Contacts of the helix formed by residues 549 - 570 (chain B) in PDB entry 3PRF
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 GLU 549 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547B LYS* 4.6 3.2 - - - +
548B PHE* 1.3 83.5 - - - +
550B MET* 1.3 67.9 + - - +
551B ILE* 3.2 23.1 - - + -
552B LYS* 2.8 24.8 + - + +
553B LEU* 3.1 12.6 + - - +
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Residues in contact with MET 550 (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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548B PHE 4.2 0.6 + - - -
549B GLU* 1.3 70.6 - - - +
551B ILE* 1.3 68.7 + - + +
553B LEU* 3.1 15.5 + - + +
554B ILE* 2.9 50.8 + - + +
650B MET* 4.0 23.8 - - - +
682B ARG* 3.8 21.1 - - - -
684B ASN* 3.7 53.1 - - + +
685B CYS* 3.9 14.8 - - + +
686B PRO* 4.4 1.8 - - + -
721B LEU* 5.4 4.3 - - + -
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Residues in contact with ILE 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B GLU* 3.5 26.5 - - + -
550B MET* 1.3 78.7 - - + +
552B LYS* 1.3 56.4 + - - +
554B ILE* 3.7 5.0 + - - +
555B ASP* 3.1 25.5 + - - +
721B LEU* 3.9 34.5 - - + +
722B PRO* 5.6 5.6 - - + -
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Residues in contact with LYS 552 (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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548B PHE* 3.7 32.3 - - + -
549B GLU* 2.8 29.9 + - + +
551B ILE* 1.3 72.2 - - - +
553B LEU* 1.3 53.5 + - - +
555B ASP* 2.8 19.2 + - - +
556B ILE* 2.7 46.2 + - + +
584B LEU* 5.9 0.4 - - + -
587B ASP* 2.8 27.7 + - - +
588B LEU* 4.0 16.1 - - - +
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Residues in contact with LEU 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B LEU* 4.7 6.1 - - + -
548B PHE* 3.9 36.1 - - + +
549B GLU 3.1 12.7 + - - +
550B MET* 3.6 37.2 - - + +
552B LYS* 1.3 73.8 - - - +
554B ILE* 1.3 51.8 + - - +
555B ASP 3.1 0.3 + - - -
556B ILE* 3.1 9.8 + - + +
557B ALA* 2.7 35.0 + - - +
649B LEU* 3.4 45.6 - - + +
650B MET* 3.7 15.5 - - + -
682B ARG* 4.6 13.7 - - - +
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Residues in contact with ILE 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B MET* 2.9 45.7 + - + +
551B ILE 3.9 4.5 - - - +
553B LEU* 1.3 74.4 - - - +
555B ASP* 1.3 57.1 + - - +
557B ALA* 3.3 8.7 - - - +
558B ARG* 2.8 25.5 + - + +
650B MET* 4.5 7.2 - - + +
686B PRO* 4.1 13.2 - - + -
689B MET* 4.7 6.7 - - + -
714B ILE* 3.8 18.7 - - + +
717B LEU* 3.9 25.8 - - + -
718B ALA* 4.5 8.5 - - + -
721B LEU* 3.7 30.5 - - + -
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Residues in contact with ASP 555 (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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551B ILE 3.1 14.7 + - - +
552B LYS* 2.8 25.5 + - + +
554B ILE* 1.3 74.3 - - - +
556B ILE* 1.3 58.8 + - + +
557B ALA 3.1 0.7 - - - -
558B ARG* 2.8 31.6 + - - +
559B GLN* 2.8 53.4 + - - +
588B LEU* 4.3 4.3 - - - +
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Residues in contact with ILE 556 (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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537B LEU* 4.1 22.0 - - + -
548B PHE* 4.3 26.2 - - + -
552B LYS* 2.7 41.6 + - + +
553B LEU* 3.6 10.3 - - - +
555B ASP* 1.3 73.5 - - + +
557B ALA* 1.3 59.8 + - - +
559B GLN* 5.4 0.7 - - - +
560B THR* 2.6 37.0 + - - +
582B ILE* 4.9 0.9 - - + -
584B LEU* 4.4 14.6 - - + -
590B VAL* 3.8 29.2 - - + +
649B LEU* 3.9 20.4 - - + -
