Contacts of the helix formed by residues 519 - 546 (chain B) in PDB entry 1JB0
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 GLY 519 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B GLU* 4.5 2.5 - - - -
460B PRO* 2.8 26.0 - - - +
464B GLN* 4.5 1.1 - - - -
518B ILE* 1.3 75.2 - - - +
520B PRO* 1.3 76.3 - - - +
521B GLY 3.2 3.1 - - - -
522B ASP* 2.7 21.9 + - - +
523B PHE 3.0 1.4 + - - -
616B ASN* 5.4 4.3 - - - +
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Residues in contact with PRO 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B LEU* 3.5 33.2 - - + -
458B ILE 3.4 22.2 - - - +
459B GLU* 3.3 15.5 - - - +
460B PRO* 3.9 0.2 - - - -
519B GLY* 1.3 82.9 - - - +
521B GLY* 1.3 63.6 + - - +
523B PHE* 3.0 11.3 + - + +
524B LEU* 3.0 20.1 + - + +
616B ASN 5.9 2.5 - - - +
620B THR* 4.2 10.1 - - + -
50F HIS* 3.4 33.0 - - + +
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Residues in contact with GLY 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B GLY 3.2 1.0 - - - -
520B PRO* 1.3 81.5 - - - +
522B ASP* 1.3 60.7 + - - +
524B LEU* 3.5 3.8 + - - +
525B VAL* 3.0 27.5 + - - +
615B PHE* 4.4 3.6 - - - -
616B ASN* 5.0 5.4 + - - +
619B SER* 3.1 32.4 + - - +
620B THR* 3.7 14.2 - - - +
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Residues in contact with ASP 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B PRO* 4.7 2.0 - - + -
518B ILE* 3.2 25.2 - - + +
519B GLY* 2.7 27.4 + - - +
521B GLY* 1.3 74.2 + - - +
523B PHE* 1.3 65.4 + - - +
525B VAL* 3.7 4.4 - - - +
526B HIS* 2.9 34.3 + - + +
599B TYR* 2.9 29.5 + - - +
603B LYS* 2.6 31.1 + - - -
615B PHE* 3.7 8.7 - - - -
616B ASN* 4.5 4.5 + - - -
1235B CLA 4.9 2.2 - - - +
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Residues in contact with PHE 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B LEU* 4.8 3.8 - - + -
458B ILE* 3.4 58.3 - - + +
460B PRO* 4.1 8.9 - - + +
519B GLY 3.0 6.4 + - - +
520B PRO 3.0 11.1 + - - +
522B ASP* 1.3 78.2 - - - +
524B LEU* 1.3 83.0 + - + +
526B HIS* 3.3 8.7 + - - +
527B HIS* 2.9 54.9 + + - -
1235B CLA 3.4 45.1 - + + -
4015J BCR 3.6 24.7 - - + -
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Residues in contact with LEU 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B THR* 3.9 11.6 - - + +
439B LEU* 3.8 35.2 - - + -
440B TYR* 3.3 37.3 + - + +
443B ASN* 3.8 13.0 - - - +
456B ILE 4.9 4.0 - - - +
457B LEU* 5.6 1.1 - - + -
458B ILE 6.3 0.4 - - - +
520B PRO* 3.0 13.1 + - + +
521B GLY* 3.5 3.6 + - - +
523B PHE* 1.3 90.9 - - + +
525B VAL* 1.3 62.0 + - - +
527B HIS* 3.0 16.0 + - + +
528B ALA* 3.1 10.2 + - - +
620B THR* 3.6 35.0 - - + +
4015J BCR 5.4 1.1 - - + -
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Residues in contact with VAL 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B TYR* 3.2 6.7 + - - +
521B GLY 3.0 19.7 - - - +
522B ASP 3.7 6.7 - - - +
524B LEU* 1.3 73.7 - - - +
526B HIS* 1.3 57.4 - - - +
528B ALA* 2.8 7.1 + - + +
529B ILE* 2.7 34.2 + - + +
595B TRP* 4.6 2.7 - - + +
599B TYR* 3.8 42.8 - - + -
615B PHE* 4.5 0.4 - - + -
625B TRP* 3.8 18.6 - - + -
1021B CLA 3.1 35.4 - - + -
