Contacts of the strand formed by residues 587 - 591 (chain A) in PDB entry 5FZ9
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 HIS 587 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ILE* 4.3 15.0 - - + -
496A PHE* 4.5 4.7 - + - -
497A CYS 3.5 2.9 - - - +
498A TRP* 3.4 6.1 - - - -
499A HIS* 3.1 50.5 + + - +
500A ILE* 4.7 1.3 - - - -
501A GLU* 2.8 23.1 - - + -
507A SER* 4.6 0.2 + - - -
519A TRP* 3.7 24.7 - + + -
520A TYR 3.1 13.9 - - - +
581A THR* 3.8 23.1 - - + +
585A ALA 3.1 20.9 + - - -
586A TYR* 1.3 74.8 - - - +
588A SER* 1.3 63.2 + - - +
1759A MN 2.2 27.7 + - - -
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Residues in contact with SER 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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411A TRP* 5.6 2.8 - - - -
496A PHE* 3.3 32.7 - - - -
497A CYS* 3.8 0.7 - - - -
498A TRP* 3.2 47.5 + - - -
519A TRP* 3.6 1.7 - - - +
520A TYR* 2.8 36.9 + - - +
555A ILE* 6.4 0.2 - - - -
556A MET 5.1 0.3 + - - -
587A HIS* 1.3 75.6 - - - +
589A GLY* 1.3 59.9 + - - +
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Residues in contact with GLY 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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410A PHE* 5.2 1.4 - - - -
411A TRP* 6.4 0.2 - - - -
495A SER* 3.2 8.3 - - - -
496A PHE* 3.0 37.9 + - - +
518A THR 3.1 13.2 - - - -
520A TYR* 4.3 11.2 - - - -
588A SER* 1.3 79.5 + - - +
590A PHE* 1.3 64.2 + - - -
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Residues in contact with PHE 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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406A VAL* 4.0 15.7 - - + -
407A GLU* 3.7 25.1 - - + -
410A PHE* 3.8 42.8 - + + -
411A TRP* 4.3 1.3 - + - -
493A PHE* 4.2 4.5 - - - +
494A SER 3.2 13.9 - - - +
495A SER* 3.8 10.3 - - - +
496A PHE* 3.6 3.0 - - - -
517A LYS* 3.8 2.6 - - - -
518A THR* 2.9 51.6 + - + +
520A TYR* 3.6 26.5 - + - -
589A GLY* 1.3 76.8 - - - +
591A ASN* 1.3 74.6 + - - +
592A GLN* 3.9 18.6 - - - -
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Residues in contact with ASN 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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406A VAL* 4.9 0.2 - - - +
490A GLY* 3.7 5.6 - - - -
491A MET 3.4 15.3 - - - +
492A CYS* 4.7 0.2 - - - -
493A PHE 2.9 29.0 + - - -
494A SER* 2.9 32.7 + - - +
495A SER* 5.4 0.2 - - - +
496A PHE* 5.4 0.8 - - - -
516A PRO 4.0 2.5 - - - -
517A LYS* 2.8 31.5 + - - +
590A PHE* 1.3 82.4 - - - +
592A GLN* 1.3 59.9 + - - +
593A GLY 3.3 5.8 - - - +
595A ASN* 2.9 25.7 + - - +
1768A NUK 3.1 23.8 + - - -
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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