +
552F LYS* 5.4 8.9 - - - +
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Residues in contact with ILE 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A ARG* 4.2 15.9 - - - +
512A VAL* 4.0 7.6 - - + -
513A CYS* 3.6 35.7 - - - -
521A LEU* 3.8 17.7 - - + -
526A TRP* 3.8 16.6 - - + -
545A TYR* 3.8 20.9 - - + +
549A VAL* 2.9 39.2 + - + +
550A ALA* 3.6 5.6 - - - +
552A LYS* 1.3 77.1 - - - +
554A ASP* 1.3 57.9 + - - +
556A GLU* 3.3 0.9 + - - +
557A VAL* 2.9 37.3 + - + +
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Residues in contact with ASP 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A ARG* 3.6 21.7 + - - -
550A ALA* 3.2 16.8 + - - +
551A SER* 3.8 10.4 - - - +
552A LYS 3.3 0.2 - - - -
553A ILE* 1.3 77.5 - - - +
555A GLU* 1.3 56.3 + - - +
557A VAL* 3.9 5.1 - - - +
558A LYS* 2.8 32.2 + - - +
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Residues in contact with GLU 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A SER* 3.2 22.7 + - - +
552A LYS* 3.2 20.7 + - - +
554A ASP* 1.3 75.8 - - - +
556A GLU* 1.3 59.4 + - + +
558A LYS* 3.5 6.6 + - - +
559A LYS* 2.8 44.8 + - - +
520E GLU* 4.3 17.8 - - - +
552E LYS* 5.1 8.5 - - - +
555E GLU* 4.5 18.3 - - - +
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Residues in contact with GLU 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A VAL* 4.1 13.4 - - + +
518A SER* 3.0 26.6 - - - +
519A GLU* 3.1 46.1 + - - +
520A GLU* 4.2 9.2 + - + +
521A LEU* 4.0 16.8 - - + -
552A LYS* 3.0 18.8 + - + +
553A ILE 3.9 2.9 - - - +
555A GLU* 1.3 75.3 - - + +
557A VAL* 1.3 69.2 + - - +
559A LYS* 2.9 19.0 + - - +
560A ILE* 2.9 33.6 + - - +
559E LYS* 5.1 1.0 + - - -
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Residues in contact with VAL 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A THR* 4.7 11.4 - - + -
508A ALA* 3.9 20.9 - - + +
509A ARG* 3.7 45.1 - - + +
512A VAL* 4.0 10.3 - - + -
553A ILE* 2.9 29.0 + - + +
554A ASP* 3.9 5.4 - - - +
556A GLU* 1.3 80.1 - - - +
558A LYS* 1.3 66.1 + - - +
560A ILE* 3.1 9.5 + - - +
561A VAL* 3.1 17.4 + - + +
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Residues in contact with LYS 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A ASP 2.8 23.6 + - - +
555A GLU* 3.8 6.5 - - - +
557A VAL* 1.3 75.7 - - - +
559A LYS* 1.3 58.2 + - - +
561A VAL* 4.1 4.1 - - - +
562A THR* 2.9 46.5 + - - +
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Residues in contact with LYS 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A GLU* 3.8 25.2 + - - +
555A GLU* 2.8 34.4 + - - +
556A GLU* 2.9 22.8 + - - +
558A LYS* 1.3 79.1 - - - +
560A ILE* 1.3 64.4 + - + +
562A THR* 4.0 2.9 - - - +
563A ASN* 3.0 45.1 + - - +
519E GLU* 4.7 21.1 - - + +
520E GLU* 4.0 22.9 + - - -
556E GLU* 5.7 2.8 + - - -
559E LYS* 5.3 9.4 - - - +
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Residues in contact with ILE 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A ARG* 5.2 10.5 - - - +
473A LEU* 3.8 20.4 - - + -
476A LEU* 3.7 25.6 - - + -
508A ALA* 4.1 9.0 - - + +
511A MET* 4.6 19.5 - - + -
512A VAL* 4.0 23.8 - - + -
517A MET 5.2 7.0 - - - +
518A SER* 5.6 0.2 - - - -
556A GLU* 2.9 26.4 + - - +
