Contacts of the strand formed by residues 954 - 957 (chain B) in PDB entry 5B2R
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 954 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757B GLU 3.1 9.6 + - - +
758B ASN* 3.2 26.4 - - - +
759B ILE 2.9 24.5 + - - +
951B ARG* 4.5 20.4 + - + +
952B GLU 5.4 1.3 + - - +
953B VAL* 1.3 72.4 - - - +
955B VAL* 1.3 60.6 + - - +
956B ILE* 3.7 2.4 + - + +
998B ILE* 3.9 13.7 - - + -
1005B GLU* 3.2 35.1 + - - +
1009B VAL* 3.9 23.1 - - + -
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Residues in contact with VAL 955 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759B ILE* 3.4 13.0 - - + +
761B ILE* 4.7 14.6 - - + -
932B ALA* 3.8 31.0 - - + +
935B LEU* 4.2 13.7 - - + -
936B ASP* 3.7 37.5 + - + +
953B VAL* 3.7 16.0 + - + +
954B LYS* 1.3 72.3 - - - +
956B ILE* 1.3 60.6 + - - +
957B THR* 4.1 1.4 + - - -
1008B PHE 3.6 0.7 - - - +
1009B VAL* 3.3 5.4 - - - +
1010B TYR* 2.8 40.3 + - + +
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Residues in contact with ILE 956 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758B ASN* 3.9 20.6 - - + +
759B ILE 2.7 12.9 + - - +
760B VAL* 3.2 16.5 - - + +
761B ILE* 2.7 34.6 + - - +
954B LYS 4.1 7.4 - - - +
955B VAL* 1.3 75.7 - - - +
957B THR* 1.3 58.5 + - - +
958B LEU* 4.0 22.9 - - + -
994B GLY* 3.9 19.7 - - - +
998B ILE* 3.6 31.6 - - + -
1008B PHE* 3.3 17.9 - - + +
1009B VAL* 4.0 16.2 - - + -
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Residues in contact with THR 957 (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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761B ILE* 3.4 24.9 - - + +
921B LEU 5.0 1.6 - - - +
923B GLU* 3.5 33.5 + - + +
928B THR* 3.7 22.7 + - + +
929B LYS* 5.9 0.3 - - - -
932B ALA* 3.9 13.9 - - - +
955B VAL 4.9 1.2 + - - -
956B ILE* 1.3 73.4 - - - +
958B LEU* 1.3 66.9 + - - +
1008B PHE* 3.0 35.1 + - - +
1010B TYR* 5.9 0.5 + - - +
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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
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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