Contacts of the helix formed by residues 569 - 589 (chain A) in PDB entry 5FBQ
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 LEU 569 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A LYS* 3.8 27.8 - - + -
567A ASP* 3.5 13.8 + - + +
568A ASP* 1.3 90.1 + - - +
570A ARG* 1.3 58.9 + - - +
571A GLN 3.4 1.6 - - - -
572A GLU* 3.6 16.6 - - + +
573A LEU* 2.8 28.8 + - - +
600A ILE* 3.8 16.6 - - + +
601A LEU 4.5 0.4 - - - +
602A VAL* 3.7 14.0 - - + +
604A SER 5.1 3.4 + - - +
607A SER 5.5 0.7 - - - +
608A GLY* 4.0 27.6 - - - +
609A MET 4.0 16.8 - - - +
610A ILE* 4.0 18.8 - - + -
801A 5W6 5.3 1.6 - - - -
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Residues in contact with ARG 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ALA* 3.5 30.7 + - - -
219A TYR* 4.3 34.7 + - + +
221A SER* 5.8 3.6 - - - -
568A ASP* 2.8 39.5 + - - +
569A LEU* 1.3 76.1 - - - +
571A GLN* 1.3 65.9 + - - +
573A LEU* 3.5 5.2 + - - +
574A LEU* 3.2 21.0 + - - +
602A VAL* 4.1 23.3 - - + -
605A ALA* 3.9 18.4 - - - +
759A GLN* 5.9 1.2 + - - +
760A LEU* 3.4 34.4 - - + +
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Residues in contact with GLN 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A ASP* 4.9 5.3 + - - +
569A LEU* 4.5 0.2 - - - +
570A ARG* 1.3 77.4 - - - +
572A GLU* 1.3 63.5 + - - +
574A LEU* 3.3 8.6 + - + +
575A ALA* 3.1 22.9 + - - +
690A PHE 3.6 15.1 + - - +
691A GLY* 4.1 3.2 - - - -
692A PHE* 3.7 8.9 - - - +
693A ILE* 3.0 48.7 + - + +
696A SER* 5.0 2.4 + - - -
760A LEU* 4.2 9.4 - - + +
761A PRO* 3.6 25.5 - - - +
762A CYS* 3.5 30.6 - - - +
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Residues in contact with GLU 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568A ASP 4.9 2.4 + - - +
569A LEU* 3.3 31.4 + - + +
570A ARG 3.2 0.4 - - - -
571A GLN* 1.3 79.7 - - - +
573A LEU* 1.3 60.5 + - - +
575A ALA* 3.4 6.5 + - - +
576A PHE* 3.2 20.4 + - - +
598A TYR* 2.4 30.7 + - + +
600A ILE* 3.7 25.4 - - + +
610A ILE* 5.0 2.7 - - + -
688A ILE 2.8 11.6 - - - +
689A ASP* 4.6 3.3 - - - +
690A PHE* 3.3 30.8 + - - +
691A GLY 4.2 1.2 + - - -
801A 5W6 4.7 10.9 - - - +
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Residues in contact with LEU 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A PRO* 4.2 20.0 - - + -
215A LEU* 4.1 21.5 - - + -
219A TYR* 3.7 20.4 - - - +
569A LEU 2.8 17.0 + - - +
570A ARG* 3.6 5.2 - - - +
572A GLU* 1.3 74.5 - - - +
574A LEU* 1.3 65.1 + - - +
576A PHE* 3.1 36.7 + - + +
577A GLN* 3.2 15.8 + - + +
600A ILE* 4.0 28.2 - - + +
602A VAL* 4.1 11.0 - - + +
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Residues in contact with LEU 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570A ARG 3.2 11.7 + - - +
571A GLN* 3.3 11.2 + - - +
573A LEU* 1.3 78.8 - - - +
575A ALA* 1.3 64.5 + - - +
576A PHE 3.3 0.2 + - - -
577A GLN* 3.4 9.5 + - - +
578A VAL* 3.3 25.8 + - + +
667A LEU* 6.0 1.6 - - + -
693A ILE* 5.0 6.3 - - + -
694A LEU* 4.7 8.1 - - + -
750A ILE* 3.7 25.6 - - + +
751A VAL* 4.0 25.8 - - + -
754A MET* 3.9 22.0 - - + -
760A LEU* 5.6 2.0 - - + -
762A CYS* 4.7 11.9 - - - -
763A PHE* 4.0 28.3 - - + -
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Residues in contact with ALA 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571A GLN 3.1 12.8 + - - +
