Contacts of the strand formed by residues 230 - 237 (chain B) in PDB entry 2O05
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 VAL 230 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B PHE* 3.9 0.5 - - - +
229B PRO* 1.3 87.3 - - - +
231B VAL* 1.3 70.2 + - - +
232B ALA* 5.6 0.9 - - + -
251B CYS* 3.4 3.8 - - - -
252B SER* 2.9 34.4 + - - +
254B ASN 3.5 17.5 - - - +
255B PRO 3.5 25.6 - - - +
257B THR 3.6 21.1 - - - +
258B ASN* 5.4 0.2 - - - -
259B PHE* 3.7 26.2 - - + +
260B GLN* 6.0 1.1 - - - +
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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
----------------------------------------------------------
221B ARG* 3.9 34.8 + - + +
224B CYS* 3.5 43.7 - - + +
225B GLN* 3.6 22.2 + - + +
228B PHE* 4.0 9.0 - - + +
229B PRO 4.4 0.4 + - - -
230B VAL* 1.3 84.3 - - - +
232B ALA* 1.3 64.7 + - - +
249B MET* 3.8 26.2 - - - -
250B LEU 3.3 7.2 - - - +
251B CYS* 4.2 2.9 - - - -
260B GLN* 5.4 0.5 - - - +
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Residues in contact with ALA 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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221B ARG* 3.7 10.1 - - - +
230B VAL* 5.6 0.4 - - + -
231B VAL* 1.3 76.4 - - - +
233B TYR* 1.3 62.4 + - - +
248B PHE 3.7 0.9 - - - +
249B MET* 3.7 7.3 - - - +
250B LEU* 2.9 33.4 + - + +
259B PHE* 4.0 15.9 - - + -
260B GLN* 3.9 17.5 - - - +
288B PHE* 3.5 26.5 - - + -
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Residues in contact with TYR 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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207B GLY 3.3 25.1 - - - -
208B GLU 2.5 21.1 + - - -
209B CYS* 4.1 0.2 - - - -
210B GLN* 3.4 28.1 + - + +
217B ILE* 3.5 28.5 - - + -
221B ARG* 3.4 19.4 + - - +
232B ALA* 1.3 75.3 - - - +
234B ALA* 1.3 64.8 + - - +
235B TYR* 4.2 6.4 - - + +
245B GLN* 5.1 0.2 + - - -
246B ILE 4.5 0.2 - - - -
247B GLY* 3.3 19.7 + - - -
248B PHE 3.3 13.9 - - - -
249B MET* 4.1 7.9 - - + -
288B PHE* 3.4 21.0 - - - +
290B LEU* 3.8 35.2 - - + +
298B LEU* 4.2 9.4 - - + -
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Residues in contact with ALA 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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86B LEU* 4.2 14.6 - - + -
233B TYR* 1.3 79.2 - - - +
235B TYR* 1.3 60.9 + - - +
247B GLY* 3.0 4.3 - - - -
248B PHE* 2.7 33.8 + - - -
250B LEU* 4.3 3.5 - - + +
287B ALA* 3.2 24.9 - - + +
288B PHE* 3.7 28.2 - - + -
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Residues in contact with TYR 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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235A TYR* 5.7 3.3 + + - -
237A THR* 4.3 17.2 + - + +
278A TYR* 4.9 6.2 + - - -
82B MET* 4.1 1.0 - - - +
210B GLN* 3.5 22.0 - - - +
233B TYR* 4.2 9.4 - - + +
234B ALA* 1.3 77.6 - - - +
236B CYS* 1.3 68.4 + - - +
237B THR* 4.6 6.5 - - + -
245B GLN* 3.4 28.0 - - - +
246B ILE 3.1 16.2 - - - +
247B GLY* 3.8 5.4 - - - -
248B PHE* 4.1 4.7 - - - -
278B TYR* 5.0 0.2 + - - -
286B ALA 4.8 1.9 + - - -
287B ALA* 3.1 52.5 + - - +
289B VAL 3.3 26.9 + - - -
290B LEU* 3.8 11.2 - - + -
291B PRO* 4.4 6.3 - - + +
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Residues in contact with CYS 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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78B SER 4.3 0.7 - - - -
79B TYR* 4.3 13.5 - - - -
82B MET* 3.7 26.7 - - + -
235B TYR* 1.3 77.8 - - - +
237B THR* 1.3 64.3 + - - +
238B ILE* 4.2 10.5 - - - -
245B GLN* 3.1 6.6 - - - +
246B ILE* 2.9 40.2 + - - -
248B PHE* 3.7 26.2 - - + -
278B TYR* 3.5 16.6 - - + +
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Residues in contact with THR 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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211A TRP* 3.5 15.7 + - - -
235A TYR* 4.3 13.0 + - + +
237A THR* 3.5 28.3 - - + -
244A GLY 5.7 0.2 - - - +
245A GLN* 3.4 27.6 + - + +
291A PRO* 4.8 1.9 - - - +
78B SER* 3.2 23.6 + - - -
235B TYR* 4.6 6.3 - - + -
236B CYS* 1.3 76.7 - - - +
238B ILE* 1.3 61.3 + - - +
244B GLY 3.5 11.9 - - - +
245B GLN* 4.4 3.1 - - + -
278B TYR* 3.0 19.2 + - - +
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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
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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