Contacts of the strand formed by residues 523 - 530 (chain B) in PDB entry 2PY5
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 ASP 523 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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505B TYR 3.9 0.2 - - - -
506B MET* 2.9 29.0 + - + +
508B GLU* 4.6 2.6 - - - +
513B LEU* 3.5 36.1 - - + +
521B TYR* 3.5 10.1 - - - -
522B THR* 1.3 102.1 + - - +
524B ILE* 1.3 66.3 + - - +
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Residues in contact with ILE 524 (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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490B LYS* 3.6 45.3 - - + +
503B ASP* 3.6 35.7 - - + +
504B ILE 3.4 11.7 - - - +
505B TYR* 4.0 19.3 - - + -
506B MET* 4.5 1.3 - - - -
513B LEU* 5.8 1.8 - - - +
521B TYR* 4.2 7.2 - - + -
523B ASP* 1.3 80.1 - - - +
525B LYS* 1.3 63.9 + - - +
526B PHE* 4.0 2.8 + - + +
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Residues in contact with LYS 525 (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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502B GLN 3.4 4.0 - - - +
503B ASP* 3.6 0.2 - - - -
504B ILE* 2.8 63.2 + - - +
506B MET* 3.5 40.6 - - + +
513B LEU* 5.9 2.0 - - + -
515B GLU* 4.2 15.1 + - - -
524B ILE* 1.3 72.6 - - - +
526B PHE* 1.3 69.5 + - - +
527B SER* 3.5 7.4 + - - +
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Residues in contact with PHE 526 (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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501B ILE* 3.9 19.5 - - + -
502B GLN 3.5 3.8 - - - -
503B ASP* 3.4 21.8 - - - +
524B ILE* 4.0 4.7 + - + -
525B LYS* 1.3 74.6 - - - +
527B SER* 1.3 60.2 + - - +
528B VAL* 3.4 29.3 + - + +
538B LYS 5.4 0.7 - - - -
541B VAL* 3.4 19.3 - - + -
542B THR* 3.9 22.2 - - - -
543B PHE* 3.5 27.1 - + - -
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Residues in contact with SER 527 (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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500B TYR* 5.6 1.5 - - - -
501B ILE* 3.3 6.9 - - - +
502B GLN* 2.9 34.6 + - - +
504B ILE* 3.8 29.3 - - - +
525B LYS* 3.5 11.0 + - - -
526B PHE* 1.3 74.5 - - - +
528B VAL* 1.3 62.7 + - - +
529B LYS* 3.6 25.5 - - - +
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Residues in contact with VAL 528 (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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500B TYR 3.9 2.5 - - - +
501B ILE* 4.0 12.6 - - + -
526B PHE* 3.4 39.0 + - + +
527B SER* 1.3 74.0 + - - +
529B LYS* 1.3 75.3 + - - +
533B MET* 3.9 29.4 - - + -
538B LYS* 3.6 32.4 + - + +
541B VAL* 4.1 14.4 - - + -
546B PHE* 4.7 3.4 - - + -
9009B EDO 3.2 20.8 + - - +
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Residues in contact with LYS 529 (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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498B LYS 3.7 4.0 - - - +
499B THR* 3.2 2.4 - - - -
500B TYR* 2.7 86.4 + - + +
527B SER* 3.6 22.0 - - - +
528B VAL* 1.3 79.5 - - - +
530B CYS* 1.3 61.2 + - - +
546B PHE* 4.8 0.3 - - - -
9009B EDO 3.6 14.8 - - - +
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Residues in contact with CYS 530 (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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498B LYS 3.2 4.9 + - - -
499B THR* 3.8 26.2 - - + +
528B VAL* 4.7 2.9 - - + -
529B LYS* 1.3 74.6 - - - +
531B ALA* 1.3 71.0 + - - +
532B GLY 3.2 0.7 + - - -
533B MET* 3.0 45.5 + - + +
546B PHE* 5.0 1.8 - - + -
572B PHE* 3.6 29.8 - - - -
574B ILE* 4.3 7.2 - - - -
9009B EDO 3.0 18.7 + - - -
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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