Contacts of the helix formed by residues 564 - 576 (chain V) in PDB entry 5IY6
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 ASN 564 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528V LYS* 5.5 6.9 - - - +
531V ILE* 5.1 13.8 - - + +
532V LEU* 5.2 9.3 - - - +
562V ALA 3.0 3.4 + - - +
563V ASP* 1.3 81.8 - - + +
565V VAL* 1.4 55.1 + - - +
566V PHE* 3.3 18.7 + - - +
567V ALA* 2.9 20.3 + - + +
568V LEU* 2.8 33.9 + - - +
608V SER* 5.7 1.3 - - - -
37Y G 4.9 11.3 + - - -
38Y T 5.4 1.8 - - - -
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Residues in contact with VAL 565 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564V ASN* 1.4 69.8 + - - +
566V PHE* 1.3 63.3 + - - +
568V LEU* 3.5 9.7 - - + +
569V LYS* 3.0 40.5 + - + +
581V TYR* 3.4 41.5 - - + -
608V SER* 5.0 11.0 - - - +
38Y T 5.5 9.9 - - - +
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Residues in contact with PHE 566 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529V LYS* 6.1 2.2 - - - -
532V LEU* 3.7 37.9 - - + -
536V MET* 6.1 0.4 - - + -
564V ASN* 3.4 14.0 + - - +
565V VAL* 1.3 78.5 - - - +
567V ALA* 1.4 61.5 + - - +
569V LYS* 3.5 4.0 + - - +
570V GLU* 3.0 52.8 + - + +
715V LYS* 4.8 23.1 - - + -
716V VAL* 5.2 7.4 - - + -
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Residues in contact with ALA 567 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532V LEU* 4.5 12.1 - - + -
535V THR* 4.2 13.7 - - + -
536V MET* 4.4 11.0 - - - -
562V ALA* 4.8 1.6 - - + -
563V ASP 5.7 0.2 - - - +
564V ASN* 2.9 22.2 + - + +
566V PHE* 1.4 79.7 - - - +
568V LEU* 1.4 54.9 - - - +
570V GLU* 3.7 0.5 - - - +
571V TYR* 3.0 40.3 + - - -
626V ILE* 3.9 20.9 - - + -
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Residues in contact with LEU 568 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562V ALA* 3.7 18.3 - - + +
564V ASN 2.8 17.2 + - - +
565V VAL* 3.5 16.6 - - - +
567V ALA* 1.4 74.6 - - - +
569V LYS* 1.3 62.0 + - + +
571V TYR* 4.0 2.1 - - - +
572V ALA* 2.9 32.6 + - - +
579V TYR* 4.1 26.9 - - + -
580V ILE 4.1 2.5 - - - +
581V TYR* 4.2 19.1 - - + -
606V PHE* 3.9 8.9 - - + +
607V ILE* 3.4 21.8 - - - +
608V SER* 3.4 33.2 - - - +
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Residues in contact with LYS 569 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565V VAL* 3.0 33.2 + - + +
566V PHE* 4.1 3.8 - - - +
568V LEU* 1.3 82.3 - - + +
570V GLU* 1.4 63.4 + - - +
572V ALA* 4.4 2.7 - - - +
573V ILE* 3.0 51.9 + - + +
579V TYR* 4.3 22.0 + - + +
581V TYR* 3.2 38.1 + - - -
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Residues in contact with GLU 570 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536V MET* 3.4 25.4 - - + -
566V PHE* 3.0 44.9 + - + +
567V ALA 3.7 1.3 - - - +
569V LYS* 1.4 79.2 - - + +
571V TYR* 1.3 60.2 + - - +
573V ILE* 5.3 4.3 - - - +
574V ARG* 2.7 65.2 + - - +
712V LEU* 4.6 4.9 - - + +
715V LYS* 3.2 28.7 + - - +
716V VAL* 6.5 0.4 - - + -
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Residues in contact with TYR 571 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535V THR 2.9 27.9 + - - -
536V MET* 3.7 19.3 - - - -
540V LYS* 4.4 5.9 + - - +
541V PHE* 3.5 49.2 + + - +
544V CYS* 3.8 30.5 - - + +
567V ALA 3.0 24.2 + - - +
568V LEU 4.0 1.1 - - - +
570V GLU* 1.3 72.3 - - - +
572V ALA* 1.4 60.7 + - - +
574V ARG* 3.4 2.4 + - - +
575V LEU* 2.9 38.4 + - + +
606V PHE* 3.5 27.8 - + + -
626V ILE* 3.6 31.8 - - + +
662V LEU* 5.3 0.3 - - - +
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Residues in contact with ALA 572 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568V LEU 2.9 23.2 + - - +
569V LYS 3.5 0.6 + - - +
571V TYR* 1.4 76.1 - - - +
573V ILE* 1.3 51.0 + - - +
575V LEU 3.2 1.2 + - - -
576V ASN* 2.7 34.7 + - - -
577V LYS 3.4 13.7 + - - +
579V TYR* 3.5 27.1 - - + -
606V PHE* 3.8 28.9 - - + -
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Residues in contact with ILE 573 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569V LYS* 3.0 36.6 + - + +
570V GLU* 4.8 4.7 - - - +
572V ALA* 1.3 72.0 - - - +
574V ARG* 1.4 69.1 + - + +
576V ASN* 3.4 15.2 + - - +
579V TYR* 4.1 23.8 - - + +
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Residues in contact with ARG 574 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536V MET* 4.5 2.5 - - - +
541V PHE* 3.8 26.9 - - + -
570V GLU* 2.7 75.0 + - - +
571V TYR 3.4 4.2 + - - +
572V ALA 3.4 0.4 - - - -
573V ILE* 1.4 84.2 - - + +
575V LEU* 1.3 62.1 + - + +
576V ASN* 3.5 2.6 + - - +
703V PHE* 4.9 15.5 - - - -
712V LEU* 4.0 21.5 - - - +
715V LYS* 4.3 12.9 - - - +
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Residues in contact with LEU 575 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541V PHE* 3.9 31.2 - - + -
544V CYS 5.1 0.2 - - - -
545V GLN* 3.9 35.9 - - + +
548V ILE* 3.6 30.3 - - + -
571V TYR* 2.9 27.2 + - + +
572V ALA 4.2 1.6 - - - +
574V ARG* 1.3 77.8 - - + +
576V ASN* 1.4 67.0 + - - +
577V LYS* 3.2 36.6 + - + +
606V PHE* 4.2 11.0 - - + -
702V ALA* 5.9 0.2 - - + -
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Residues in contact with ASN 576 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572V ALA 2.7 11.1 + - - -
573V ILE* 3.8 11.5 - - - +
574V ARG 3.3 4.2 - - - +
575V LEU* 1.4 78.0 - - - +
577V LYS* 1.3 59.4 + - - +
578V PRO* 4.4 2.8 - - - +
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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