Contacts of the strand formed by residues 565 - 569 (chain B) in PDB entry 5IY8
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 565 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563B ASP 3.6 1.7 + - - -
564B ALA* 1.3 71.7 - - - +
566B LYS* 1.3 75.7 + - - +
567B ILE* 5.0 0.8 - - + +
576B ILE* 3.3 5.2 - - - -
577B HIS* 2.8 41.8 + - + +
580B PRO* 3.5 26.4 - - + +
605B ARG* 5.1 1.1 + - - +
610B ARG* 3.3 30.3 + - - +
611B GLU 3.7 3.1 - - - -
612B ILE* 3.6 32.5 - - + +
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Residues in contact with LYS 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B TYR* 3.2 43.2 + - - +
367B TYR* 4.7 24.0 - - + -
370B HIS* 5.2 10.7 + - - -
564B ALA 4.7 1.1 - - - +
565B THR* 1.3 78.2 - - - +
567B ILE* 1.3 59.7 + - - +
568B PHE* 4.0 15.5 - - + -
573B TRP* 3.1 36.8 - - + +
575B GLY 3.7 4.7 - - - -
576B ILE* 4.6 2.7 - - + +
609B GLU 5.8 2.2 + - - -
610B ARG* 3.5 8.3 + - - +
611B GLU* 3.6 10.6 - - + +
612B ILE 2.8 26.0 + - - +
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Residues in contact with ILE 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B LEU* 3.5 39.3 - - + -
550B MET* 3.9 13.5 - - + -
565B THR* 5.0 1.6 - - + +
566B LYS* 1.3 74.3 - - - +
568B PHE* 1.3 68.6 + - - +
573B TRP* 3.9 4.7 - - - -
574B VAL* 3.2 25.5 + - + -
575B GLY* 3.0 34.5 + - - +
576B ILE* 3.9 7.0 - - - +
577B HIS* 5.0 4.5 - - + +
583B LEU* 4.9 11.9 - - + -
587B LEU* 5.5 0.7 - - + -
612B ILE* 3.2 22.7 - - + +
614B ILE* 4.1 10.8 - - + -
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Residues in contact with PHE 568 (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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364B PHE* 4.2 9.9 - + - -
367B TYR* 3.9 33.0 - + - -
566B LYS* 4.0 9.6 - - + -
567B ILE* 1.3 77.8 - - - +
569B VAL* 1.3 65.0 + - - +
571B GLY* 4.0 16.2 - - - -
572B CYS 3.1 7.2 - - - +
573B TRP* 3.4 48.7 - + + -
611B GLU* 2.9 35.4 - - + -
612B ILE 3.0 15.8 + - - +
613B ARG* 4.2 20.0 - - + -
614B ILE* 2.9 32.0 + - - +
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Residues in contact with VAL 569 (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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538B PRO* 3.7 31.2 - - + +
541B ILE* 5.3 4.7 - - + -
542B LEU* 3.6 28.7 - - + -
545B LEU* 4.0 14.6 - - + -
567B ILE* 4.8 0.4 - - + -
568B PHE* 1.3 79.0 - - - +
570B ASN* 1.3 68.9 + - - +
571B GLY 3.2 0.2 - - - -
572B CYS* 2.6 38.5 + - - +
574B VAL* 3.9 17.7 - - + -
614B ILE* 3.6 18.8 - - + +
616B THR* 5.0 1.6 - - + -
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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