Contacts of the helix formed by residues 521 - 547 (chain B) in PDB entry 4DAJ
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 PRO 521 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B CYS 4.1 2.7 - - - +
520B ILE* 1.3 97.9 - - + +
522B LYS* 1.3 66.8 + - - +
523B THR* 3.0 18.9 + - - +
524B TYR* 3.1 43.3 + - + +
525B TRP* 3.0 14.0 - - - -
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Residues in contact with LYS 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B TYR* 4.0 26.8 + - - -
219B GLU* 5.3 4.9 - - - +
520B ILE 4.2 0.6 + - - -
521B PRO* 1.3 72.0 - - - +
523B THR* 1.3 58.7 + - - +
525B TRP* 3.4 14.2 + - + +
526B ASN* 2.6 53.3 + - - +
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Residues in contact with THR 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B PRO* 3.0 9.7 - - - +
522B LYS* 1.3 80.9 - - - +
524B TYR* 1.3 84.0 + - + +
526B ASN* 3.0 6.0 + - - +
527B LEU* 2.9 45.3 + - + +
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Residues in contact with TYR 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B MET* 3.6 14.9 - - - +
520B ILE* 3.6 23.6 - - + -
521B PRO* 3.1 37.0 + - + +
523B THR* 1.3 98.3 - - + +
525B TRP* 1.3 62.8 + - - +
527B LEU* 3.5 13.1 + - + +
528B GLY* 2.9 18.0 + - - -
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Residues in contact with TRP 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B TYR* 4.3 22.3 - + + -
509B MET* 3.4 44.9 - - + +
510B VAL* 4.1 18.6 - - + -
513B ASN* 3.3 47.3 - - + -
520B ILE* 3.3 27.7 + - + +
521B PRO 3.0 26.9 + - - -
522B LYS* 3.4 13.7 - - + +
523B THR 3.2 0.2 - - - -
524B TYR* 1.3 76.5 - - - +
526B ASN* 1.3 68.7 + - - +
528B GLY* 2.7 14.4 + - - -
529B TYR* 2.9 13.8 + - + +
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Residues in contact with ASN 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PHE* 4.1 26.9 - - + -
128B ILE* 4.9 14.9 - - + +
522B LYS* 2.6 44.5 + - - +
523B THR* 3.5 7.1 - - - +
525B TRP* 1.3 76.3 - - - +
527B LEU* 1.3 67.5 + - + +
529B TYR* 2.9 10.3 + - - +
530B TRP* 2.9 26.1 + - + +
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Residues in contact with LEU 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B THR* 2.9 37.7 + - + +
524B TYR* 3.7 15.9 - - + +
526B ASN* 1.3 79.1 - - + +
528B GLY* 1.3 62.4 + - - +
530B TRP* 3.2 11.5 + - + +
531B LEU* 2.9 34.0 + - + +
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Residues in contact with GLY 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B THR 4.3 0.3 - - - +
505B PRO* 4.9 2.0 - - - -
506B TYR* 3.9 20.8 - - - +
509B MET* 4.4 6.3 - - - -
524B TYR 2.9 10.7 + - - -
525B TRP 2.7 14.8 + - - -
527B LEU* 1.3 71.6 - - - +
529B TYR* 1.3 60.6 + - - -
531B LEU* 3.1 14.8 + - - +
532B CYS* 3.0 25.7 + - - -
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Residues in contact with TYR 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PHE* 4.0 26.5 - + + -
143B TRP* 5.0 7.4 - + - -
144B LEU* 4.8 6.9 - - - +
147B ASP* 3.5 9.8 + - - -
148B TYR* 3.3 32.6 + - - -
506B TYR* 3.5 39.4 - + - -
525B TRP* 2.9 10.9 + - + -
526B ASN* 3.1 13.5 - - - +
528B GLY* 1.3 74.4 - - - +
530B TRP* 1.3 58.0 + - - +
532B CYS* 3.0 12.0 + - - +
533B TYR* 3.0 65.1 + + - -
2000B 0HK 3.6 18.8 - - - -
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Residues in contact with TRP 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B THR* 3.5 39.0 - - + +
77B LEU* 4.8 15.0 - - + -
121B MET* 3.1 62.6 - - + -
124B PHE* 2.9 40.6 - + - -
125B THR* 3.4 11.9 - - - -
128B ILE* 3.6 13.5 - - + +
526B ASN* 2.9 15.8 + - + +
527B LEU* 3.2 12.3 + - + +
