Contacts of the strand formed by residues 238 - 246 (chain L) in PDB entry 1OEY
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 ASN 238 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236L MSE 4.3 8.9 + - - +
237L THR* 1.3 81.7 - - - +
239L TRP* 1.3 65.8 + - - +
256L ALA* 3.6 0.2 - - - -
257L VAL* 2.8 37.3 + - - +
258L GLU 4.5 1.2 + - - -
259L GLU 3.0 22.6 + - - -
260L ASP* 4.1 2.2 + - - +
261L LEU* 3.6 40.9 - - + +
318L ARG* 3.5 29.2 + - - +
320L PHE* 4.0 8.1 - - + -
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Residues in contact with TRP 239 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237L THR* 4.0 24.2 + - + +
238L ASN* 1.3 80.1 - - - +
240L LEU* 1.3 59.8 + - - +
241L ARG 4.0 0.2 - - - -
254L ASP* 3.6 31.4 - - + -
255L ILE 3.3 6.7 - - - -
256L ALA* 3.4 37.9 - - + -
318L ARG* 2.9 24.0 + - + +
319L LEU* 3.3 16.3 - - + +
320L PHE* 3.0 28.6 + - - -
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Residues in contact with LEU 240 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239L TRP* 1.3 72.1 - - - +
241L ARG* 1.3 66.9 + - - +
242L VAL* 3.6 23.8 + - + +
254L ASP* 4.4 1.6 - - - -
255L ILE* 2.9 35.0 + - + +
257L VAL* 4.2 10.3 - - + +
270L LEU* 4.7 2.0 - - + -
273L LEU* 4.3 23.6 - - + -
320L PHE* 4.0 15.2 - - + -
322L TRP* 3.4 59.9 - - + +
324L LEU* 4.3 16.2 - - + +
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Residues in contact with ARG 241 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239L TRP 4.0 2.8 + - - -
240L LEU* 1.3 73.4 - - - +
242L VAL* 1.3 62.6 + - - +
243L TYR* 4.1 24.7 - - + -
252L ILE* 3.8 24.5 - - + +
253L LYS 3.7 0.2 - - - -
254L ASP* 2.9 42.8 + - - +
319L LEU* 3.7 38.6 - - + +
320L PHE 5.6 0.4 + - - -
322L TRP 5.1 1.4 + - - -
323L LYS* 3.5 26.8 - - + +
324L LEU 3.1 22.2 + - - -
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Residues in contact with VAL 242 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240L LEU* 3.6 28.7 - - + +
241L ARG* 1.3 79.2 - - - +
243L TYR* 1.3 68.5 + - - +
244L TYR* 4.7 0.6 - - - +
251L THR 3.6 0.7 - - - +
252L ILE* 3.4 7.4 - - - +
253L LYS* 2.9 35.7 + - - +
255L ILE* 3.7 17.9 - - + -
273L LEU* 5.3 2.0 - - + -
278L PHE* 3.9 16.8 - - + -
324L LEU* 3.2 16.4 - - + +
326L ILE* 3.3 35.7 - - + -
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Residues in contact with TYR 243 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241L ARG* 4.1 22.9 - - + -
242L VAL* 1.3 75.3 - - - +
244L TYR* 1.3 59.8 + - - +
245L TYR* 3.5 21.8 - - + -
250L SER* 3.5 17.7 - - - +
251L THR 3.4 2.0 - - - -
252L ILE* 3.7 34.0 - - + +
323L LYS* 4.1 25.0 - - + +
324L LEU 2.8 8.3 + - - +
325L HIS* 3.4 32.3 - + - +
326L ILE* 2.8 28.1 + - - +
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Residues in contact with TYR 244 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242L VAL* 5.1 1.1 - - + +
243L TYR* 1.3 72.0 - - - +
245L TYR* 1.3 67.8 + - - +
246L GLU* 3.9 0.7 + - - +
249L ILE 3.9 0.5 - - - +
250L SER* 3.2 2.6 - - - -
251L THR* 2.8 49.0 + - - +
253L LYS* 6.2 0.7 - - + +
278L PHE* 4.0 49.6 + + + -
280L ARG* 3.0 48.6 + - + +
283L ILE* 5.2 1.1 - - + -
326L ILE* 3.8 27.8 - - + -
327L THR* 6.3 0.4 - - - -
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Residues in contact with TYR 245 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243L TYR* 3.5 21.4 - - + +
244L TYR* 1.3 78.9 - - - +
246L GLU* 1.3 60.1 + - - +
247L ASP 3.8 12.3 + - - +
248L THR 4.2 17.5 - - - -
249L ILE 3.4 3.6 - - - -
250L SER* 3.9 18.4 + - - -
280L ARG* 4.3 15.2 + - - -
288L ARG* 2.9 26.0 + - - -
294L LEU* 4.9 3.1 - - + -
325L HIS* 2.8 42.3 + - + -
326L ILE 2.9 27.3 + - - +
327L THR* 3.9 17.7 - - + -
328L GLN* 4.7 9.0 + - - +
331L ASN* 4.7 2.0 + - - +
334L VAL* 3.9 22.2 - - + -
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Residues in contact with GLU 246 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244L TYR 3.9 1.7 + - - +
245L TYR* 1.3 72.0 - - - +
247L ASP* 1.3 72.4 + - + +
248L THR 3.2 1.7 + - - -
249L ILE* 2.9 22.4 + - + +
280L ARG* 5.8 1.8 - - - +
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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