Contacts of the strand formed by residues 696 - 700 (chain A) in PDB entry 1B0K
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 LYS 696 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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554A ASP* 3.8 35.9 - - + +
555A LEU 3.4 12.3 - - - +
556A GLN* 3.0 37.8 + - - +
608A ALA* 5.6 0.2 - - - +
694A VAL* 3.5 22.2 + - - +
695A ASP* 1.3 82.7 + - - +
697A LEU* 1.4 64.9 + - - +
714A ILE 3.8 0.2 - - - +
716A LYS* 2.9 45.4 + - + +
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Residues in contact with LEU 697 (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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552A LEU 3.4 3.1 - - - +
554A ASP 4.3 0.4 - - - -
555A LEU* 3.0 45.5 + - + +
557A ILE* 4.0 21.5 - - + -
631A VAL* 4.1 12.8 - - + -
633A ILE* 3.9 28.5 - - + -
660A ILE* 4.3 10.8 - - + -
691A ILE* 4.4 11.9 - - + -
695A ASP* 4.9 1.6 - - + -
696A LYS* 1.4 82.3 - - - +
698A THR* 1.3 61.1 + - - +
699A ILE* 5.3 2.2 - - + -
713A CYS* 3.9 22.4 - - - -
714A ILE 3.4 1.8 - - - -
715A ILE* 3.9 25.6 - - + -
716A LYS* 5.8 0.4 - - - -
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Residues in contact with THR 698 (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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551A ASP* 5.0 0.7 - - + -
552A LEU 3.4 2.7 - - - -
553A GLU* 3.3 38.3 - - + +
554A ASP 3.3 5.9 + - - -
697A LEU* 1.3 71.0 - - - +
699A ILE* 1.3 74.4 + - - +
700A GLN* 3.6 21.9 + - + +
712A LYS 3.5 1.0 - - - +
713A CYS* 3.3 6.1 - - - -
714A ILE* 2.9 46.9 + - - +
716A LYS* 3.6 17.3 + - - +
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Residues in contact with ILE 699 (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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551A ASP* 3.4 5.9 - - - +
552A LEU* 3.2 51.1 + - + -
555A LEU* 4.0 13.9 - - + -
658A ALA* 5.1 4.0 - - + -
660A ILE* 4.0 17.7 - - + -
678A LEU* 4.9 2.7 - - + -
680A LEU* 4.3 12.6 - - + -
697A LEU* 5.3 1.8 - - + -
698A THR* 1.3 77.1 - - - +
700A GLN* 1.3 61.1 + - - +
702A LEU* 4.3 12.2 - - + +
711A LEU* 4.1 33.0 - - + -
712A LYS 3.6 3.8 - - - +
713A CYS* 4.4 8.5 - - - -
727A LEU* 3.9 24.0 - - + -
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Residues in contact with GLN 700 (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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551A ASP* 3.8 13.9 + - - +
698A THR* 4.1 18.0 - - + +
699A ILE* 1.3 78.3 - - - +
701A GLY* 1.3 65.4 + - - +
702A LEU 3.6 0.9 - - - -
711A LEU* 3.8 8.7 - - - +
712A LYS* 3.1 67.8 + - + +
714A ILE* 3.2 17.5 - - + +
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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
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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