529B TYR* 1.3 73.7 - - - +
531B LEU* 1.3 62.4 + - + +
533B TYR* 3.0 24.9 + + + +
534B ILE* 2.9 34.0 + - + +
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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
----------------------------------------------------------
502B THR* 3.2 23.7 - - - +
505B PRO* 3.7 31.4 - - + -
527B LEU* 2.9 24.5 + - + +
528B GLY* 3.1 7.6 + - - +
530B TRP* 1.3 72.5 - - + +
532B CYS* 1.3 67.8 + - - +
534B ILE* 3.0 44.4 + - + +
535B ASN 3.0 4.5 + - - -
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Residues in contact with CYS 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ILE* 4.7 2.8 - - - +
502B THR 3.8 0.4 - - - -
503B TRP* 3.2 58.9 + - + +
506B TYR* 3.9 18.4 - - - -
528B GLY 3.0 18.4 + - - -
529B TYR 3.1 10.3 - - - +
531B LEU* 1.3 75.9 - - - +
533B TYR* 1.3 61.1 + - - +
535B ASN* 3.4 8.0 - - - +
536B SER* 4.0 6.2 + - - -
2000B 0HK 3.7 31.8 - - - -
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Residues in contact with TYR 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ILE* 3.3 36.8 - - + -
120B SER* 3.7 13.2 + - - -
121B MET* 3.6 32.1 - - + +
124B PHE* 4.0 23.0 - + - +
143B TRP* 4.3 4.7 - - - -
147B ASP* 2.5 25.5 + - - -
529B TYR* 3.0 30.6 + + - -
530B TRP* 3.2 35.4 - + + +
531B LEU 3.0 0.4 - - - -
532B CYS* 1.3 76.6 - - - +
534B ILE* 1.3 57.3 + - - +
535B ASN 2.9 4.7 - - - -
536B SER* 2.8 23.2 + - - -
537B THR* 3.0 13.2 + - - -
2000B 0HK 3.8 16.2 - - - -
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Residues in contact with ILE 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 4.4 26.2 - - + -
121B MET* 5.9 0.2 - - + -
502B THR* 3.7 13.5 - - + -
530B TRP* 2.9 28.0 + - + +
531B LEU* 3.0 41.0 + - + +
533B TYR* 1.3 69.3 - - + +
535B ASN* 1.3 59.8 + - - +
537B THR* 3.5 14.7 - - + +
538B VAL* 2.9 41.9 + - + +
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Residues in contact with ASN 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ASP* 5.2 0.3 - - - +
154B SER* 5.1 5.0 + - - -
498B ALA* 3.5 5.3 - - - +
499B PHE* 3.1 41.6 - - - +
502B THR* 2.7 29.3 + - - +
503B TRP* 3.7 13.7 + - - +
531B LEU 3.0 6.1 + - - -
532B CYS 3.4 12.3 - - - +
533B TYR 2.9 0.6 - - - -
534B ILE* 1.3 79.2 - - - +
536B SER* 1.3 60.6 + - - +
538B VAL* 3.1 3.6 + - - +
539B ASN* 3.0 47.6 + - - +
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Residues in contact with SER 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B THR* 3.8 7.1 - - - +
113B ASP* 2.6 47.8 + - - +
116B ILE* 3.6 33.5 - - - +
121B MET* 5.6 0.2 - - - -
154B SER* 5.6 0.3 + - - -
503B TRP* 6.0 1.4 - - - -
532B CYS 4.3 3.1 + - - -
533B TYR 2.8 13.0 + - - -
535B ASN* 1.3 76.6 + - - +
537B THR* 1.3 58.8 + - - +
539B ASN* 4.2 0.7 - - - +
540B PRO* 3.2 22.7 - - - +
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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
----------------------------------------------------------
77B LEU* 3.5 24.9 + - + +
80B VAL* 3.7 26.1 - - + +
81B THR* 2.5 29.3 + - - +
121B MET* 3.6 9.0 - - - +
533B TYR 3.0 12.6 + - - -
534B ILE* 3.5 16.4 - - - +
535B ASN 3.2 0.2 - - - -
536B SER* 1.3 79.4 - - - +
538B VAL* 1.3 61.1 + - + +
540B PRO* 3.6 10.6 - - - +
541B VAL* 4.1 11.8 - - - +
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Residues in contact with VAL 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B ALA* 4.2 13.9 - - + -
502B THR* 5.4 3.6 - - + -
534B ILE* 2.9 32.9 + - + +
535B ASN* 3.1 5.6 + - - +
537B THR* 1.3 79.6 - - + +
539B ASN* 1.3 66.7 + - - +
541B VAL* 2.8 22.8 + - + +
542B CYS* 2.9 29.1 + - - -
