Contacts of the strand formed by residues 239 - 243 (chain A) in PDB entry 2WXF
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 TYR 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A TRP* 3.8 12.1 - - - -
196A PHE* 3.9 23.3 - + - -
217A MET* 3.4 27.6 - - - +
221A LEU* 3.7 29.5 - - + +
224A LYS* 4.4 5.4 + - - -
235A GLN 3.7 18.2 - - - -
236A PRO 3.1 8.5 + - - +
237A GLU* 3.3 2.0 - - - +
238A GLU* 1.3 84.5 - - + +
240A ALA* 1.3 62.5 + - - +
251A TYR* 5.6 1.0 - - - +
276A MET* 3.5 21.3 - - + -
277A VAL 3.3 26.0 - - - -
278A HIS* 3.6 35.0 + + + +
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Residues in contact with ALA 240 (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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159A TRP* 4.4 2.6 - - + -
163A LEU* 3.7 30.7 - - + -
217A MET* 4.1 5.4 - - - -
239A TYR* 1.3 73.9 - - - +
241A LEU* 1.3 63.7 + - - +
249A TYR* 4.0 13.7 - - + -
250A LEU 4.3 2.5 - - - -
251A TYR* 4.3 13.9 - - + -
275A THR 3.4 0.5 - - - +
276A MET* 3.8 1.9 - - - -
277A VAL* 2.9 34.2 + - - +
282A ILE* 4.2 7.4 - - + -
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Residues in contact with LEU 241 (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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194A VAL* 4.2 3.4 - - + -
213A PRO* 4.0 23.1 - - + +
216A LEU* 3.8 28.5 - - + -
217A MET* 3.7 23.3 - - + -
240A ALA* 1.3 71.5 - - - +
242A GLN* 1.3 62.2 + - - +
243A VAL 3.9 0.2 + - - -
249A TYR* 3.2 4.0 - - - -
250A LEU* 2.6 52.7 + - + +
256A LEU* 5.5 0.7 - - + -
274A LEU* 4.0 30.5 - - + +
275A THR 3.3 5.8 - - - +
276A MET* 3.7 28.3 - - + -
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Residues in contact with GLN 242 (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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197A GLU* 5.0 4.0 - - - +
240A ALA 3.8 0.8 + - - -
241A LEU* 1.3 72.4 - - - +
243A VAL* 1.3 74.3 + - - +
244A ASN* 3.4 1.4 + - - +
245A GLY* 4.6 5.6 - - - +
246A ARG 2.8 27.9 + - - +
247A HIS* 4.4 11.3 + - - -
248A GLU 3.6 7.9 - - - +
249A TYR* 3.6 35.7 + - + -
274A LEU* 3.3 6.4 - - - -
275A THR* 2.8 46.7 + - - +
277A VAL* 3.9 10.6 - - + +
740A LEU* 5.6 1.4 - - - +
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Residues in contact with VAL 243 (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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242A GLN* 1.3 72.0 - - - +
244A ASN* 1.3 72.2 + - - +
245A GLY 3.2 0.9 + - - -
246A ARG* 3.0 46.0 + - + +
248A GLU* 2.9 30.7 + - + +
250A LEU* 3.8 23.1 - - + -
261A TYR* 3.7 53.4 - - + +
273A HIS 3.9 4.3 - - - -
274A LEU* 4.1 3.4 - - + -
771A ALA* 6.1 1.6 - - + -
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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