Contacts of the strand formed by residues 558 - 561 (chain V) 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 ILE 558 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548V ILE* 4.1 7.6 - - + +
551V HIS* 3.6 25.6 - - + -
552V GLU* 3.6 17.0 - - + +
556V ASP 3.4 17.7 - - - +
557V LYS* 1.3 79.1 - - - +
559V ILE* 1.3 65.4 + - - +
560V VAL* 4.1 13.2 - - + -
596V PHE* 3.3 8.2 - - - -
603V ASN 2.8 8.8 + - - +
604V THR* 3.3 25.8 - - + +
605V ILE 3.1 24.4 + - - -
622V VAL* 3.4 21.1 - - + +
624V ILE* 3.8 29.2 - - + -
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Residues in contact with ILE 559 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558V ILE* 1.3 78.2 - - - +
560V VAL* 1.3 69.2 + - - +
561V PHE* 5.5 1.3 - - + -
596V PHE* 3.7 16.6 - - + -
605V ILE* 3.4 7.4 - - + +
607V ILE* 3.8 29.4 - - + -
617V LEU* 4.9 2.9 - - + -
618V PRO* 3.8 38.4 - - + +
620V ALA* 3.9 6.5 - - + -
622V VAL 3.1 6.9 + - - +
623V LEU* 3.3 20.6 - - + +
624V ILE 3.1 21.3 + - - -
643V VAL* 3.7 29.6 - - + -
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Residues in contact with VAL 560 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544V CYS* 4.6 2.5 - - - -
548V ILE* 4.4 5.2 - - + -
558V ILE* 4.1 10.1 - - + -
559V ILE* 1.3 79.7 - - - +
561V PHE* 1.3 60.4 + - - +
604V THR* 3.9 26.5 - - + -
605V ILE 2.9 11.4 + - - +
606V PHE* 3.4 38.9 - - + +
607V ILE* 2.9 27.2 + - - -
624V ILE* 3.3 29.4 - - + +
626V ILE* 3.9 17.3 - - + -
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Residues in contact with PHE 561 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559V ILE* 4.1 2.4 + - + -
560V VAL* 1.3 74.3 - - - +
562V ALA* 1.4 58.7 + - - +
563V ASP* 3.5 42.8 - - + -
607V ILE* 3.4 15.9 - - + +
608V SER 3.8 22.9 - - - -
609V LYS* 4.1 10.5 - - + -
612V ASP* 5.8 0.2 - - - -
623V LEU* 4.6 7.2 - - + -
624V ILE 2.8 12.9 + - - +
625V GLN* 4.2 21.8 - - + -
626V ILE* 3.5 26.2 + - - +
627V SER* 5.6 2.7 - - - -
629V HIS* 4.3 11.0 - + - -
639V ARG* 3.5 48.7 - - - +
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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