Contacts of the helix formed by residues 558 - 583 (chain B) in PDB entry 5CTR
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 558 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A ARG* 4.4 4.9 - - - +
528B ARG* 4.9 1.2 - - - +
557B GLY* 1.3 77.2 - - - +
559B LEU* 1.3 80.1 + - - +
560B GLU* 3.0 17.0 + - - +
561B ASP* 3.2 21.6 + - - -
562B TRP* 2.9 26.5 + - - +
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Residues in contact with LEU 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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390A GLU* 4.3 20.9 - - + +
391A ARG* 4.2 29.2 - - + -
430A ARG* 3.9 26.3 - - + +
558B SER* 1.3 87.1 + - - +
560B GLU* 1.3 75.8 + - + +
562B TRP* 3.3 9.7 + - + +
563B ASP* 2.7 40.7 + - - +
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Residues in contact with GLU 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B SER* 3.0 8.7 + - - +
559B LEU* 1.3 91.2 - - + +
561B ASP* 1.3 61.2 + - - +
563B ASP* 3.2 9.7 + - - +
564B ILE* 2.9 63.3 + - + +
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Residues in contact with ASP 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B ARG* 3.9 28.3 + - - -
532B HIS* 5.8 1.0 - - - -
553B GLU* 3.2 25.7 - - - +
558B SER* 3.2 30.7 + - - +
560B GLU* 1.3 82.5 - - - +
562B TRP* 1.3 57.3 + - - +
564B ILE* 3.4 14.7 + - - +
565B ALA* 2.9 28.4 + - - +
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Residues in contact with TRP 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A LEU* 4.9 15.6 - - + +
391A ARG* 5.4 3.2 - - - +
430A ARG* 4.9 12.3 - - - +
550B LEU* 3.1 54.3 - - + -
553B GLU* 4.0 14.3 - - + +
554B ARG* 3.6 38.8 - - + -
558B SER 2.9 13.0 + - - +
559B LEU* 3.5 13.7 - - + +
561B ASP* 1.3 77.4 - - - +
563B ASP* 1.3 70.0 + - - +
565B ALA* 3.1 3.5 + - - +
566B VAL* 2.9 49.5 + - + +
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Residues in contact with ASP 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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391A ARG* 2.7 47.5 + - - +
559B LEU* 2.7 34.2 + - - +
560B GLU* 3.2 12.8 + - - +
562B TRP* 1.3 83.9 - - - +
564B ILE* 1.3 61.7 + - + +
566B VAL* 3.0 26.8 - - - +
567B GLN* 3.3 9.4 + - - +
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Residues in contact with ILE 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B HIS* 4.7 8.3 - - - +
560B GLU* 2.9 52.2 + - + +
561B ASP* 3.6 14.1 - - - +
563B ASP* 1.3 75.7 - - + +
565B ALA* 1.3 63.4 + - - +
567B GLN* 3.3 7.5 + - + +
568B LYS* 3.1 45.3 + - + +
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Residues in contact with ALA 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B HIS* 4.6 6.3 - - + -
549B LEU* 4.0 23.2 - - + +
550B LEU* 4.1 11.2 - - + -
553B GLU* 3.9 21.3 - - + -
561B ASP 2.9 14.4 + - - +
562B TRP* 3.3 9.6 - - - +
564B ILE* 1.3 75.5 - - - +
566B VAL* 1.3 65.0 + - - +
568B LYS* 3.4 2.8 + - - +
569B THR* 3.2 28.2 + - - +
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Residues in contact with VAL 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ARG* 4.6 16.4 - - - +
550B LEU* 3.6 11.7 - - + -
562B TRP* 2.9 53.1 + - + +
563B ASP* 3.0 31.0 - - - +
565B ALA* 1.3 74.5 - - - +
567B GLN* 1.3 60.2 + - + +
569B THR* 3.1 16.5 + - - -
570B GLU* 3.0 23.2 + - - +
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Residues in contact with GLN 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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356A ARG* 4.3 10.2 + - - +
563B ASP 3.3 9.6 + - - +
564B ILE* 3.5 11.7 - - + +
565B ALA 3.2 0.2 - - - -
566B VAL* 1.3 83.5 - - + +
568B LYS* 1.3 64.0 + - + +
570B GLU* 3.2 24.7 - - - +
571B THR* 2.8 42.8 + - - +
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Residues in contact with LYS 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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529B LYS* 5.5 4.8 - - - +
532B HIS* 3.4 52.8 + - + +
535B VAL* 4.4 13.5 - - + +
549B LEU* 5.3 1.1 - - + -
564B ILE* 3.1 27.2 + - + +
565B ALA* 4.0 4.5 - - - +
566B VAL 3.4 0.4 - - - -
567B GLN* 1.3 80.1 - - + +
569B THR* 1.3 61.0 + - + +
571B THR* 3.6 5.7 - - - -
572B ARG* 3.1 26.5 + - - +
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Residues in contact with THR 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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535B VAL* 4.5 6.7 - - + -
546B CYS* 3.5 42.2 - - + -
549B LEU* 4.2 16.2 - - + -
550B LEU* 3.9 16.8 - - + +
565B ALA 3.2 13.9 + - - +
566B VAL* 3.1 14.0 + - - -
568B LYS* 1.3 73.9 - - - +
570B GLU* 1.3 55.7 + - - +
571B THR 3.2 1.6 - - - -
572B ARG* 3.1 4.7 + - - +
573B LEU* 2.7 44.0 + - - +
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Residues in contact with GLU 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A GLN* 5.4 0.7 - - - +
356A ARG* 2.9 34.6 + - - -
566B VAL* 3.0 20.0 - - - +
567B GLN* 3.2 28.2 - - - +
569B THR* 1.3 80.1 + - - +
571B THR* 1.3 59.2 + - - +
573B LEU* 3.8 7.9 - - - +
574B ALA* 2.7 39.4 + - + +
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Residues in contact with THR 571 (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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567B GLN* 2.8 37.2 + - - +
