Contacts of the strand formed by residues 56 - 59 (chain R) in PDB entry 2WUB
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 ALA 56 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C LYS* 5.0 0.2 - - - -
88C TYR 3.8 10.3 - - - +
89C ILE* 3.6 28.0 - - + -
90C PRO* 4.4 3.1 - - + -
51R ILE* 3.4 6.1 - - - +
52R TYR* 2.9 35.2 + - + +
55R GLY* 1.3 79.0 - - - +
57R THR* 1.3 61.7 + - - +
58R TYR* 3.6 26.4 - - + +
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Residues in contact with THR 57 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LYS* 5.4 5.4 + - - +
89C ILE* 5.8 0.2 - - - +
241C ARG* 2.6 38.0 + - - +
50R GLY 3.4 6.1 - - - +
51R ILE* 4.1 14.1 - - + -
55R GLY 4.2 1.3 + - - -
56R ALA* 1.3 77.0 - - - +
58R TYR* 1.3 61.9 + - - +
59R TYR* 3.6 27.4 + - + +
69R ILE* 3.4 26.7 - - + +
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Residues in contact with TYR 58 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ILE* 3.3 17.6 - - + +
90C PRO* 2.7 50.1 + - - +
92C THR* 3.1 39.5 - - + -
237C TRP* 4.3 2.9 - + - -
241C ARG* 3.4 19.5 - - - +
33R TYR* 5.7 6.7 - + - -
35R HIS* 5.0 6.1 - + + -
47R TRP* 3.9 20.2 - - + -
49R GLY* 3.1 2.8 - - - -
50R GLY* 2.9 43.4 + - - +
51R ILE* 4.6 0.9 - - - -
52R TYR* 4.7 9.9 - - + +
56R ALA* 3.6 18.2 - - + +
57R THR* 1.3 78.4 - - - +
59R TYR* 1.3 69.9 + - - +
69R ILE* 4.2 0.5 - - - +
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Residues in contact with TYR 59 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C ARG* 5.1 1.2 - - - +
47R TRP* 3.5 14.0 - - - -
48R VAL* 3.8 7.0 - - + +
57R THR* 3.6 29.5 + - + +
58R TYR* 1.3 81.2 - - - +
60R ALA* 1.3 66.0 + - - +
61R ASP* 4.0 1.2 + - - +
63R VAL* 4.8 3.6 - - + -
64R LYS* 4.2 41.6 - - + +
65R GLY 5.7 1.6 - - - -
67R PHE* 3.4 31.6 - - + -
68R THR* 3.4 12.8 - - - +
69R ILE* 2.8 53.0 + - + -
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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
------------------------------------------------------------
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