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Residues in contact with ALA 557 (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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553B LEU 2.7 13.4 + - - +
554B ILE* 3.3 15.7 - - - +
556B ILE* 1.3 78.0 - - - +
558B ARG* 1.3 61.7 + - - +
560B THR* 4.7 2.0 - - - -
561B ALA* 3.1 23.2 + - - +
642B PHE* 3.7 8.8 - - - -
646B LEU* 3.8 27.1 - - + -
649B LEU* 3.8 11.8 - - + +
650B MET* 5.5 1.6 - - + -
689B MET* 4.4 10.8 - - + -
714B ILE* 3.9 4.0 - - + +
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Residues in contact with ARG 558 (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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512B ASN* 5.4 0.6 + - - -
554B ILE* 2.8 16.2 + - + +
555B ASP* 2.8 42.0 + - - +
557B ALA* 1.3 75.7 - - - +
559B GLN* 1.3 84.8 + - - +
561B ALA* 3.3 5.4 + - - +
562B GLN* 2.9 40.6 + - - +
711B LEU* 3.7 6.0 - - + +
714B ILE* 3.8 24.9 - - + +
715B GLU* 4.3 28.8 + - + +
718B ALA* 5.2 9.0 - - + -
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Residues in contact with GLN 559 (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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512B ASN* 3.3 26.9 + - - +
555B ASP* 2.8 45.7 + - - +
556B ILE* 5.2 0.4 - - - +
558B ARG* 1.3 91.8 - - - +
560B THR* 1.3 60.1 + - - +
562B GLN* 3.0 10.4 + - - +
563B GLY 2.9 25.1 + - - -
588B LEU 3.3 12.3 + - - +
589B THR* 3.2 11.9 - - - +
590B VAL* 2.7 44.2 + - + +
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Residues in contact with THR 560 (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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556B ILE* 2.6 27.5 + - - +
557B ALA* 3.8 3.8 - - - -
558B ARG 3.3 0.2 - - - -
559B GLN* 1.3 73.9 - - - +
561B ALA* 1.3 67.2 + - - +
562B GLN 3.3 0.2 + - - -
563B GLY 3.3 1.0 + - - -
564B MET* 3.0 31.2 + - + +
577B LEU* 4.7 5.2 - - + -
582B ILE* 3.8 28.5 - - + +
590B VAL* 3.5 18.2 - - - +
592B ILE* 3.6 16.5 - - + +
642B PHE* 4.0 21.5 - - + -
645B VAL* 4.8 4.5 - - + +
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Residues in contact with ALA 561 (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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557B ALA 3.1 14.7 + - - +
558B ARG 3.5 8.5 - - - +
559B GLN 3.3 0.2 - - - -
560B THR* 1.3 75.5 - - - +
562B GLN* 1.3 57.2 + - - +
564B MET* 3.4 1.7 + - - +
565B ASP* 2.9 32.2 + - - +
642B PHE* 3.8 13.3 - - + -
707B PHE* 4.1 11.2 - - + -
710B ILE* 4.2 11.0 - - + -
711B LEU* 3.7 15.7 - - + +
714B ILE* 3.9 17.7 - - + -
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Residues in contact with GLN 562 (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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475A LYS* 5.1 0.2 + - - -
477A HIS* 3.1 40.6 + - - +
478A GLY* 3.3 18.2 + - - +
510B HIS* 3.8 4.5 - - + -
512B ASN* 3.5 15.0 - - - +
558B ARG* 2.9 27.7 + - - +
559B GLN* 3.0 14.8 + - - +
561B ALA* 1.3 78.4 - - - +
563B GLY* 1.3 60.1 + - - +
565B ASP* 3.4 3.1 + - - +
566B TYR* 3.1 20.3 + - - +
711B LEU* 3.5 30.9 - - + +
715B GLU* 4.3 9.0 - - - +
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Residues in contact with GLY 563 (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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510B HIS* 4.7 0.9 - - - -
512B ASN* 3.7 21.6 - - - +
513B ILE* 3.8 8.9 - - - +
559B GLN 2.9 11.3 + - - -
560B THR 3.3 0.2 + - - -
562B GLN* 1.3 75.4 - - - +
564B MET* 1.3 62.2 + - - +
566B TYR* 3.0 9.9 + - - +
567B LEU* 3.0 24.7 + - - +
592B ILE* 3.8 15.0 - - - -
