Contacts of the strand formed by residues 229 - 238 (chain B) in PDB entry 5DQE
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 GLN 229 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223B LEU 4.5 1.1 - - - +
224B GLY* 4.0 11.0 - - - -
225B THR 2.6 28.5 + - - +
226B ALA* 3.5 18.6 + - - +
227B ARG 4.3 0.8 - - - -
228B LEU* 1.3 75.6 - - - +
230B LEU* 1.3 67.6 + - - +
231B VAL* 3.5 2.1 + - + -
256B GLN* 5.4 0.9 - - - +
333B TYR* 3.0 11.8 - - - +
334B GLU* 2.7 64.5 + - + +
335B SER* 4.5 2.8 + - - +
336B LEU 5.9 0.2 - - - +
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Residues in contact with LEU 230 (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* 3.3 48.3 + - + +
224B GLY* 4.6 0.4 - - - -
229B GLN* 1.3 76.7 - - - +
231B VAL* 1.3 62.0 + - - +
232B GLU 3.6 25.4 - - - +
233B PHE* 4.1 14.4 - - + -
254B ILE* 4.0 27.8 - - + -
256B GLN* 3.0 26.9 + - - +
331B SER* 5.0 2.0 - - - +
332B GLN 3.7 6.5 - - - +
333B TYR* 3.6 32.3 - - + +
410B GLN* 6.2 0.2 - - - +
422B LEU* 4.8 2.4 - - + +
426B TYR* 4.9 6.3 - - - +
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Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B GLN* 3.5 2.9 + - + +
230B LEU* 1.3 77.8 - - - +
232B GLU* 1.3 75.0 + - + +
255B SER* 3.6 0.7 - - - -
256B GLN* 2.8 40.7 + - - +
332B GLN* 2.6 36.2 + - + +
333B TYR 4.4 0.7 - - - -
334B GLU* 3.1 51.1 - - + +
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Residues in contact with GLU 232 (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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230B LEU* 3.6 6.4 - - - +
231B VAL* 1.3 93.6 - - + +
233B PHE* 1.3 65.1 + - - +
234B SER* 5.9 0.7 - - - +
253B HIS* 3.5 19.4 - - + -
254B ILE 3.2 18.2 - - - +
255B SER* 3.6 21.7 + - - -
330B SER 4.4 0.9 - - - -
331B SER* 3.4 3.3 - - - -
332B GLN* 2.9 36.4 + - + +
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Residues in contact with PHE 233 (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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230B LEU* 4.1 20.9 - - + -
232B GLU* 1.3 76.8 - - - +
234B SER* 1.3 68.8 + - - +
252B VAL* 4.0 21.1 - - + -
253B HIS* 3.2 2.5 + - - -
254B ILE* 2.7 45.7 + - + +
302B PHE* 4.3 18.2 - + - -
329B VAL* 3.6 27.6 - - + -
330B SER 3.3 6.7 - - - -
331B SER* 3.2 23.3 - - - -
333B TYR* 5.9 0.2 - - - -
410B GLN* 4.2 16.8 - - - -
426B TYR* 4.7 8.5 - - - -
501B 5E4 3.6 40.8 - + + -
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Residues in contact with SER 234 (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* 5.9 0.8 - - - +
233B PHE* 1.3 85.4 - - - +
235B ALA* 1.3 60.8 + - - +
236B PHE* 4.0 12.4 - - - -
248B ARG* 4.8 4.3 + - - -
250B LEU* 4.1 14.2 - - - +
252B VAL 3.3 10.1 - - - -
253B HIS* 3.6 19.3 - - - -
328B GLY 4.1 0.2 - - - +
329B VAL* 3.4 5.5 - - - +
330B SER* 2.9 41.0 + - - +
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Residues in contact with ALA 235 (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* 5.0 0.2 - - + -
234B SER* 1.3 73.8 - - - +
236B PHE* 1.3 63.9 + - - +
250B LEU* 3.7 1.6 - - - +
251B PHE* 2.9 32.1 + - + -
252B VAL* 3.1 28.7 + - + +
328B GLY 3.3 6.5 - - - +
329B VAL* 4.3 4.5 - - + -
379B MET* 3.9 13.7 - - + -
501B 5E4 3.8 24.0 - - + -
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Residues in contact with PHE 236 (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* 4.0 11.4 - - - -
235B ALA* 1.3 76.6 - - - +
237B VAL* 1.3 65.2 + - - +
238B GLU* 3.7 30.1 - - + -
248B ARG* 3.8 42.6 - - - -
249B HIS 3.2 13.9 - - - +
250B LEU* 4.1 5.8 - - + -
251B PHE* 3.6 11.8 - - - -
326B PHE* 3.8 28.9 - + - -
327B TYR* 3.4 3.6 - - - -
328B GLY* 2.8 47.7 + - - -
329B VAL 4.1 0.7 - - - -
330B SER* 3.6 25.4 - - - -
376B ARG* 4.1 13.7 - - + -
379B MET* 4.2 0.7 - - - +
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Residues in contact with VAL 237 (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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236B PHE* 1.3 77.4 - - - +
238B GLU* 1.3 75.3 + - - +
239B PRO* 4.0 4.3 - - + +
248B ARG* 3.4 1.0 - - - -
249B HIS* 2.9 51.2 + - + +
251B PHE* 3.5 26.7 - - + -
308B TRP* 3.8 19.7 - - + +
324B GLY 5.3 0.9 - - - +
325B GLY* 4.8 2.0 - - - -
326B PHE 3.2 11.0 - - - +
327B TYR* 3.7 30.1 - - + +
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Residues in contact with GLU 238 (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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236B PHE* 3.7 11.4 - - + -
237B VAL* 1.3 79.0 - - - +
239B PRO* 1.3 71.4 - - + +
242B ALA* 4.3 6.5 - - + +
246B TYR* 2.6 40.1 + - + +
247B GLN 3.8 11.0 - - - +
248B ARG* 3.7 6.8 + - + -
325B GLY* 3.5 2.4 - - - -
326B PHE* 2.8 41.8 + - + +
376B ARG* 2.6 44.5 + - - -
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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