Contacts of the helix formed by residues 496 - 524 (chain L) in PDB entry 6ULG
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 496 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350L ARG* 3.3 4.0 - - - +
494L ASN 3.4 5.8 + - - -
495L LEU* 1.3 77.7 - - - +
497L VAL* 1.3 66.6 + - - +
498L ASP* 4.3 4.8 + - - +
499L VAL* 3.1 26.1 + - - +
500L VAL* 3.1 18.0 + - - +
1071N GLU* 5.4 1.0 + - - -
1072N TYR* 5.0 1.7 - - - -
1078N ARG* 5.6 4.3 + - - +
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Residues in contact with VAL 497 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347L LYS 6.1 0.7 - - - +
348L SER* 4.4 25.4 - - - +
350L ARG* 3.5 32.3 - - + +
496L SER* 1.3 74.8 - - - +
498L ASP* 1.3 66.0 + - + +
500L VAL* 3.2 6.1 + - + +
501L ASP* 2.9 36.6 + - - +
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Residues in contact with ASP 498 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496L SER* 3.3 4.9 + - - +
497L VAL* 1.3 83.9 - - - +
499L VAL* 1.3 60.9 + - - +
501L ASP* 3.2 17.3 + - - +
502L GLN* 2.9 29.3 + - - +
1071N GLU* 3.2 30.4 - - - +
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Residues in contact with VAL 499 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495L LEU* 3.7 18.1 - - + +
496L SER* 3.1 27.3 + - - +
498L ASP* 1.3 73.7 - - - +
500L VAL* 1.3 61.1 + - - +
502L GLN* 3.3 4.5 + - - +
503L CYS* 2.9 28.3 + - + +
1068N MET* 4.1 17.8 - - + +
1071N GLU* 3.3 17.9 - - - +
1072N TYR* 3.7 53.2 - - + -
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Residues in contact with VAL 500 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350L ARG* 3.4 22.0 - - + +
486L ILE* 4.7 9.7 - - + +
489L ALA* 3.8 24.9 - - + +
490L LEU* 3.9 29.2 - - + -
495L LEU* 4.0 11.2 - - + -
496L SER 3.1 15.5 + - - +
497L VAL* 3.2 8.7 + - - +
499L VAL* 1.3 78.6 - - - +
501L ASP* 1.3 59.5 + - - +
503L CYS* 3.4 5.4 + - - +
504L LEU* 2.9 29.3 + - + +
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Residues in contact with ASP 501 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347L LYS 5.7 0.9 - - - +
348L SER* 5.5 6.2 - - - -
497L VAL* 2.9 20.7 + - - +
498L ASP* 3.2 20.5 + - - +
500L VAL* 1.3 81.8 - - - +
502L GLN* 1.3 62.8 + - - +
504L LEU* 3.3 16.5 + - + +
505L VAL* 3.0 28.2 + - - +
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Residues in contact with GLN 502 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498L ASP 2.9 19.7 + - - +
499L VAL* 3.7 6.1 - - - +
500L VAL 3.3 0.2 - - - -
501L ASP* 1.3 81.2 - - - +
503L CYS* 1.3 59.1 + - - +
505L VAL* 3.3 20.3 - - - +
506L CYS* 2.9 29.5 + - - +
1064N LEU* 5.0 3.5 - - - +
1067N LYS* 3.4 26.4 - - - +
1068N MET* 3.8 28.5 + - + +
1071N GLU* 4.3 19.4 - - + +
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Residues in contact with CYS 503 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486L ILE* 5.1 0.9 - - + -
489L ALA* 4.8 16.6 - - + -
495L LEU* 6.4 2.5 - - + -
499L VAL* 2.9 17.0 + - + +
500L VAL* 3.8 7.2 - - - +
502L GLN* 1.3 72.3 - - - +
504L LEU* 1.3 59.7 + - - +
506L CYS* 3.8 6.3 - - - +
507L LEU* 2.9 41.1 + - + +
1068N MET* 4.3 18.0 - - + +
1110N ALA* 5.1 8.5 - - + +
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Residues in contact with LEU 504 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349L LEU* 4.4 11.7 - - + -
393L THR* 3.4 45.3 - - - +
