Contacts of the strand formed by residues 244 - 249 (chain B) in PDB entry 4PAR
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 THR 244 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B THR* 4.1 0.9 + - - +
238B ILE* 3.4 2.7 - - - -
239B SER* 2.9 45.1 + - - -
242B GLY 3.5 0.8 - - - -
243B LEU* 1.3 80.0 - - - +
245B ILE* 1.3 67.3 + - - +
246B THR* 4.3 3.3 + - - +
303B VAL* 4.2 24.2 - - + -
304B TRP 3.6 2.7 - - - +
305B LYS* 3.0 27.6 + - + +
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Residues in contact with ILE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B TRP* 4.4 19.5 - - + -
228B LEU* 4.1 24.5 - - + -
236B ASN* 5.5 0.2 - - + -
237B THR 3.3 11.0 - - - +
238B ILE* 4.2 16.2 - - + -
244B THR* 1.3 77.2 - - - +
246B THR* 1.3 70.8 + - - +
271B VAL* 4.3 15.9 - - + -
288B MET* 5.4 0.4 - - + -
291B TYR* 3.5 46.2 - - + +
302B ALA 3.8 0.2 - - - +
303B VAL* 3.5 5.7 - - - +
304B TRP* 2.9 45.0 + - + +
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Residues in contact with THR 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ILE* 5.0 2.7 - - + +
236B ASN* 3.2 9.1 - - - +
237B THR* 2.9 70.2 + - + +
244B THR* 4.3 3.8 + - - -
245B ILE* 1.3 76.7 - - - +
247B GLU* 1.3 59.9 + - - +
248B LYS* 4.2 3.7 - - + +
300B ASP* 3.0 26.2 + - - +
302B ALA 3.1 7.5 + - - -
303B VAL* 4.3 8.2 - - - +
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Residues in contact with GLU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B TRP* 3.5 24.9 + - + -
234B TRP* 3.6 26.3 - - + -
236B ASN* 3.2 15.3 - - - +
245B ILE 4.3 0.2 - - - -
246B THR* 1.3 74.0 + - - +
248B LYS* 1.3 61.4 + - - +
262B TRP* 3.3 34.6 + - + -
269B ARG* 3.0 28.6 + - - -
302B ALA* 2.9 41.3 + - + -
304B TRP* 3.2 16.7 + - + +
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Residues in contact with LYS 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B TRP* 3.3 17.4 - - - +
235B ILE* 2.9 47.7 + - + +
236B ASN* 3.5 0.6 + - - -
246B THR* 5.4 3.4 - - + +
247B GLU* 1.3 73.9 - - - +
249B SER* 1.3 74.9 + - - +
255B THR* 3.8 13.9 - - + +
262B TRP* 4.9 3.4 - - - -
298B LEU 5.1 1.6 - - - +
299B LYS* 2.8 29.3 + - - +
300B ASP* 3.6 19.7 + - - +
301B GLY* 4.0 12.8 - - - +
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Residues in contact with SER 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ASP 3.9 10.9 + - - -
234B TRP* 4.5 8.3 - - - +
235B ILE* 4.6 6.3 - - - +
248B LYS* 1.3 89.4 - - - +
250B THR* 1.3 66.1 + - - +
251B ASP* 2.7 33.5 + - - +
252B GLU* 4.4 1.2 + - - -
254B ILE* 3.4 28.5 - - - +
255B THR* 3.3 13.3 + - - -
262B TRP* 6.3 0.2 - - - -
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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