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Residues in contact with MET 564 (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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560B THR* 3.0 23.4 + - + +
561B ALA 3.6 4.5 - - - +
563B GLY* 1.3 74.9 - - - +
565B ASP* 1.3 56.9 + - - +
567B LEU* 3.0 21.0 + - + +
568B HIS* 2.9 47.3 + - + +
574B HIS* 4.4 6.3 - - + -
577B LEU* 4.0 26.9 - - + -
592B ILE* 3.7 19.4 - - + +
638B ASP* 3.6 36.3 - - + +
642B PHE* 5.0 0.2 - - + -
707B PHE* 3.6 33.0 - - + -
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Residues in contact with ASP 565 (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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477A HIS* 3.9 17.3 + - - -
561B ALA 2.9 18.3 + - - +
562B GLN* 3.6 6.1 + - - +
564B MET* 1.3 72.6 - - - +
566B TYR* 1.3 65.0 + - - +
568B HIS* 4.7 3.8 - - - +
569B ALA* 3.4 22.5 + - - +
707B PHE* 4.0 12.8 - - + +
708B PRO* 3.5 37.5 - - - +
711B LEU* 3.4 27.5 - - + +
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Residues in contact with TYR 566 (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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450A TRP* 4.2 3.6 - - - -
476A TRP* 4.2 20.9 - + - -
477A HIS* 4.1 23.1 + + + -
517A MET 5.2 1.7 + - - -
507B LYS 3.3 11.4 + - - -
508B THR* 3.9 20.9 - - + -
509B ARG 2.9 35.1 + - - -
510B HIS* 3.5 43.5 - + + +
513B ILE* 4.0 10.1 - - + -
562B GLN 3.1 9.3 + - - +
563B GLY 3.0 9.0 + - - +
565B ASP* 1.3 77.8 - - - +
567B LEU* 1.3 68.6 + - + +
569B ALA* 3.3 13.0 + - - +
570B LYS* 3.4 40.7 + - + +
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Residues in contact with LEU 567 (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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508B THR* 3.8 28.0 - - + -
513B ILE* 3.9 21.8 - - + -
563B GLY 3.0 13.2 + - - +
564B MET* 3.0 32.1 + - + +
566B TYR* 1.3 80.4 - - + +
568B HIS* 1.3 59.1 + - + +
570B LYS* 2.9 21.1 + - - -
572B ILE* 2.9 46.9 + - + +
574B HIS* 4.3 14.8 - - + -
592B ILE* 4.7 1.3 - - + -
595B PHE* 4.2 18.6 - - + -
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Residues in contact with HIS 568 (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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564B MET* 2.9 28.5 + - + +
565B ASP* 4.6 6.5 - - - +
567B LEU* 1.3 73.9 - - + +
569B ALA* 1.3 59.5 + - - +
571B SER* 3.3 9.9 + - - +
572B ILE 3.0 27.8 - - - -
573B ILE* 4.5 0.2 - - - -
635B PHE* 3.4 76.3 - + + +
638B ASP* 2.7 30.2 + - + +
706B LEU* 5.7 0.4 - - - +
707B PHE* 3.5 28.0 + + + +
708B PRO* 6.4 0.7 - - + -
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Residues in contact with ALA 569 (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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477A HIS* 3.5 26.5 - - + +
565B ASP* 3.4 20.3 + - - +
566B TYR 3.3 5.1 + - - +
567B LEU 3.2 0.8 - - - -
568B HIS* 1.3 76.9 - - - +
570B LYS* 1.3 60.2 + - + +
571B SER* 3.4 2.9 + - - -
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Residues in contact with LYS 570 (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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448A ASP 5.8 1.6 - - - -
449A ASP 5.5 4.0 + - - -
450A TRP* 4.5 15.9 - - - +
476A TRP* 4.7 11.3 - - - -
517A MET 5.7 0.6 + - - -
507B LYS* 2.9 45.1 + - + +
566B TYR* 3.4 49.1 + - + +
567B LEU 2.9 8.6 + - - +
569B ALA* 1.3 80.0 - - + +
571B SER* 1.3 72.0 + - - +
572B ILE* 3.1 19.2 + - + +
599B THR* 4.3 6.2 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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