572A GLU 3.7 8.5 - - - +
574A LEU* 1.3 77.9 - - - +
576A PHE* 1.3 58.6 + - - +
578A VAL* 3.3 4.5 + - - +
579A LEU* 2.9 36.1 + - + +
667A LEU* 4.2 21.7 - - + +
690A PHE* 3.7 36.6 - - + -
693A ILE* 5.1 4.5 - - + +
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Residues in contact with PHE 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A PHE* 4.7 13.9 - + - -
572A GLU 3.2 12.9 + - - +
573A LEU* 3.1 27.5 + - + +
575A ALA* 1.3 76.9 - - - +
577A GLN* 1.3 64.2 + - + +
579A LEU* 3.2 11.0 + - - +
580A LYS* 2.9 64.0 + - + +
597A PRO* 4.0 14.8 - - + -
598A TYR* 3.3 30.5 - - + +
599A LYS* 4.1 17.5 - - + -
600A ILE* 4.2 13.2 - - + -
690A PHE* 5.5 0.4 - - - -
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Residues in contact with GLN 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A PHE* 2.8 54.2 + - + -
175A TYR* 4.4 0.2 - - - +
177A PRO* 3.6 15.1 - - - +
178A GLN* 2.7 40.5 + - - +
573A LEU* 3.2 18.0 + - + +
574A LEU* 3.7 11.2 - - - +
576A PHE* 1.3 87.2 - - + +
578A VAL* 1.3 57.3 + - - +
580A LYS* 3.3 2.1 + - - +
581A GLN* 2.9 30.0 + - - +
750A ILE* 3.6 16.1 - - + +
754A MET* 4.2 6.4 - - - +
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Residues in contact with VAL 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A LEU* 3.3 15.5 + - + +
575A ALA* 3.3 9.8 + - - +
576A PHE 3.2 0.4 - - - -
577A GLN* 1.3 76.7 - - - +
579A LEU* 1.3 57.6 + - + +
581A GLN* 3.4 6.2 + - - +
582A LEU* 2.9 49.1 + - + +
666A LEU* 6.3 1.8 - - + -
667A LEU* 4.4 26.5 - - + -
747A VAL* 4.4 19.1 - - + +
750A ILE* 4.3 12.3 - - + -
751A VAL* 4.1 26.5 - - + -
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Residues in contact with LEU 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A ALA* 2.9 23.0 + - + +
576A PHE* 3.6 8.5 - - - +
578A VAL* 1.3 76.7 - - + +
580A LYS* 1.3 58.6 + - - +
582A LEU* 3.5 2.8 + - + +
583A GLN* 2.9 29.6 + - - +
595A ILE* 3.4 16.5 - - + +
596A LYS 5.2 3.4 - - - +
597A PRO* 4.0 26.2 - - + -
598A TYR* 5.4 2.0 - - + -
660A TYR* 4.9 9.4 - - + -
663A VAL* 3.2 47.6 - - + -
667A LEU* 5.5 1.3 - - + -
690A PHE* 3.4 36.1 - - + -
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Residues in contact with LYS 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A PHE* 4.0 27.7 - - + -
576A PHE* 2.9 48.0 + - + +
577A GLN 3.6 4.5 - - - +
578A VAL 3.2 0.2 - - - -
579A LEU* 1.3 75.7 - - - +
581A GLN* 1.3 59.4 + - - +
583A GLN* 3.3 16.9 + - - +
584A SER* 3.0 33.1 + - - +
597A PRO* 4.1 13.4 - - + +
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Residues in contact with GLN 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A PHE* 4.8 9.8 - - + -
175A TYR* 4.4 11.4 + - - +
577A GLN 2.9 15.0 + - - +
578A VAL* 3.7 5.4 - - - +
580A LYS* 1.3 73.7 - - - +
582A LEU* 1.3 54.9 + - - +
584A SER* 3.0 13.2 + - - -
585A ILE* 2.8 52.4 + - - +
746A LYS* 3.5 44.3 - - + +
747A VAL* 4.7 8.5 - - + -
750A ILE* 3.7 24.9 - - + -
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Residues in contact with LEU 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578A VAL* 2.9 39.9 + - + +
579A LEU* 3.8 6.1 - - + +
581A GLN* 1.3 77.3 - - - +
583A GLN* 1.3 61.4 + - - +
