Contacts of the strand formed by residues 590 - 593 (chain B) in PDB entry 6RY4
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 THR 590 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559B HIS* 3.9 18.8 - - + -
574B PHE* 3.8 19.7 + - + +
575B ASN 4.0 4.2 + - - -
576B ARG* 3.6 25.5 + - - +
579B ALA* 4.5 7.8 - - + +
589B GLY* 1.3 71.1 - - - -
591B TYR* 1.3 61.0 - - - +
592B PHE* 3.4 36.0 - - + -
660B PHE 3.7 0.2 - - - +
661B VAL* 3.3 3.1 - - - -
662B VAL* 3.0 39.1 + - - +
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Residues in contact with TYR 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B HIS* 2.8 33.7 + - + -
579B ALA* 5.8 0.7 - - + -
580B GLY 5.1 6.7 - - - -
582B ASN* 3.6 46.0 - - + +
584B VAL 3.9 5.4 - - - -
585B SER* 3.2 5.9 + - - -
586B TYR 2.8 22.0 + - - -
587B GLY 2.5 30.2 + - - -
589B GLY 3.3 17.9 - - - -
590B THR* 1.3 74.3 - - - +
592B PHE* 1.3 59.8 + - - +
598B TYR* 5.9 0.4 - + - -
659B LEU* 4.0 20.4 - - + -
660B PHE 3.4 3.8 - - - -
661B VAL* 3.5 24.7 - - + -
801B DMS 3.9 23.5 - - + -
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Residues in contact with PHE 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B LEU* 3.6 25.7 - - + +
558B PHE 3.3 4.9 - - - -
559B HIS* 3.8 20.9 - - + -
574B PHE* 3.9 12.1 - + + -
590B THR* 3.4 37.0 - - + -
591B TYR* 1.3 76.5 - - - +
593B ALA* 1.3 59.0 + - - +
618B VAL* 3.7 27.1 - - + -
620B VAL* 3.8 22.4 - - + -
659B LEU* 3.1 7.8 - - - +
660B PHE* 2.9 36.3 + - - +
662B VAL* 3.7 20.2 - - + -
668B ALA* 3.7 21.3 - - + -
801B DMS 4.9 2.7 - - - -
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Residues in contact with ALA 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B LEU* 3.4 7.5 - - - +
558B PHE* 2.8 31.1 + - + +
592B PHE* 1.3 72.5 - - - +
594B VAL* 1.3 63.3 + - - +
595B ASP 3.5 16.6 - - - +
598B TYR* 3.5 28.5 - - + -
599B SER* 3.3 23.1 - - - +
658B LYS 3.6 6.3 - - - +
659B LEU* 4.5 0.4 - - - +
801B DMS 4.8 1.7 - - - +
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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
------------------------------------------------------------
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