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Residues in contact with ASN 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 5.0 11.1 - - - +
113B ASP* 3.2 25.6 + - - +
154B SER* 5.4 1.4 + - - -
158B LEU* 5.9 1.4 - - - +
495B ILE* 3.6 39.7 - - + +
498B ALA* 4.2 4.3 - - - +
499B PHE* 5.9 0.4 - - - +
535B ASN* 3.0 42.5 + - - +
538B VAL* 1.3 75.9 - - - +
540B PRO* 1.3 71.7 - - + +
542B CYS* 2.9 14.4 + - - +
543B TYR* 2.9 28.6 + - - +
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Residues in contact with PRO 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B THR* 4.6 2.2 - - - +
84B GLY* 3.7 28.7 - - - +
85B ASN* 2.8 35.2 - - - +
88B VAL* 4.0 4.5 - - + +
536B SER 3.2 17.7 - - - +
537B THR 3.6 8.1 - - - +
538B VAL 3.6 2.9 - - - -
539B ASN* 1.3 92.1 - - + +
541B VAL* 1.3 60.1 - - + +
543B TYR* 3.5 27.3 - - + +
544B ALA* 3.8 7.4 + - - +
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Residues in contact with VAL 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL* 5.6 7.6 - - + -
537B THR 4.1 13.2 - - - +
538B VAL* 2.8 22.1 + - + +
540B PRO* 1.3 75.9 - - + +
542B CYS* 1.3 63.7 + - - +
543B TYR 3.1 2.1 + - - -
544B ALA* 3.2 8.2 + - - +
545B LEU* 2.9 45.3 + - + +
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Residues in contact with CYS 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491B THR* 5.4 1.8 - - - +
494B ALA* 4.1 30.1 - - + -
495B ILE* 3.3 29.4 - - + -
498B ALA* 4.3 3.1 - - - -
538B VAL* 2.9 37.0 + - - -
539B ASN* 2.9 3.2 + - - +
541B VAL* 1.3 74.6 - - - +
543B TYR* 1.3 63.8 + - - +
545B LEU* 3.1 17.1 + - - +
546B CYS* 2.9 28.1 + - - +
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Residues in contact with TYR 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B VAL* 3.5 38.6 - - + -
106B LEU* 3.0 55.6 + - + +
109B LEU* 3.4 20.3 - - + +
110B ALA* 3.8 5.6 + - + -
491B THR* 5.0 4.7 - - + -
495B ILE* 3.7 19.5 - - + -
539B ASN* 2.9 19.6 + - + +
540B PRO* 3.5 28.0 - - + +
542B CYS* 1.3 79.0 - - - +
544B ALA* 1.3 64.9 + - - +
546B CYS 3.3 0.3 + - - -
547B ASN* 3.0 29.1 + - - +
550B PHE* 4.0 11.0 - - + -
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Residues in contact with ALA 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B PRO 3.8 7.3 + - - +
541B VAL* 3.2 9.9 + - - +
543B TYR* 1.3 78.2 - - - +
545B LEU* 1.3 64.7 + - + +
547B ASN 2.8 18.0 - - - +
548B LYS* 4.7 0.2 - - - -
550B PHE* 3.6 20.5 - - + +
551B ARG* 4.5 16.9 - - + +
554B PHE* 5.9 2.7 - - + -
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Residues in contact with LEU 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B ALA* 5.9 3.1 - - + -
541B VAL* 2.9 40.4 + - + +
542B CYS* 3.2 22.2 - - + +
543B TYR 3.0 0.2 + - - -
544B ALA* 1.3 81.6 - - + +
546B CYS* 1.3 65.3 + - + +
547B ASN* 3.2 1.6 + - - -
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Residues in contact with CYS 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B GLN* 5.2 3.2 - - + +
491B THR* 3.2 46.8 + - + +
493B SER* 6.1 1.1 - - - -
494B ALA* 3.9 24.7 - - - -
542B CYS 2.9 14.3 + - - +
545B LEU* 1.3 75.2 - - - +
547B ASN* 1.3 65.9 + - - +
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Residues in contact with ASN 547 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ASN* 5.7 1.6 - - - +
106B LEU* 5.8 1.4 - - - +
490B GLN* 4.3 12.8 + - - +
491B THR* 2.6 38.8 + - - +
543B TYR* 3.0 13.4 + - - +
544B ALA 2.8 18.8 - - - +
545B LEU 3.1 1.9 - - - -
546B CYS* 1.3 83.8 + - - +
548B LYS* 1.3 63.8 + - - +
549B THR* 4.2 15.8 + - - +
550B PHE* 3.2 18.9 + - + +
551B ARG 3.4 3.5 + - - -
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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