557A VAL* 3.7 4.0 - - - +
559A LYS* 1.3 80.7 - - + +
561A VAL* 1.3 63.2 + - - +
563A ASN* 3.3 6.1 + - - +
564A CYS* 3.0 23.6 + - - -
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Residues in contact with VAL 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A LEU* 4.3 6.3 - - + -
480A LEU* 3.6 23.5 - - + +
501A ILE* 6.5 1.3 - - + -
504A ALA* 4.2 14.6 - - + +
505A THR* 4.4 14.4 - - - +
508A ALA* 3.8 21.5 - - + -
557A VAL* 3.1 19.0 + - + +
558A LYS* 4.2 3.8 - - - +
560A ILE* 1.3 76.3 - - - +
562A THR* 1.3 59.8 + - - +
564A CYS* 3.3 4.8 + - - +
565A TYR* 2.9 28.0 + - + +
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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
----------------------------------------------------------
558A LYS* 2.9 32.7 + - - +
559A LYS* 4.0 4.0 - - - -
561A VAL* 1.3 80.0 - - - +
563A ASN* 1.3 66.4 + - - +
565A TYR* 3.3 8.9 + - + +
566A GLU* 3.1 35.4 + - + +
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Residues in contact with ASN 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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559A LYS* 3.0 33.9 + - - +
560A ILE* 3.7 6.4 - - - +
562A THR* 1.3 81.6 - - - +
564A CYS* 1.3 62.6 + - - +
566A GLU* 3.5 7.3 + - - +
567A ARG* 3.2 20.4 + - - +
519E GLU* 3.3 26.4 + - - +
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Residues in contact with CYS 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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473A LEU* 3.4 35.2 - - - -
476A LEU* 4.1 9.9 - - + -
477A THR* 3.3 29.5 - - - +
480A LEU* 3.9 11.7 - - + -
560A ILE* 3.0 27.5 + - - +
561A VAL* 3.8 4.7 - - - +
563A ASN* 1.3 75.0 - - - +
565A TYR* 1.3 68.2 + - - +
567A ARG* 3.1 9.3 + - - +
568A ALA* 3.0 22.2 + - - +
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Residues in contact with TYR 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LEU* 3.4 28.9 - - + +
483A ARG* 3.8 21.3 + - + +
484A ALA* 3.8 25.1 - - + -
487A GLU* 2.0 46.8 + - - +
493A VAL* 4.8 0.7 - - - +
561A VAL* 2.9 16.2 + - + +
562A THR* 3.3 13.4 + - + +
564A CYS* 1.3 77.3 - - - +
566A GLU* 1.3 69.2 + - - +
568A ALA* 3.1 6.3 + - - +
569A LYS* 3.0 43.2 + - + +
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Residues in contact with GLU 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A THR* 3.1 26.4 + - + +
563A ASN* 3.9 7.4 - - - +
564A CYS 3.2 0.4 - - - -
565A TYR* 1.3 87.3 - - - +
567A ARG* 1.3 62.6 + - - +
569A LYS* 3.0 42.7 + - - +
570A GLU* 3.0 31.6 + - + +
573A ARG* 5.0 4.5 + - - -
566D GLU* 4.8 9.0 - - - +
569D LYS* 5.5 2.9 + - - -
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Residues in contact with ARG 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A VAL* 3.4 21.0 - - - +
435A PRO* 3.8 10.5 - - - +
473A LEU* 3.9 14.3 + - - +
474A ASP* 2.5 35.8 + - - +
477A THR* 3.3 24.3 + - + -
563A ASN 3.2 11.2 + - - +
564A CYS* 3.1 12.7 + - - +
566A GLU* 1.3 79.1 - - - +
568A ALA* 1.3 62.3 + - - +
570A GLU* 3.1 22.8 + - - +
571A ILE* 3.1 23.2 + - + +
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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
----------------------------------------------------------
