Contacts of the strand formed by residues 849 - 851 (chain B) in PDB entry 1ZY5
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 VAL 849 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653B GLN 3.8 0.3 - - - +
654B TYR* 3.2 36.6 - - + +
796B LEU* 5.6 1.3 - - + -
815B LEU* 3.8 25.1 - - + +
818B GLN* 2.9 34.3 + - + +
819B ILE* 4.3 17.0 - - + +
841B ILE* 3.9 16.2 - - + -
842B PHE 3.2 9.4 - - - +
843B ILE* 3.7 17.7 - - + -
848B ASN* 1.3 74.2 - - - +
850B LYS* 1.3 65.9 + - - +
851B ILE* 4.7 3.8 - - + +
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Residues in contact with LYS 850 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B HIS 4.7 2.2 + - - -
653B GLN* 2.7 34.0 + - - +
654B TYR 3.4 7.4 - - - -
655B VAL 4.7 5.2 + - - +
656B VAL* 3.9 13.5 - - + +
789B GLU* 3.7 31.9 + - - +
791B CYS* 4.6 10.1 - - - -
841B ILE* 4.6 0.7 - - - -
842B PHE* 2.9 44.0 + - + +
844B ASP* 4.6 23.9 + - + +
848B ASN 4.7 4.3 - - - +
849B VAL* 1.3 79.1 - - - +
851B ILE* 1.3 66.4 + - - +
852B GLY 3.3 1.2 + - - -
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Residues in contact with ILE 851 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654B TYR 2.9 15.1 + - - +
655B VAL* 3.6 7.7 - - - +
656B VAL* 2.9 21.8 + - - +
819B ILE* 4.0 24.2 - - + +
822B ALA* 3.4 27.1 - - + -
823B LEU* 4.2 15.5 - - + +
826B ILE* 4.4 7.9 - - + -
833B HIS* 3.3 32.1 - - + +
836B LEU* 4.2 15.0 - - + -
840B ASN 3.9 4.7 - - - +
841B ILE* 4.5 13.9 - - + +
849B VAL* 4.9 4.5 - - + -
850B LYS* 1.3 69.4 - - - +
852B GLY* 1.3 58.6 + - - +
854B PHE* 4.0 10.5 - - + -
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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