Contacts of the strand formed by residues 249 - 257 (chain J) 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 ILE 249 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245J TYR* 3.5 2.5 - - - -
246J GLU* 3.0 33.1 + - - +
248J THR* 1.3 87.7 - - - +
250J SER* 1.3 65.0 + - - +
251J THR* 5.6 2.8 - - + +
262K SER* 3.5 11.9 - - - +
264K THR* 3.4 23.3 - - - +
307K VAL* 4.0 22.4 - - + +
308K ARG* 4.5 15.3 - - + +
311K ARG* 3.4 42.8 - - + +
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Residues in contact with SER 250 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243J TYR* 3.7 27.9 - - - +
244J TYR 3.2 11.9 - - - -
245J TYR* 3.9 20.6 + - - +
249J ILE* 1.3 75.2 - - - +
251J THR* 1.3 63.8 + - - +
260K ASP* 5.3 0.3 + - - -
262K SER 3.1 7.3 + - - -
263K SER* 3.1 27.0 + - - -
264K THR* 2.9 32.6 + - - -
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Residues in contact with THR 251 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242J VAL 3.6 0.3 - - - +
243J TYR* 3.5 3.6 - - - -
244J TYR* 2.8 50.4 + - - +
246J GLU* 6.1 1.3 - - + +
249J ILE* 5.6 2.7 - - + +
250J SER* 1.3 79.7 - - - +
252J ILE* 1.3 67.1 + - - +
264K THR* 4.3 20.0 - - + +
304K ALA* 5.9 4.5 - - + -
308K ARG* 6.4 0.4 - - - +
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Residues in contact with ILE 252 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241J ARG* 3.5 42.2 - - + +
242J VAL 3.5 3.1 - - - -
243J TYR* 3.8 19.1 - - + -
251J THR* 1.3 79.3 - - - +
253J LYS* 1.3 67.5 + - - +
254J ASP* 4.3 0.2 - - - +
259K GLU* 4.0 27.6 - - + +
263K SER* 4.3 3.4 - - - +
264K THR 3.2 23.7 + - - +
265K PRO* 3.7 16.4 - - + -
266K LEU* 3.9 32.6 - - + +
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Residues in contact with LYS 253 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240J LEU 3.8 0.3 - - - +
241J ARG* 3.7 0.7 - - - -
242J VAL* 2.9 35.2 + - + +
244J TYR* 5.9 0.4 - - + -
251J THR 4.1 0.4 + - - +
252J ILE* 1.3 75.3 - - - +
254J ASP* 1.3 69.4 + - - +
255J ILE* 3.9 12.0 + - + -
277J GLU* 2.6 48.0 + - - +
278J PHE* 3.6 39.0 - - + -
266K LEU* 6.1 0.4 - - - -
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Residues in contact with ASP 254 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239J TRP* 3.8 30.8 - - + -
240J LEU 3.7 3.1 - - - +
241J ARG* 2.7 58.8 + - - +
252J ILE* 4.9 1.3 - - - -
253J LYS* 1.3 79.8 - - - +
255J ILE* 1.3 61.9 + - - +
319J LEU* 4.4 7.5 - - - +
266K LEU* 4.2 8.5 - - - +
268K LYS* 4.9 8.3 + - - -
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Residues in contact with ILE 255 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239J TRP* 3.4 5.0 - - - -
240J LEU* 2.9 37.9 + - + +
242J VAL* 3.7 35.2 - - + -
253J LYS* 3.9 11.4 - - + +
254J ASP* 1.3 78.7 - - - +
256J ALA* 1.3 75.1 + - - +
257J VAL* 3.4 3.5 + - - +
273J LEU* 4.0 27.1 - - + -
277J GLU* 3.7 44.2 - - + +
278J PHE* 4.0 12.1 - - + -
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Residues in contact with ALA 256 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237J THR* 3.8 18.8 - - + -
238J ASN 3.5 7.4 - - - -
239J TRP* 3.5 17.0 - - + -
255J ILE* 1.3 80.0 - - - +
257J VAL* 1.3 63.7 + - - +
258J GLU 4.4 0.2 - - - -
273J LEU* 5.2 0.9 - - - +
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Residues in contact with VAL 257 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237J THR* 4.8 1.4 - - - +
238J ASN* 2.9 32.1 + - - +
240J LEU* 4.0 20.0 - - + -
255J ILE 3.4 11.4 - - - +
256J ALA* 1.3 81.1 - - - +
258J GLU* 1.3 65.8 + - - +
259J GLU* 3.4 29.8 - - + +
273J LEU* 4.0 22.2 - - + -
320J PHE* 3.9 23.6 - - + -
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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