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Residues in contact with HIS 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B ILE* 5.8 0.7 - - + -
522B ASP* 2.9 27.6 + - + +
523B PHE 3.6 4.7 - - - +
524B LEU 3.2 0.2 - - - -
525B VAL* 1.3 79.4 - - - +
527B HIS* 1.3 58.6 + - - +
529B ILE* 3.5 9.2 + - + +
530B ALA 3.0 19.6 + - - -
599B TYR* 3.1 34.6 + + - -
1234B CLA 2.2 67.2 + + + -
1235B CLA 3.5 53.2 - - + +
1236B CLA 4.8 0.6 - - - +
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Residues in contact with HIS 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B LEU* 4.1 6.1 - - + +
436B THR* 3.6 23.0 + - + +
523B PHE* 2.9 51.7 + + + +
524B LEU* 3.0 9.8 + - - +
526B HIS* 1.3 74.4 - - - +
528B ALA* 1.3 60.5 + - - +
529B ILE 3.2 0.4 - - - -
530B ALA* 3.5 5.5 - - - +
531B LEU* 2.9 26.5 + - - +
1235B CLA 2.3 69.2 + + + -
4015J BCR 3.4 29.5 - - + +
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Residues in contact with ALA 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B THR* 4.1 7.4 - - + +
440B TYR* 4.9 0.9 - - - +
524B LEU 3.1 10.4 + - - +
525B VAL* 2.8 16.1 + - + +
527B HIS* 1.3 76.8 - - - +
529B ILE* 1.3 59.7 + - + +
531B LEU* 3.1 9.2 + - - +
532B GLY 2.9 23.6 + - - -
595B TRP* 3.3 20.1 - - + -
1021B CLA 3.5 37.0 - - + -
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Residues in contact with ILE 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B VAL* 2.7 20.0 + - + +
526B HIS* 3.6 11.2 - - + +
528B ALA* 1.3 75.3 - - - +
530B ALA* 1.3 66.0 + - - +
532B GLY* 3.2 1.9 + - - +
533B LEU* 2.9 30.0 + - + +
592B THR* 4.4 3.9 - - + +
595B TRP* 4.8 9.2 - - + -
596B VAL* 4.0 28.0 - - + +
599B TYR* 4.0 19.3 - - + -
1234B CLA 3.3 65.3 - - + -
1236B CLA 4.9 1.8 - - - -
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Residues in contact with ALA 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B LEU* 3.6 16.6 - - + -
526B HIS 3.0 15.5 + - - +
527B HIS* 3.6 12.3 - - - +
528B ALA 3.2 0.2 - - - -
529B ILE* 1.3 78.3 - - - +
531B LEU* 1.3 63.0 + - - +
533B LEU* 3.3 2.6 + - - -
534B HIS* 2.8 29.1 + - - -
1235B CLA 4.1 15.5 - - + -
1236B CLA 3.5 28.3 - - - +
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Residues in contact with LEU 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013A CLA 2.9 24.5 - - - +
429B SER* 3.3 16.4 - - - +
432B LEU* 3.6 16.3 - - + +
433B GLY* 3.6 17.0 - - - +
436B THR* 5.5 0.7 - - - +
527B HIS 2.9 14.6 + - - +
528B ALA* 3.1 8.7 + - - +
530B ALA* 1.3 77.2 - - - +
532B GLY* 1.3 59.6 + - - +
534B HIS* 4.0 0.8 - - - -
535B THR* 2.7 44.3 + - - +
588B TRP* 4.4 2.9 - - + -
595B TRP* 4.2 5.4 - - + -
1012B CLA 3.4 29.8 - - + -
1021B CLA 4.1 20.0 - - + -
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Residues in contact with GLY 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B ALA 2.9 13.4 + - - -
529B ILE 3.2 3.3 + - - -
531B LEU* 1.3 75.8 - - - +
533B LEU* 1.3 62.0 + - - +
536B THR* 2.7 32.7 + - - -
588B TRP* 3.8 13.9 - - - -
592B THR* 3.1 24.9 - - - -
595B TRP* 4.6 2.9 - - - -
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Residues in contact with LEU 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B ILE* 2.9 21.9 + - + +