585A ILE* 3.6 20.4 - - + +
586A TRP* 3.0 55.2 + - + -
595A ILE* 4.7 0.7 - - + -
663A VAL* 3.9 26.7 - - + -
666A LEU* 4.1 30.7 - - + -
667A LEU* 6.2 0.2 - - + -
740A ALA* 4.6 9.4 - - + -
747A VAL* 4.0 13.2 - - + -
776A PHE* 5.5 0.4 - - + -
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Residues in contact with GLN 583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579A LEU 2.9 18.9 + - - +
580A LYS* 3.3 17.6 - - - +
581A GLN 3.1 0.4 - - - -
582A LEU* 1.3 77.4 - - - +
584A SER* 1.3 59.0 + - - +
586A TRP* 3.4 7.0 + - - +
587A GLU* 2.8 30.3 + - + +
595A ILE* 3.2 39.4 + - + +
596A LYS* 4.9 0.2 - - - +
597A PRO* 3.7 21.1 - - - +
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Residues in contact with SER 584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580A LYS* 3.0 16.6 + - - +
581A GLN* 3.0 19.6 + - - -
583A GLN* 1.3 75.7 - - - +
585A ILE* 1.3 54.1 + - - +
587A GLU* 3.0 8.8 + - - +
588A GLN* 2.6 38.1 + - - +
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Residues in contact with ILE 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581A GLN* 2.8 37.6 + - - +
582A LEU* 3.6 18.8 - - + +
584A SER* 1.3 71.6 - - - +
586A TRP* 1.3 61.4 + - + +
588A GLN* 3.3 6.1 + - - +
589A GLU* 3.0 30.7 + - - +
739A ALA* 3.5 36.3 - - + +
740A ALA* 4.1 7.2 - - - +
743A HIS* 3.7 37.0 - - + +
746A LYS* 5.5 0.7 - - + -
747A VAL* 3.8 25.1 - - + -
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Residues in contact with TRP 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582A LEU* 3.0 45.3 + - + +
583A GLN* 3.9 5.2 - - - +
585A ILE* 1.3 79.8 - - + +
587A GLU* 1.3 52.7 + - - +
589A GLU* 2.7 24.3 - - - +
590A ARG* 4.2 0.2 - - - -
591A VAL* 3.5 30.9 + - + +
593A LEU* 3.4 36.1 - - + +
595A ILE* 3.7 37.9 - - + -
659A GLY* 3.7 20.4 - - - -
662A LEU* 3.8 16.6 - - + -
663A VAL* 4.2 7.4 - - + -
666A LEU* 5.5 2.0 - - + -
736A GLY* 2.9 31.8 + - - -
739A ALA* 3.8 15.7 - - + -
740A ALA* 4.6 4.6 - - + +
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Residues in contact with GLU 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583A GLN* 2.8 20.3 + - + +
584A SER* 3.0 11.4 + - - +
586A TRP* 1.3 73.3 - - - +
588A GLN* 1.3 57.0 + - - +
589A GLU 2.7 16.8 - - - +
590A ARG* 5.3 1.4 - - - +
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Residues in contact with GLN 588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584A SER 2.6 19.0 + - - +
585A ILE* 3.3 5.8 + - - +
587A GLU* 1.3 71.3 - - - +
589A GLU* 1.3 70.5 + - - +
590A ARG* 4.8 5.7 - - - +
743A HIS* 3.0 37.6 + - - +
746A LYS* 6.2 0.3 - - - -
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Residues in contact with GLU 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A ILE 3.0 14.6 + - - +
586A TRP 2.7 19.9 - - - +
587A GLU 2.7 14.0 - - - +
588A GLN* 1.3 83.8 + - - +
590A ARG* 1.3 61.3 + - - +
591A VAL* 4.2 7.0 - - + -
739A ALA* 3.9 27.8 - - + -
742A LYS* 3.6 29.1 + - - +
743A HIS* 3.6 23.9 + - + -
41B LYS* 4.3 16.5 - - - +
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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) + - + + + + + -
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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