568B LYS* 3.6 6.1 - - - +
570B GLU* 1.3 82.0 - - - +
572B ARG* 1.3 65.1 + - - +
574B ALA* 4.0 4.8 - - - +
575B ARG* 3.4 19.5 + - + +
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Residues in contact with ARG 572 (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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535B VAL* 3.4 38.2 + - + +
536B GLN* 3.9 16.0 + - - +
537B CYS 5.2 0.2 + - - -
538B THR 3.0 25.7 + - - -
539B SER* 4.2 13.1 + - - +
542B PRO* 4.3 9.6 - - + +
568B LYS 3.1 16.0 + - - +
569B THR 3.1 6.5 + - - +
571B THR* 1.3 78.9 - - - +
573B LEU* 1.3 65.7 + - + +
575B ARG* 3.1 37.8 + - - +
576B VAL* 3.0 52.0 + - + +
579B GLN* 5.6 4.6 + - - -
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Residues in contact with LEU 573 (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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542B PRO* 4.5 5.6 - - + -
543B GLU* 4.4 31.0 - - + +
546B CYS* 3.9 31.0 - - + -
569B THR* 2.7 28.2 + - - +
570B GLU* 3.8 6.3 - - - +
572B ARG* 1.3 80.1 - - + +
574B ALA* 1.3 57.7 - - - +
576B VAL* 3.4 9.7 - - + +
577B ASN* 2.9 43.6 + - - +
580B ARG* 5.9 0.9 - - - +
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Residues in contact with ALA 574 (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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570B GLU* 2.7 22.6 + - + +
571B THR* 4.0 5.4 - - - +
573B LEU* 1.3 73.7 - - - +
575B ARG* 1.3 58.3 + - - +
577B ASN* 3.4 10.4 + - - +
578B GLU* 3.1 24.9 + - - +
581B MET* 5.5 0.5 - - - +
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Residues in contact with ARG 575 (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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536B GLN* 5.1 8.1 + - - +
571B THR 3.4 11.1 + - - +
572B ARG* 3.1 44.6 + - - +
573B LEU 3.3 0.2 - - - -
574B ALA* 1.3 76.3 - - - +
576B VAL* 1.3 61.7 + - - +
578B GLU* 2.9 27.7 - - + +
579B GLN* 2.9 27.5 + - + +
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Residues in contact with VAL 576 (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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542B PRO* 4.5 17.7 - - + -
543B GLU* 5.2 0.9 - - - +
572B ARG* 3.0 51.9 + - + +
573B LEU* 3.4 14.8 - - + +
574B ALA 3.3 0.2 - - - -
575B ARG* 1.3 77.7 - - + +
577B ASN* 1.3 56.7 + - - +
579B GLN* 2.9 29.0 + - + +
580B ARG* 3.1 39.8 + - - +
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Residues in contact with ASN 577 (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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573B LEU* 2.9 29.9 + - - +
574B ALA* 3.4 9.3 + - - +
576B VAL* 1.3 74.2 - - - +
578B GLU* 1.3 56.7 + - - +
580B ARG* 2.8 45.3 + - + +
581B MET* 3.0 42.2 + - + +
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Residues in contact with GLU 578 (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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574B ALA 3.1 13.8 + - - +
575B ARG* 2.9 34.3 + - + +
577B ASN* 1.3 78.7 - - - +
579B GLN* 1.3 68.9 + - - +
581B MET* 3.3 20.3 - - + +
582B LYS* 3.2 38.3 + - - +
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Residues in contact with GLN 579 (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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572B ARG* 5.6 4.2 + - - -
575B ARG* 2.9 14.6 + - + +
576B VAL* 2.9 16.7 + - - +
578B GLU* 1.3 86.4 - - - +
580B ARG* 1.3 57.6 + - - +
582B LYS* 3.2 29.6 - - + +
583B ALA* 3.3 15.1 + - - +
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Residues in contact with ARG 580 (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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543B GLU* 4.0 20.6 + - - +
573B LEU* 5.9 1.6 - - - +
576B VAL* 3.1 28.2 + - - +
577B ASN* 2.8 47.5 + - + +
579B GLN* 1.3 75.1 - - - +
581B MET* 1.3 58.0 + - + +
583B ALA* 3.9 6.6 - - - +
584B ALA* 3.3 24.3 + - - +
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Residues in contact with MET 581 (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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574B ALA 5.5 0.4 - - - +
577B ASN* 3.0 31.9 + - + +
578B GLU* 3.3 24.2 - - + +
579B GLN 3.3 0.2 - - - -
580B ARG* 1.3 77.0 - - + +
582B LYS* 1.3 68.1 + - + +
583B ALA 3.1 1.3 - - - -
584B ALA* 3.3 22.3 + - - +
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Residues in contact with LYS 582 (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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578B GLU* 3.2 27.4 + - - +
579B GLN* 3.2 28.5 - - + +
581B MET* 1.3 84.8 - - + +
583B ALA* 1.3 60.2 + - + +
584B ALA 3.3 2.6 - - - -
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Residues in contact with ALA 583 (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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579B GLN 3.3 17.9 + - - +
580B ARG* 4.1 7.2 - - - +
581B MET 3.1 0.6 - - - -
582B LYS* 1.3 80.4 - - + +
584B ALA* 1.3 60.9 + - - +
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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) + - + + + + + -
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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