Contacts of the helix formed by residues 563 - 573 (chain N) in PDB entry 5GJQ
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 ALA 563 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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529N ILE* 6.3 0.4 - - - -
556N MET* 3.4 40.4 - - + -
559N ARG* 4.4 6.9 - - + +
560N MET 3.3 5.6 + - - +
562N GLU* 1.3 76.7 - - - +
564N ASP* 1.3 53.2 + - - +
565N ALA* 3.0 1.1 - - - -
566N LEU* 2.8 11.8 + - + +
567N ILE* 2.4 49.3 + - + +
585N THR* 3.8 6.5 - - + -
589N ALA* 5.3 2.0 - - + -
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Residues in contact with ASP 564 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560N MET 2.8 19.9 - - - +
561N GLU* 2.8 35.0 - - - +
562N GLU 2.8 2.0 + - - +
563N ALA* 1.3 75.3 - - - +
565N ALA* 1.3 52.4 + - - +
567N ILE* 3.1 20.1 - - + +
568N GLU* 2.3 40.6 + - - +
590N TYR* 3.7 10.4 + - - -
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Residues in contact with ALA 565 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562N GLU 3.6 9.0 + - - +
563N ALA 2.9 0.4 + - - +
564N ASP* 1.3 75.5 - - - +
566N LEU* 1.3 52.6 + - - +
568N GLU* 2.8 9.0 + - - +
569N SER* 2.4 41.0 + - - +
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Residues in contact with LEU 566 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529N ILE* 3.5 40.6 - - + -
533N VAL* 3.9 27.8 - - + -
552N ILE* 3.7 30.7 - - + +
556N MET* 4.6 8.5 - - + -
563N ALA* 2.8 13.4 + - + +
565N ALA* 1.3 76.3 - - - +
567N ILE* 1.3 53.9 + - - +
569N SER* 3.1 13.3 + - - -
570N LEU* 2.3 54.7 + - + +
578N LEU* 6.3 0.9 - - + -
585N THR* 5.2 4.3 - - + -
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Residues in contact with ILE 567 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560N MET 4.2 3.6 - - - +
563N ALA* 2.4 29.0 + - + +
564N ASP* 3.1 40.4 - - - +
566N LEU* 1.3 71.7 - - - +
568N GLU* 1.3 53.9 + - - +
570N LEU* 2.9 6.8 + - - +
571N CYS* 2.4 46.5 + - - -
582N GLY* 5.0 2.5 - - - +
585N THR* 3.8 20.4 - - + -
586N VAL* 3.6 40.6 - - + -
589N ALA* 4.9 1.6 - - + -
590N TYR* 4.8 4.3 - - + -
601N ARG* 3.6 20.0 - - - +
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Residues in contact with GLU 568 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564N ASP 2.3 33.0 + - - +
565N ALA* 3.2 6.1 - - - +
567N ILE* 1.3 68.1 - - - +
569N SER* 1.3 51.7 + - - +
571N CYS* 3.3 9.3 - - + +
572N ARG* 2.5 44.4 + - + +
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Residues in contact with SER 569 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533N VAL* 5.5 5.6 - - - -
565N ALA* 2.4 31.9 + - - +
566N LEU* 3.1 23.0 - - - +
568N GLU* 1.3 67.9 - - - +
570N LEU* 1.3 58.7 + - - +
572N ARG* 2.9 9.1 + - - +
573N ASP* 2.8 27.4 + - - +
578N LEU* 5.0 3.6 - - - +
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Residues in contact with LEU 570 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549N ALA* 5.1 5.2 - - + -
552N ILE* 5.5 1.6 - - + -
566N LEU* 2.3 54.3 + - + +
567N ILE* 3.3 3.8 - - - +
569N SER* 1.3 66.1 - - - -
571N CYS* 1.3 62.7 + - - +
573N ASP* 3.0 6.9 + - - +
578N LEU* 3.0 47.3 - - + +
579N ARG* 2.9 26.0 + - - +
582N GLY* 4.0 15.3 - - - +
585N THR* 5.2 4.0 - - - +
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Residues in contact with CYS 571 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567N ILE* 2.4 59.1 + - - +
568N GLU* 3.3 9.6 - - + +
570N LEU* 1.3 69.3 - - - +
572N ARG* 1.3 58.7 + - - +
573N ASP 3.0 4.9 + - - -
579N ARG* 3.2 27.6 + - - +
582N GLY* 5.5 4.9 - - - -
601N ARG* 3.8 28.5 - - - -
605N VAL* 4.9 10.5 - - + -
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Residues in contact with ARG 572 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568N GLU* 2.5 27.2 + - + +
569N SER* 3.4 6.7 - - - +
571N CYS* 1.3 71.2 - - - +
573N ASP* 1.3 64.7 + - - +
574N LYS 3.3 2.4 + - - -
579N ARG* 4.6 3.6 + - - +
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Residues in contact with ASP 573 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537N GLN* 5.9 1.8 - - - +
569N SER 2.8 7.4 + - - +
570N LEU 3.1 15.5 - - - +
571N CYS 3.0 1.4 + - - -
572N ARG* 1.3 76.3 - - - +
574N LYS* 1.3 61.4 + - - +
575N ASP* 2.7 55.2 - - - +
578N LEU* 3.3 33.2 - - + -
579N ARG* 2.3 38.5 + - - -
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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
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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