394L MET* 4.6 14.8 - - + -
482L ILE* 5.7 6.1 - - + -
486L ILE* 3.7 32.9 - - + +
500L VAL* 2.9 18.8 + - + +
501L ASP* 3.3 17.7 - - + +
502L GLN 3.2 0.2 - - - -
503L CYS* 1.3 76.2 - - - +
505L VAL* 1.3 57.4 + - - +
507L LEU* 3.4 2.5 + - - +
508L LYS* 2.9 40.3 + - + +
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Residues in contact with VAL 505 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281L ASP* 5.1 10.5 - - - +
501L ASP 3.0 14.2 + - - +
502L GLN* 3.3 31.9 - - - +
504L LEU* 1.3 78.4 - - - +
506L CYS* 1.3 61.0 + - + +
508L LYS* 3.9 15.2 - - + +
509L GLU* 2.9 35.2 + - - +
1064N LEU* 4.5 18.3 - - + +
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Residues in contact with CYS 506 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502L GLN 2.9 17.4 + - - +
503L CYS* 3.8 7.0 - - - +
505L VAL* 1.3 78.9 - - - +
507L LEU* 1.3 57.9 + - + +
509L GLU* 3.4 5.0 + - - +
510L GLU* 2.9 29.7 + - - +
1061N GLU* 5.1 2.7 - - - +
1064N LEU* 4.4 29.2 - - + +
1065N LYS* 4.6 15.9 - - + +
1068N MET* 5.4 5.4 - - + -
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Residues in contact with LEU 507 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482L ILE* 3.7 26.0 - - + -
485L LYS* 3.5 63.9 - - + +
486L ILE* 4.5 10.8 - - + +
489L ALA* 5.6 0.7 - - + -
503L CYS* 2.9 26.4 + - + +
504L LEU* 3.9 3.4 - - - +
506L CYS* 1.3 73.6 - - + +
508L LYS* 1.3 62.0 + - - +
510L GLU* 3.4 13.7 + - - +
511L TRP* 3.0 39.7 + - + +
1110N ALA* 4.7 15.0 - - + +
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Residues in contact with LYS 508 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281L ASP* 4.3 16.3 + - - -
393L THR* 3.3 32.0 + - - +
394L MET 4.2 10.5 - - - +
395L LEU 3.4 24.1 + - - -
396L PRO* 4.5 7.8 - - + +
397L VAL* 5.9 2.2 - - - +
482L ILE* 4.7 4.2 - - + +
504L LEU* 2.9 30.2 + - + +
505L VAL* 3.9 14.7 - - + +
507L LEU* 1.3 76.5 - - - +
509L GLU* 1.3 58.4 + - - +
511L TRP 3.8 0.2 - - - -
512L MET* 2.9 30.5 + - - +
553L TRP* 4.2 25.2 - - + -
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Residues in contact with GLU 509 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279L THR* 3.3 43.3 + - + +
280L GLU* 4.7 5.2 + - - +
281L ASP* 5.4 4.7 - - - +
505L VAL* 2.9 24.0 + - + +
506L CYS 3.8 2.9 - - - +
507L LEU 3.3 0.2 - - - -
508L LYS* 1.3 74.0 - - - +
510L GLU* 1.3 60.9 + - - +
512L MET* 4.2 11.7 - - - +
513L ASN* 2.9 29.8 + - - +
1057N ASP* 4.6 14.2 - - - +
1060N GLN* 5.9 1.8 - - + -
1061N GLU* 4.1 8.9 - - + +
1064N LEU* 3.7 27.3 - - + +
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Residues in contact with GLU 510 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485L LYS* 3.8 21.1 + - - -
506L CYS 2.9 17.8 + - - +
507L LEU* 3.7 8.1 - - - +
509L GLU* 1.3 76.4 - - - +
511L TRP* 1.3 79.6 + - - +
513L ASN* 3.2 5.9 + - - +
514L LYS* 3.0 49.2 + - - +
1061N GLU* 3.4 32.3 - - + +
1065N LYS* 4.4 17.7 + - - -
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Residues in contact with TRP 511 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481L THR* 4.0 25.2 - - + +
482L ILE* 4.0 34.4 - - + +
485L LYS* 5.4 0.6 - - - +
507L LEU* 3.0 26.4 + - + +
510L GLU* 1.3 96.5 + - - +
512L MET* 1.3 57.2 + - - +
514L LYS* 3.2 35.1 + - + +
515L VAL* 2.9 31.9 + - - +
539L LEU 5.0 0.2 - - - -
540L GLY 3.8 22.4 - - - -
541L ALA* 4.1 15.9 - - + -