530B ALA* 3.8 4.3 - - - +
532B GLY* 1.3 76.3 - - - +
534B HIS* 1.3 58.8 + - - +
536B THR* 4.2 3.1 - - - -
537B THR* 2.7 35.2 + - - -
592B THR* 3.8 17.3 - - + -
1222B CLA 3.5 58.3 - - + +
1234B CLA 4.0 26.7 - - + -
1236B CLA 4.1 34.2 - - + +
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Residues in contact with HIS 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B LEU* 4.1 11.0 - - + +
428B VAL* 3.6 21.1 - - + +
429B SER* 3.6 16.0 + - - +
432B LEU* 3.7 11.8 - - + +
530B ALA 2.8 27.4 + - - +
531B LEU 4.1 2.2 - - - +
533B LEU* 1.3 76.3 - - - +
535B THR* 1.3 56.0 + - - +
537B THR* 3.4 5.4 + - - -
538B LEU* 2.7 34.3 + - - +
1235B CLA 3.9 10.3 - - + -
1236B CLA 2.2 88.0 + + + -
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Residues in contact with THR 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013A CLA 3.6 32.5 - - + +
429B SER* 3.6 12.1 + - - +
531B LEU* 2.7 38.8 + - - +
534B HIS* 1.3 73.6 - - - +
536B THR* 1.3 65.7 + - - +
538B LEU* 3.4 3.4 - - - +
539B ILE* 3.0 31.5 + - + +
588B TRP* 3.4 40.8 - - + +
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Residues in contact with THR 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B VAL* 4.7 0.9 - - + -
532B GLY 2.7 23.8 + - - -
533B LEU 4.2 0.7 - - - -
535B THR* 1.3 77.2 - - - +
537B THR* 1.3 62.4 + - - +
539B ILE* 3.5 4.1 + - - +
540B LEU* 3.1 38.9 + - + +
585B ALA* 4.0 17.7 - - + +
588B TRP* 3.4 23.4 + - - +
589B MET* 3.8 6.5 + - + +
592B THR* 3.6 8.3 + - - -
1222B CLA 3.4 38.3 - - + +
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Residues in contact with THR 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B PHE* 4.5 2.4 - - + -
425B LEU* 3.9 13.2 - - + -
533B LEU 2.7 21.9 + - - -
534B HIS* 3.6 5.4 - - - -
536B THR* 1.3 78.0 - - - +
538B LEU* 1.3 59.3 + - - +
540B LEU* 4.5 3.8 - - - +
541B VAL* 2.8 45.6 + - + +
1222B CLA 3.3 56.1 - - + +
1236B CLA 4.0 7.9 - - + +
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Residues in contact with LEU 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A TYR* 4.8 0.2 - - - +
700A LEU* 4.2 10.3 - - + -
1013A CLA 3.1 53.2 - - + +
422B ILE* 3.8 27.8 - - + +
425B LEU* 3.7 31.6 - - + -
426B SER* 3.9 10.5 - - - +
429B SER* 4.2 7.4 - - - +
534B HIS 2.7 21.8 + - - +
535B THR* 3.4 5.8 - - - +
537B THR* 1.3 74.0 - - - +
539B ILE* 1.3 58.9 + - - +
541B VAL* 4.0 0.5 - - - +
542B LYS* 2.9 34.9 + - + +
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Residues in contact with ILE 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A TYR* 3.6 20.1 - - + +
1013A CLA 3.4 43.1 - - + +
535B THR 3.0 17.6 + - - +
536B THR* 3.8 3.8 - - - +
538B LEU* 1.3 75.5 - - - +
540B LEU* 1.3 56.8 + - - +
542B LYS* 4.1 0.9 - - - +
543B GLY* 2.9 25.3 + - - -
581B ALA* 3.5 27.1 - - - +
584B LEU* 4.1 3.1 - - + +
585B ALA* 3.7 14.8 - - + +
588B TRP* 3.3 39.9 - - + +
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Residues in contact with LEU 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B VAL* 4.2 22.4 - - + +
390B PHE* 3.6 52.6 - - + +
391B ALA* 5.5 0.4 - - - -
