Contacts of the helix formed by residues 546 - 575 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543D ARG* 4.5 1.8 - - - -
545D TYR* 1.3 83.4 - - - +
547D GLU* 1.3 60.2 + - - +
548D GLU* 3.7 12.0 + - - +
549D VAL* 3.2 25.6 + - - +
550D ALA* 3.0 23.4 + - - +
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Residues in contact with GLU 547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543D ARG* 3.6 22.8 + - - +
546D SER* 1.3 74.2 - - - +
548D GLU* 1.3 65.5 + - - +
550D ALA* 4.0 1.8 - - - -
551D SER* 3.1 22.6 + - - -
543E ARG* 5.0 1.6 + - - -
546E SER* 2.9 15.9 - - - -
547E GLU* 2.7 45.6 + - + +
548E GLU* 3.6 5.2 + - - +
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Residues in contact with GLU 548 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546D SER* 3.1 11.5 + - - +
547D GLU* 1.3 81.1 - - - +
549D VAL* 1.3 63.5 + - + +
551D SER* 3.3 6.1 - - - -
552D LYS* 2.9 54.2 + - - +
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Residues in contact with VAL 549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521D LEU* 4.6 9.2 - - + -
526D TRP* 3.7 46.2 - - + -
545D TYR* 4.0 9.0 - - + -
546D SER* 3.2 18.9 + - - +
548D GLU* 1.3 80.6 - - + +
550D ALA* 1.3 64.0 + - - +
552D LYS* 3.0 15.3 + - + +
553D ILE* 2.9 43.2 + - + +
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Residues in contact with ALA 550 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543D ARG* 3.5 28.9 - - - +
545D TYR* 3.7 15.9 - - + +
546D SER 3.0 17.3 + - - +
547D GLU* 3.7 7.0 - - - +
548D GLU 3.3 0.4 - - - -
549D VAL* 1.3 77.1 - - - +
551D SER* 1.3 60.6 + - - +
553D ILE* 3.5 5.9 + - - +
554D ASP* 3.1 28.8 + - - +
545E TYR 5.2 0.4 - - - -
546E SER* 3.8 13.2 - - - +
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Residues in contact with SER 551 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547D GLU* 3.1 12.2 + - - -
548D GLU* 3.3 12.1 - - - -
550D ALA* 1.3 77.0 - - - +
552D LYS* 1.3 66.8 + - - +
554D ASP* 3.2 4.4 + - - +
555D GLU* 3.1 30.5 + - - +
546E SER* 3.6 17.2 - - - -
548E GLU* 3.2 33.9 + - - +
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Residues in contact with LYS 552 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520D GLU* 6.2 6.7 - - + -
521D LEU* 3.9 25.8 - - + -
548D GLU* 2.9 48.6 + - - +
549D VAL* 3.0 16.5 + - + +
551D SER* 1.3 78.4 - - - +
553D ILE* 1.3 64.0 + - - +
555D GLU* 3.3 16.5 + - - +
556D GLU* 2.9 28.6 + - + +
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Residues in contact with ILE 553 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509D ARG* 3.9 15.5 - - - +
512D VAL* 4.1 7.4 - - + -
513D CYS* 3.8 22.2 - - - -
521D LEU* 3.8 23.3 - - + -
526D TRP* 4.0 17.5 - - + -
545D TYR* 3.8 26.2 - - + +
549D VAL* 2.9 35.0 + - + +
550D ALA* 3.5 7.0 - - - +
552D LYS* 1.3 77.4 - - - +
554D ASP* 1.3 62.7 + - - +
556D GLU* 3.4 1.6 + - - +
557D VAL* 2.9 37.1 + - + +
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Residues in contact with ASP 554 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509D ARG* 3.6 21.8 + - - -
550D ALA 3.1 9.3 + - - +
551D SER 3.2 7.6 + - - +
553D ILE* 1.3 80.7 - - - +
555D GLU* 1.3 62.0 + - + +
557D VAL* 3.3 6.1 + - - +
558D LYS* 2.9 24.8 + - - +
526E TRP* 4.1 18.7 - - + -
544E ASN 4.3 0.2 - - - +
545E TYR* 3.6 9.0 - - - +
546E SER* 2.8 42.5 + - - +
549E VAL* 3.7 21.1 - - + +
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Residues in contact with GLU 555 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551D SER* 3.1 29.3 + - - +
552D LYS* 3.6 15.4 - - - +
554D ASP* 1.3 72.6 - - + +
556D GLU* 1.3 69.0 + - + +
558D LYS* 3.2 10.0 + - - +
559D LYS* 2.8 34.8 + - - +
548E GLU* 4.1 11.7 - - - +
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Residues in contact with GLU 556 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512D VAL* 3.9 16.9 - - + +
518D SER* 2.7 27.7 + - - +
519D GLU* 3.8 14.3 + - - +
520D GLU* 4.1 19.2 + - + +
521D LEU* 3.9 11.9 - - + -
552D LYS* 2.9 20.6 + - + +
553D ILE 3.7 3.8 - - - +
555D GLU* 1.3 76.2 - - + +
