Contacts of the strand formed by residues 586 - 592 (chain A) in PDB entry 5JBJ
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 TYR 586 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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582A PHE* 3.5 48.0 - + + -
583A ARG* 3.1 47.3 - - + +
584A PHE 4.2 1.6 - - - +
585A TYR* 1.3 78.1 - - - +
587A THR* 1.3 64.2 + - - +
588A VAL* 4.9 9.9 - - + -
608A ILE* 3.7 34.3 - - + -
609A VAL 3.3 10.3 - - - +
611A SER* 4.0 0.2 - - - -
617A TRP* 3.8 17.7 - - + -
620A GLU* 5.5 3.8 - - + -
627A THR* 5.7 4.7 - - - +
628A LEU 5.4 0.3 - - - -
629A PRO* 3.7 27.8 - - + +
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Residues in contact with THR 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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586A TYR* 1.3 73.9 - - - +
588A VAL* 1.3 73.6 + - - +
589A SER* 3.4 1.9 + - - -
608A ILE* 3.4 3.0 - - - -
609A VAL* 2.9 43.6 + - + +
610A CYS 5.1 0.2 - - - -
611A SER* 3.1 27.8 + - - -
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Residues in contact with VAL 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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586A TYR* 4.9 9.6 - - + +
587A THR* 1.3 80.2 - - - +
589A SER* 1.3 64.9 + - - +
590A SER 4.0 4.7 - - - +
606A CYS* 3.4 38.6 - - + -
607A ARG 3.6 4.9 - - - +
608A ILE* 4.6 6.5 - - + -
620A GLU* 3.2 19.1 - - - +
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Residues in contact with SER 589 (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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587A THR* 3.4 4.1 + - - -
588A VAL* 1.3 75.9 - - - +
590A SER* 1.3 70.9 + - - +
607A ARG* 3.4 30.3 + - - +
609A VAL* 3.9 31.3 - - - +
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Residues in contact with SER 590 (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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588A VAL* 4.0 3.8 - - - +
589A SER* 1.3 86.5 + - - +
591A GLY* 1.3 70.1 + - - +
593A ILE* 4.4 1.9 - - - +
606A CYS* 3.3 18.4 - - - +
607A ARG* 3.2 30.2 + - - +
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Residues in contact with GLY 591 (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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590A SER* 1.3 88.7 + - - +
592A LYS* 1.3 66.1 + - - +
593A ILE* 3.7 8.9 - - - +
606A CYS* 3.4 11.9 - - - -
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Residues in contact with LYS 592 (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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591A GLY* 1.3 73.8 - - - +
593A ILE* 1.3 67.8 + - - +
594A HIS* 3.9 2.1 + - - +
603A GLU* 3.7 21.5 + - - +
604A PRO* 2.7 49.1 + - - +
605A GLY* 3.8 9.2 - - - -
606A CYS* 3.4 14.4 - - - +
622A ILE* 3.5 29.2 - - + -
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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