394B ALA* 5.5 0.2 - - - +
536B THR* 3.1 26.4 + - + +
537B THR* 3.9 2.7 - - - +
539B ILE* 1.3 77.2 - - - +
541B VAL* 1.3 57.3 + - - +
543B GLY* 3.4 1.1 + - - -
544B ALA* 3.0 28.6 + - - +
581B ALA* 4.5 1.6 - - + +
582B PHE* 4.2 18.8 - - + +
585B ALA* 3.4 22.9 - - + -
1222B CLA 3.9 16.2 - - + -
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Residues in contact with VAL 541 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B PHE* 3.5 25.8 - - + -
421B ILE* 4.4 6.1 - - + -
422B ILE* 4.7 3.4 - - + -
425B LEU* 4.0 16.6 - - + -
537B THR* 2.8 36.8 + - + +
540B LEU* 1.3 69.9 - - - +
542B LYS* 1.3 63.2 + - - +
544B ALA* 3.2 5.0 + - - +
545B LEU* 2.8 47.1 + - + +
4009B BCR 3.4 34.5 - - + -
4010B BCR 5.5 1.3 - - + -
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Residues in contact with LYS 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A TYR* 2.5 68.8 + - + +
699A GLU* 3.4 25.6 + - - +
700A LEU* 3.8 14.4 - - + +
703A SER* 5.7 0.2 - - - +
422B ILE* 3.9 37.0 - - + +
538B LEU* 2.9 22.0 + - + +
539B ILE* 4.1 1.8 - - - +
541B VAL* 1.3 79.1 - - - +
543B GLY* 1.3 64.6 + - - +
546B ASP* 3.1 48.5 + - - +
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Residues in contact with GLY 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A TYR* 6.0 0.2 - - - -
394B ALA* 4.7 0.9 - - - -
539B ILE 2.9 12.2 + - - -
540B LEU 3.8 0.9 - - - -
542B LYS* 1.3 82.5 - - - +
544B ALA* 1.3 55.2 + - - +
546B ASP* 3.8 2.5 - - - +
547B ALA* 3.2 20.4 + - - -
556B LYS* 5.6 0.5 + - - -
578B ALA* 3.6 20.0 - - - +
581B ALA* 3.4 29.6 - - - -
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Residues in contact with ALA 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B PHE 4.6 1.1 - - - +
394B ALA* 3.6 27.5 - - + +
397B LEU* 3.2 21.3 - - + +
540B LEU 3.0 17.2 + - - +
541B VAL 3.6 3.4 - - - +
543B GLY* 1.3 73.4 - - - +
545B LEU* 1.3 65.3 + - + +
546B ASP 3.1 1.8 - - - -
547B ALA* 3.1 15.8 + - - +
548B ARG* 4.6 0.7 + - - +
4010B BCR 3.7 29.4 - - + -
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Residues in contact with LEU 545 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B LEU* 4.5 9.0 - - + -
414B VAL* 4.5 13.5 - - + -
415B LEU* 3.9 28.0 - - + +
418B LYS* 3.4 49.2 + - + +
421B ILE* 4.5 11.2 - - + -
422B ILE* 4.1 15.5 - - + -
541B VAL* 2.8 41.7 + - + +
544B ALA* 1.3 75.5 - - + +
546B ASP* 1.3 63.7 + - - +
547B ALA 3.4 0.2 - - - -
548B ARG* 4.9 3.4 + - - +
549B GLY 4.4 0.7 + - - +
4009B BCR 4.5 15.9 - - + -
4010B BCR 5.6 0.7 - - + -
141F ARG 5.2 4.7 - - - +
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Residues in contact with ASP 546 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A GLU* 3.8 29.2 - - - +
702A GLU* 5.5 0.3 - - - +
703A SER* 5.1 1.0 + - - -
418B LYS* 2.9 30.9 + - - +
422B ILE* 3.9 10.0 - - - +
542B LYS* 3.1 39.8 + - - +
543B GLY* 3.8 2.2 - - - +
545B LEU* 1.3 78.1 - - - +
547B ALA* 1.3 66.2 + - - +
548B ARG 3.3 2.7 - - - -
549B GLY 3.1 20.8 + - - +
550B SER* 4.5 6.1 - - - -
556B LYS* 3.1 16.7 + - - +
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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