557D VAL* 1.3 64.7 + - - +
559D LYS* 2.9 35.2 + - - +
560D ILE* 2.9 21.3 + - - +
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Residues in contact with VAL 557 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505D THR* 4.6 12.6 - - + -
508D ALA* 3.9 18.6 - - + +
509D ARG* 3.9 36.1 - - + +
512D VAL* 3.9 17.7 - - + -
553D ILE* 2.9 27.3 + - + +
554D ASP* 3.6 6.1 - - - +
556D GLU* 1.3 75.0 - - - +
558D LYS* 1.3 64.6 + - - +
560D ILE* 2.9 14.7 + - - +
561D VAL* 3.1 14.0 + - + +
524E LEU* 3.7 19.3 - - + -
526E TRP* 5.7 2.9 - - + -
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Residues in contact with LYS 558 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554D ASP 2.9 16.6 + - - +
555D GLU* 3.5 7.9 - - - +
557D VAL* 1.3 78.8 - - - +
559D LYS* 1.3 59.0 + - - +
561D VAL* 4.2 0.3 - - - +
562D THR* 2.9 49.4 + - - +
520E GLU* 4.0 25.4 + - - +
521E LEU* 4.4 15.3 - - + +
522E GLY* 5.2 1.6 - - - +
524E LEU* 3.6 25.6 - - + -
526E TRP* 4.7 8.7 - - + -
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Residues in contact with LYS 559 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555D GLU* 2.8 23.8 + - - +
556D GLU* 2.9 29.8 + - - +
558D LYS* 1.3 74.4 - - - +
560D ILE* 1.3 65.5 + - + +
562D THR* 4.1 2.6 - - - -
563D ASN* 3.1 45.3 + - - +
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Residues in contact with ILE 560 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469D ARG* 5.3 7.6 - - - +
473D LEU* 4.0 26.0 - - + -
476D LEU* 4.1 19.7 - - + -
508D ALA* 4.1 15.9 - - + +
511D MET* 4.4 21.1 - - + -
512D VAL* 3.9 27.1 - - + -
517D MET 5.1 6.7 - - - +
518D SER* 5.9 0.4 - - - -
556D GLU* 2.9 19.1 + - - +
557D VAL 3.5 4.9 - - - +
559D LYS* 1.3 77.5 - - + +
561D VAL* 1.3 65.3 + - - +
563D ASN* 3.2 6.6 + - - +
564D CYS* 3.0 23.2 + - - -
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Residues in contact with VAL 561 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476D LEU* 4.1 11.4 - - + -
480D LEU* 3.7 19.0 - - + +
504D ALA* 4.1 13.9 - - + +
505D THR* 4.6 3.8 - - - +
508D ALA* 3.8 21.5 - - + -
557D VAL* 3.1 13.3 + - + +
560D ILE* 1.3 75.0 - - - +
562D THR* 1.3 64.5 + - - +
564D CYS* 3.2 2.6 + - - +
565D TYR* 2.9 21.7 + - - +
523E PRO* 3.6 28.9 - - + +
524E LEU* 3.7 26.7 - - + -
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Residues in contact with THR 562 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558D LYS* 2.9 41.7 + - - +
559D LYS* 4.1 3.8 - - - -
561D VAL* 1.3 77.3 - - - +
563D ASN* 1.3 68.5 + - - +
565D TYR* 3.1 11.1 + - + +
566D GLU* 2.9 32.8 + - + +
522E GLY* 5.1 1.6 - - - -
523E PRO* 4.6 9.3 - - + +
524E LEU* 4.6 5.7 - - - +
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Residues in contact with ASN 563 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559D LYS* 3.1 37.2 + - - +
560D ILE* 3.6 5.6 - - - +
562D THR* 1.3 80.8 - - - +
564D CYS* 1.3 63.9 + - - +
566D GLU* 3.4 6.5 + - - +
567D ARG* 3.0 23.3 + - - +
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Residues in contact with CYS 564 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473D LEU* 3.7 42.6 - - - -
476D LEU* 3.4 34.1 - - + -
477D THR* 3.5 18.5 - - - +
480D LEU* 3.9 3.4 - - + -
560D ILE* 3.0 19.1 + - - +
561D VAL 3.6 0.4 - - - +
563D ASN* 1.3 78.7 - - - +
565D TYR* 1.3 57.9 + - - +
567D ARG* 3.1 7.5 + - - +
568D ALA* 2.8 25.6 + - - +
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Residues in contact with TYR 565 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480D LEU* 3.7 30.5 - - + +
483D ARG* 3.6 34.4 + - + +
484D ALA* 3.9 13.7 - - + -
487D GLU* 1.9 45.7 + - - +
561D VAL 2.9 16.7 + - - +
562D THR* 3.4 10.5 - - + +
564D CYS* 1.3 74.2 - - - +
566D GLU* 1.3 70.7 + - + +
568D ALA* 3.2 5.4 + - - +
569D LYS* 3.0 43.0 + - + +
523E PRO* 4.0 25.8 - - + -
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Residues in contact with GLU 566 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A GLU* 4.8 9.5 - - - +
569A LYS* 5.6 2.4 + - - -
562D THR* 2.9 28.1 + - + +
