Contacts of the strand formed by residues 236 - 240 (chain B) in PDB entry 3PU3
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 236 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B EDO 3.6 42.8 + - - +
193B THR 4.8 0.4 - - - +
194B ASN* 3.9 18.1 + - - -
195B LEU 3.3 3.8 - - - +
196B GLU* 3.7 28.3 - - + -
197B PHE* 3.4 8.3 - - - -
232B LYS 3.6 2.8 + - - -
233B VAL* 3.3 52.5 - - - +
235B LYS* 1.3 73.5 - - - +
237B CYS* 1.3 59.9 + - - +
238B LEU* 4.0 11.4 - - + -
332B PHE* 3.3 8.0 - - - -
333B ALA 2.7 43.0 + - - +
334B GLY* 4.1 2.0 - - - -
335B HIS* 3.4 21.1 - + - -
361B THR* 5.0 6.2 + - - -
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Residues in contact with CYS 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B VAL* 4.2 10.3 - - - -
192B VAL 3.9 4.5 - - - +
195B LEU* 2.8 43.6 + - + +
197B PHE* 3.6 4.9 - - + -
202B MET* 3.8 30.5 - - + -
236B TYR* 1.3 73.8 - - - +
238B LEU* 1.3 62.0 + - - +
239B ILE* 3.8 13.6 - - - +
330B LEU* 3.4 31.0 - - - -
331B ALA 3.6 2.0 - - - -
332B PHE* 4.0 8.3 - - - -
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B OGA 3.1 33.0 - - - +
49B EDO 4.4 0.4 - - - +
192B VAL 3.4 1.8 - - - +
193B THR* 3.3 33.0 - - - +
236B TYR* 3.8 15.9 - - + +
237B CYS* 1.3 77.0 - - - +
239B ILE* 1.3 61.4 + - - +
240B CYS* 4.0 5.1 - - - -
259B TYR* 3.4 24.5 - - + +
329B CYS 3.7 1.0 - - - +
330B LEU* 3.3 9.5 - - - +
331B ALA* 2.8 46.8 + - + +
333B ALA* 3.8 22.9 - - + -
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Residues in contact with ILE 239 (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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146B VAL* 3.9 22.2 - - + -
149B VAL* 4.7 8.3 - - + -
174B LEU* 5.6 3.8 - - + -
177B PHE* 3.9 29.0 - - + -
181B TYR* 3.9 26.0 - - + -
191B ASN* 3.7 3.6 - - - -
192B VAL* 2.8 58.1 + - + -
195B LEU* 4.6 6.7 - - + -
237B CYS* 3.8 20.0 - - + +
238B LEU* 1.3 78.0 - - - +
240B CYS* 1.3 62.1 + - - +
329B CYS 3.7 4.9 - - - +
330B LEU* 4.0 12.8 - - + -
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Residues in contact with CYS 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B OGA 3.6 17.3 - - - -
181B TYR* 4.9 0.9 - - - -
191B ASN* 3.4 19.1 - - - +
193B THR* 4.2 4.0 - - - -
238B LEU* 4.5 3.8 - - - -
239B ILE* 1.3 82.6 - - - +
241B VAL* 1.3 62.6 + - - +
244B SER* 3.3 17.0 - - - +
266B LYS* 2.9 28.9 - - - +
325B THR* 3.5 12.4 - - + +
328B ASP* 3.4 2.3 - - - +
329B CYS 2.8 39.0 + - - +
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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
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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