546L ASN* 3.8 22.2 - - + -
549L LEU* 4.6 12.8 - - + -
550L LEU* 4.5 13.5 - - + -
553L TRP* 3.6 23.1 - - + -
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Residues in contact with MET 512 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280L GLU* 3.7 27.4 - - + -
396L PRO* 3.8 33.4 - - + -
508L LYS 2.9 20.3 + - - +
509L GLU* 3.9 13.0 - - - +
510L GLU 3.3 0.2 - - - -
511L TRP* 1.3 74.3 - - - +
513L ASN* 1.3 60.5 + - - +
515L VAL* 3.3 10.3 + - - +
516L LYS* 2.9 29.4 + - - +
553L TRP* 3.6 31.6 - - - +
556L GLY* 3.3 27.1 - - - +
557L LEU* 3.8 11.6 - - + +
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Residues in contact with ASN 513 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509L GLU* 2.9 11.6 + - - +
510L GLU 3.2 3.4 + - - +
512L MET* 1.3 74.1 - - - +
514L LYS* 1.3 64.7 + - - +
516L LYS* 3.3 10.9 + - - +
517L VAL* 3.0 29.3 + - - +
1054N HIS* 3.2 38.9 + - - -
1057N ASP* 3.3 39.4 + - - +
1058N ARG* 4.4 4.8 - - - +
1061N GLU* 2.9 29.0 + - - +
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Residues in contact with LYS 514 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510L GLU* 3.0 37.8 + - - +
511L TRP* 3.2 39.9 + - + +
513L ASN* 1.3 86.3 - - - +
515L VAL* 1.3 56.1 + - - +
517L VAL* 3.3 1.5 + - - -
518L LEU* 3.0 26.7 + - - +
539L LEU* 3.2 59.1 + - + +
550L LEU* 3.9 6.1 - - + -
1054N HIS* 5.4 2.9 - - + -
1058N ARG* 5.2 14.6 - - - +
1061N GLU* 5.3 1.1 - - - -
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Residues in contact with VAL 515 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511L TRP 2.9 20.2 + - - +
512L MET* 3.5 10.8 - - - +
513L ASN 3.3 0.2 - - - -
514L LYS* 1.3 74.6 - - - +
516L LYS* 1.3 57.4 + - - +
518L LEU* 3.2 3.1 + - + +
519L PHE* 2.9 29.1 + - - +
549L LEU* 5.7 0.9 - - + -
550L LEU* 3.6 27.8 - - + +
553L TRP* 3.5 50.5 - - + +
554L MET* 3.7 14.2 - - + +
557L LEU* 3.6 17.9 - - + -
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Residues in contact with LYS 516 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277L ALA* 5.5 9.1 - - - +
279L THR* 5.0 10.7 + - - +
280L GLU* 4.8 14.6 - - - -
512L MET 2.9 17.2 + - - +
513L ASN* 3.6 11.4 - - - +
515L VAL* 1.3 76.5 - - - +
517L VAL* 1.3 62.1 + - + +
519L PHE* 3.7 1.9 + - - +
520L LYS 3.7 7.1 + - - -
557L LEU* 4.2 15.0 - - + -
561L TYR* 3.1 51.0 + - + +
1050N PHE* 3.2 15.0 - - + -
1053N MET* 5.0 18.4 - - + +
1054N HIS* 6.2 2.5 - - - -
1057N ASP* 3.1 27.9 + - + +
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Residues in contact with VAL 517 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513L ASN* 3.0 23.7 + - - +
514L LYS* 3.7 4.5 - - - +
516L LYS* 1.3 77.0 - - + +
518L LEU* 1.3 65.1 + - - +
520L LYS* 3.2 18.0 + - - +
521L PHE* 3.8 5.5 + - + +
535L LEU* 3.7 28.1 - - + +
539L LEU* 4.1 13.7 - - + -
1041N LEU* 4.7 11.2 - - + -
1050N PHE* 3.6 24.0 - - + -
1054N HIS* 3.4 34.8 - - + +
----------------------------------------------------------
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Residues in contact with LEU 518 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514L LYS 3.0 16.8 + - - +
515L VAL* 3.2 4.7 + - - +
517L VAL* 1.3 76.9 - - - +
519L PHE* 1.3 55.7 - - - +
520L LYS 3.2 0.3 + - - -
521L PHE* 3.3 2.4 + - - -
522L THR* 2.5 51.5 + - - +
532L THR* 5.2 9.0 - - + +
535L LEU* 3.7 23.6 - - + -