430A VAL* 4.5 4.3 - - + -
477A THR* 3.9 27.5 - - + +
480A LEU* 4.4 3.4 - - + +
481A GLY* 4.4 7.0 - - - -
484A ALA* 3.7 19.5 - - + -
564A CYS 3.0 10.2 + - - +
565A TYR* 3.4 9.9 - - - +
567A ARG* 1.3 77.5 - - - +
569A LYS* 1.3 65.0 + - - +
571A ILE* 2.9 18.3 + - - +
572A ILE* 3.0 14.8 + - - +
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Residues in contact with LYS 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A ALA* 3.8 18.1 - - + +
487A GLU* 3.2 33.1 + - - +
488A VAL* 4.1 19.0 - - + +
565A TYR* 3.0 31.4 + - + +
566A GLU* 3.0 47.9 + - - +
568A ALA* 1.3 77.1 - - - +
570A GLU* 1.3 56.4 + - - +
572A ILE* 3.3 2.6 + - - +
573A ARG* 2.9 55.5 + - - +
566D GLU* 5.6 3.0 + - - -
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Residues in contact with GLU 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A GLU* 3.0 23.3 + - + +
567A ARG* 3.1 15.0 + - + +
569A LYS* 1.3 76.8 - - - +
571A ILE* 1.3 60.3 + - + +
573A ARG* 3.7 23.2 - - - +
574A LYS* 3.0 30.5 + - - +
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Residues in contact with ILE 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A VAL* 3.9 12.1 - - + -
430A VAL* 3.8 33.0 - - + -
433A VAL* 3.9 34.3 - - + -
434A VAL* 4.4 11.7 - - + -
477A THR* 4.8 0.2 - - + -
567A ARG* 3.1 26.9 + - + +
568A ALA* 2.9 7.2 + - - +
570A GLU* 1.3 75.3 - - + +
572A ILE* 1.3 59.9 + - - +
574A LYS* 3.1 6.2 + - + -
575A TYR* 2.9 51.1 + - + +
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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
----------------------------------------------------------
426A GLY* 4.2 16.8 - - - +
429A VAL* 4.7 10.3 - - + -
430A VAL* 4.2 14.4 - - + -
481A GLY 4.5 0.4 - - - +
484A ALA* 4.2 7.9 - - + -
485A ALA* 4.0 36.1 - - + +
488A VAL* 4.0 23.6 - - + -
489A VAL* 5.1 0.9 - - + -
568A ALA 3.0 16.2 + - - +
569A LYS* 3.7 8.3 - - - +
571A ILE* 1.3 77.7 - - - +
573A ARG* 1.3 63.6 + - - +
575A TYR* 3.2 3.1 + - - -
576A ARG* 3.0 24.5 + - - -
579A LEU* 3.7 25.8 - - + -
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Residues in contact with ARG 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A VAL* 3.9 27.4 - - + +
566A GLU* 5.0 4.4 + - - -
569A LYS* 2.9 45.8 + - - +
570A GLU* 3.7 32.3 - - - +
572A ILE* 1.3 78.1 - - - +
574A LYS* 1.3 62.0 + - - +
575A TYR 3.4 0.3 + - - -
576A ARG* 3.6 16.7 + - - +
573D ARG* 3.3 56.2 - - - +
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Residues in contact with LYS 574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A GLU 3.0 20.3 + - - +
571A ILE* 3.1 6.9 + - + +
573A ARG* 1.3 78.1 - - - +
575A TYR* 1.3 90.9 + - + +
576A ARG 3.5 1.4 + - - -
577A LYS* 5.8 3.1 - - - -
578A GLN* 4.2 3.8 - - - +
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Residues in contact with TYR 575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A VAL* 4.1 16.6 - - + -
433A VAL* 3.7 33.4 - - + +
571A ILE* 2.9 35.6 + - + +
572A ILE* 3.2 4.0 + - - +
574A LYS* 1.3 113.3 + - + +
576A ARG* 1.3 64.2 + - - +
577A LYS 3.2 2.5 - - - -
578A GLN* 3.2 29.7 + - + -
579A LEU* 2.9 21.1 + - - +
601A LEU* 4.3 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