Contacts of the strand formed by residues 249 - 255 (chain B) in PDB entry 5DQ8
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 HIS 249 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236B PHE* 3.1 7.3 - - - +
237B VAL* 2.8 44.6 + - + +
239B PRO* 5.3 1.9 - - + +
248B ARG* 1.3 73.2 - - - +
250B LEU* 1.3 65.3 + - - +
251B PHE* 3.8 21.5 - + - -
305B ASP* 2.7 57.6 + - + -
307B ASN 3.4 18.7 + - - -
308B TRP* 3.5 25.5 - + + +
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Residues in contact with LEU 250 (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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234B SER* 4.1 24.5 - - - +
235B ALA 3.6 3.1 - - - +
236B PHE* 4.2 4.7 - - + -
248B ARG* 4.0 31.6 + - + +
249B HIS* 1.3 77.1 + - - +
251B PHE* 1.3 63.8 + - - +
252B VAL* 4.4 6.5 - - - +
253B HIS* 3.9 31.6 - - + +
305B ASP* 3.6 18.0 - - - +
437B ALA* 4.3 5.9 - - + +
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Residues in contact with PHE 251 (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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235B ALA* 2.8 23.8 + - + +
236B PHE* 3.8 28.0 - - - -
237B VAL* 3.8 22.0 - - + -
249B HIS* 3.8 5.6 - + - -
250B LEU* 1.3 72.1 - - - +
252B VAL* 1.3 72.0 + - + +
304B ALA* 3.4 1.7 - - + -
305B ASP 3.0 40.7 + - - -
306B LEU* 3.7 13.9 - - + -
308B TRP* 3.4 35.4 - + - -
327B TYR* 3.9 13.2 - + - -
379B MET* 4.2 8.7 - - + -
387B LEU* 3.9 25.8 - - + -
437B ALA* 3.3 7.1 - - - +
501B FLF 5.8 0.2 - - - -
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Residues in contact with VAL 252 (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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233B PHE* 3.9 20.0 - - + -
234B SER* 3.3 2.1 - - - -
235B ALA* 3.0 46.4 + - + +
250B LEU* 4.4 1.9 - - - +
251B PHE* 1.3 87.0 + - + +
253B HIS* 1.3 66.0 + - - +
302B PHE* 3.8 35.4 - - + -
303B TRP 5.0 0.7 - - - +
304B ALA* 3.9 19.3 - - + -
428B PHE* 4.4 7.0 - - + -
437B ALA* 3.9 8.5 - - + -
501B FLF 3.9 10.3 - - - -
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Residues in contact with HIS 253 (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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232B GLU* 3.4 27.1 - - + -
233B PHE* 3.2 14.7 + - - -
234B SER* 3.6 11.3 - - - -
250B LEU* 3.9 32.1 - - + +
252B VAL* 1.3 79.7 - - - +
254B ILE* 1.3 76.4 + - - +
255B SER* 4.1 14.4 - - - -
302B PHE* 4.3 3.7 - - - -
437B ALA* 4.6 9.1 - - + +
438B GLN* 5.6 0.7 - - - -
439B HIS* 3.2 22.3 + - - -
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Residues in contact with ILE 254 (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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223B LEU* 4.6 3.1 - - + -
230B LEU* 4.0 25.1 - - + -
231B VAL 5.6 0.4 - - - +
232B GLU* 3.3 7.1 - - - +
233B PHE* 2.6 51.8 + - + +
253B HIS* 1.3 81.0 - - - +
255B SER* 1.3 63.5 + - - +
256B GLN* 4.1 22.7 - - + -
300B VAL* 4.4 20.0 - - + -
302B PHE* 3.8 30.3 - - + -
426B TYR* 4.7 3.8 - - + -
439B HIS* 4.1 24.5 - - + +
441B ILE* 4.6 6.7 - - + -
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Residues in contact with SER 255 (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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231B VAL 3.7 4.6 + - - -
232B GLU* 4.2 10.1 - - - +
253B HIS* 4.1 18.6 + - - -
254B ILE* 1.3 77.0 - - - +
256B GLN* 1.3 68.9 + - - +
439B HIS* 4.9 4.5 + - - -
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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