536L LEU* 3.8 20.2 - - + -
539L LEU* 4.6 3.8 - - + +
547L VAL* 5.5 2.0 - - + -
550L LEU* 3.7 40.4 - - + -
551L LYS* 4.8 7.4 - - + +
554L MET* 3.8 18.6 - - + -
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Residues in contact with PHE 519 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515L VAL 2.9 17.7 + - - +
516L LYS* 3.9 4.9 - - - +
517L VAL 3.3 0.4 - - - -
518L LEU* 1.3 77.1 - - - +
520L LYS* 1.3 63.4 + - - +
522L THR* 3.8 5.2 - - - -
523L LYS* 3.3 53.3 + - + +
524L VAL* 5.9 0.2 - - - +
554L MET* 4.0 26.7 - - + +
557L LEU* 4.7 9.0 - - + -
561L TYR* 3.8 20.9 - + - -
562L LYS* 3.6 45.3 - - + -
565L LEU* 3.7 28.6 - - + +
566L MET* 4.8 7.4 - - - -
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Residues in contact with LYS 520 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516L LYS 3.7 3.2 + - - -
517L VAL 3.2 12.0 + - - +
518L LEU 3.2 1.0 - - - -
519L PHE* 1.3 81.3 - - - +
521L PHE* 1.3 78.8 + - + +
522L THR 3.3 0.2 + - - -
524L VAL* 3.2 51.6 + - + +
527L ARG* 5.8 1.2 - - - +
565L LEU* 3.8 37.2 - - + -
568L THR* 5.5 7.1 + - - -
1046N LEU 4.5 13.5 + - - -
1047N PRO* 5.1 5.8 - - - -
1049N ASP* 6.2 0.2 - - - -
1050N PHE* 3.6 44.2 - - + -
----------------------------------------------------------
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Residues in contact with PHE 521 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517L VAL* 3.8 3.7 + - + -
518L LEU 3.3 2.6 + - - -
520L LYS* 1.3 95.9 - - + +
522L THR* 1.3 60.9 + - - +
523L LYS 3.5 0.2 - - - -
524L VAL* 5.8 0.4 - - + -
525L ASP* 3.2 22.8 - - - +
527L ARG* 3.9 44.8 - - - +
531L ASP* 4.9 4.3 - - + -
532L THR* 4.1 11.6 - - + +
535L LEU* 3.6 46.0 - - + -
1041N LEU* 5.0 7.2 - - + -
1044N LEU* 3.8 41.5 - - + -
1045N HIS 4.3 4.5 - - - -
1046N LEU 5.0 1.6 - - - -
1047N PRO* 4.2 21.5 - - + -
1050N PHE* 6.0 2.2 - + - -
----------------------------------------------------------
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Residues in contact with THR 522 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518L LEU* 2.5 42.8 + - - +
519L PHE 4.1 2.2 - - - -
520L LYS 3.2 0.2 - - - -
521L PHE* 1.3 81.6 - - - +
523L LYS* 1.3 89.3 + - - +
524L VAL 3.8 0.2 - - - -
525L ASP* 3.7 17.7 - - - +
532L THR* 4.8 10.6 - - + +
551L LYS* 6.5 0.2 - - + -
554L MET* 4.0 10.9 - - + +
----------------------------------------------------------
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Residues in contact with LYS 523 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519L PHE* 3.3 44.7 + - + +
522L THR* 1.3 96.9 - - + +
524L VAL* 1.3 60.5 + - + +
525L ASP* 3.4 6.9 - - - +
554L MET* 3.3 24.7 - - - -
566L MET* 3.6 25.0 - - + +
----------------------------------------------------------
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Residues in contact with VAL 524 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520L LYS* 3.2 44.5 + - + +
521L PHE* 5.2 0.9 - - - -
523L LYS* 1.3 81.1 - - + +
525L ASP* 1.3 66.0 + - - +
526L SER* 3.5 5.1 + - - -
527L ARG* 5.2 6.2 + - - +
565L LEU* 4.3 17.7 - - + +
566L MET* 3.7 29.6 - - + +
568L THR* 5.7 0.9 - - - +
----------------------------------------------------------
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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).
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