563D ASN* 3.8 6.3 - - - +
565D TYR* 1.3 80.8 - - + +
567D ARG* 1.3 60.9 + - - +
569D LYS* 2.5 45.6 + - - +
570D GLU* 2.8 37.8 + - - +
573D ARG* 4.8 6.9 + - - -
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Residues in contact with ARG 567 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434D VAL* 2.9 30.2 - - - +
435D PRO* 3.8 10.5 - - - +
473D LEU* 4.0 10.9 + - - +
474D ASP* 2.9 22.4 + - - -
477D THR* 3.2 27.1 + - + +
563D ASN 3.0 14.8 + - - +
564D CYS* 3.1 11.8 + - - +
566D GLU* 1.3 75.2 - - - +
568D ALA* 1.3 64.6 + - - +
570D GLU* 3.2 12.3 + - + +
571D ILE* 3.2 32.5 + - + +
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Residues in contact with ALA 568 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430D VAL* 4.4 4.3 - - + +
477D THR* 3.6 28.4 - - + +
480D LEU* 4.3 6.5 - - + +
481D GLY* 4.5 3.4 - - - -
484D ALA* 3.7 19.1 - - + -
564D CYS 2.8 13.3 + - - +
565D TYR* 3.3 11.9 - - - +
567D ARG* 1.3 75.6 - - - +
569D LYS* 1.3 63.2 + - - +
571D ILE* 3.0 17.1 + - - +
572D ILE* 3.1 16.1 + - - +
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Residues in contact with LYS 569 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A GLU* 5.5 3.0 + - - -
484D ALA* 3.7 20.6 - - + -
487D GLU* 4.0 24.4 + - + +
488D VAL* 4.0 21.3 - - + +
565D TYR* 3.0 36.4 + - + +
566D GLU* 2.5 42.8 + - - +
567D ARG 3.3 0.2 - - - -
568D ALA* 1.3 75.2 - - - +
570D GLU* 1.3 63.7 + - - +
572D ILE* 3.4 3.1 + - - +
573D ARG* 3.0 49.1 + - - +
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Residues in contact with GLU 570 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566D GLU* 2.8 33.9 + - - +
567D ARG* 3.2 9.7 + - - +
569D LYS* 1.3 76.1 - - - +
571D ILE* 1.3 59.3 + - + +
573D ARG* 3.3 23.3 + - - +
574D LYS* 2.9 29.9 + - - +
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Residues in contact with ILE 571 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429D VAL* 4.1 17.0 - - + -
430D VAL* 4.2 29.6 - - + +
433D VAL* 4.1 26.2 - - + -
434D VAL* 5.2 5.8 - - + -
477D THR* 4.3 6.3 - - + -
567D ARG* 3.2 31.1 + - + +
568D ALA* 3.0 6.9 + - - +
570D GLU* 1.3 76.0 - - + +
572D ILE* 1.3 66.4 + - - +
574D LYS* 3.2 6.6 + - + -
575D TYR* 2.9 41.8 + - + +
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Residues in contact with ILE 572 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426D GLY* 4.1 14.6 - - - +
429D VAL* 5.1 7.9 - - + -
430D VAL* 4.6 7.2 - - + -
481D GLY 4.0 6.1 - - - +
484D ALA* 4.2 6.7 - - + -
485D ALA* 3.4 37.5 - - + +
488D VAL* 4.1 26.0 - - + -
489D VAL* 5.3 0.7 - - + -
568D ALA 3.1 12.3 + - - +
569D LYS* 3.6 8.1 - - - +
571D ILE* 1.3 78.6 - - - +
573D ARG* 1.3 63.7 + - - +
575D TYR* 3.3 4.1 - - - -
576D ARG* 2.9 25.7 + - - +
579D LEU* 3.7 25.8 - - + -
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Residues in contact with ARG 573 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A ARG* 3.3 58.5 - - - +
488D VAL* 3.8 30.8 - - + +
566D GLU* 4.8 8.9 + - - -
569D LYS* 3.0 51.2 + - - +
570D GLU* 3.7 25.3 - - - +
572D ILE* 1.3 77.6 - - - +
574D LYS* 1.3 63.5 + - - +
575D TYR 3.2 0.5 + - - -
576D ARG* 3.4 16.6 + - - +
----------------------------------------------------------
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Residues in contact with LYS 574 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570D GLU 2.9 16.9 + - - +
571D ILE* 3.5 7.4 - - + +
573D ARG* 1.3 78.2 - - - +
575D TYR* 1.3 96.1 + - + +
576D ARG 3.8 0.5 + - - -
----------------------------------------------------------
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Residues in contact with TYR 575 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429D VAL* 4.2 15.2 - - + +
433D VAL* 3.8 30.3 - - + +
571D ILE* 2.9 36.0 + - + +
572D ILE* 3.3 4.3 - - - -
574D LYS* 1.3 115.8 + - + +
576D ARG* 1.3 64.6 + - - +
577D LYS 3.3 2.5 - - - -
578D GLN* 3.3 35.7 + - + +
579D LEU* 3.1 21.3 + - - +
605D PHE* 4.1 16.2 - + + -
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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