Contacts of the strand formed by residues 227 - 229 (chain J) in PDB entry 2WQT
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 227 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G ASP* 4.1 22.4 - - + +
57J VAL* 2.9 38.9 + - + +
58J GLY* 3.1 2.9 - - - -
59J ARG 3.1 24.8 + - - +
82J LEU* 4.2 9.2 - - + -
109J ALA* 4.2 19.3 - - + -
110J LEU 3.2 10.1 - - - +
111J VAL* 4.4 12.6 - - + -
134J LEU* 5.0 1.6 - - + -
164J TYR* 4.1 9.0 - - + +
166J ILE* 3.6 31.4 - - + -
225J GLY 3.7 0.9 + - - +
226J ASP* 1.3 74.9 - - - +
228J ILE* 1.3 66.9 + - - +
229J LEU* 4.2 4.3 - - + -
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Residues in contact with ILE 228 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59J ARG 3.4 3.8 - - - +
61J VAL* 4.5 3.1 - - + -
108J ILE 3.8 0.3 - - - +
109J ALA* 3.3 4.7 - - - -
110J LEU* 2.8 44.2 + - + +
112J LEU* 3.9 27.4 - - + -
116J LEU* 5.6 1.1 - - + -
126J LEU* 5.6 0.9 - - + -
208J ALA* 4.6 20.9 - - + +
211J LEU* 3.7 26.9 - - + -
222J LEU* 3.6 30.7 - - + -
226J ASP* 5.2 0.7 - - + -
227J ILE* 1.3 79.1 - - - +
229J LEU* 1.3 70.3 + - - +
230J THR* 3.6 21.7 + - + +
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Residues in contact with LEU 229 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59J ARG 3.0 7.9 + - - -
60J LYS* 4.1 9.9 - - + -
61J VAL* 2.8 33.3 + - - +
82J LEU* 3.9 24.0 - - + -
107J GLU* 3.3 13.6 - - + +
108J ILE 4.0 1.6 - - - +
109J ALA* 3.7 26.5 - - + +
136J ALA* 3.9 17.7 - - + -
137J LEU 5.3 0.2 - - - +
138J GLU* 3.8 36.8 - - + +
164J TYR* 3.8 25.1 - - + -
166J ILE* 5.6 0.2 - - + -
227J ILE* 5.0 4.5 - - + -
228J ILE* 1.3 71.4 - - - +
230J THR* 1.3 60.5 + - - +
231J GLY 3.3 2.0 + - - -
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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
------------------------------------------------------------
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