Contacts of the strand formed by residues 249 - 257 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245M TYR* 4.3 1.8 - - - -
246M GLU* 2.9 36.7 + - + +
247M ASP 3.4 0.2 - - - -
248M THR* 1.3 90.8 - - - +
250M SER* 1.3 71.4 + - - +
251M THR* 5.8 2.6 - - + +
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Residues in contact with SER 250 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243M TYR* 3.7 26.6 - - - +
244M TYR 3.1 13.5 - - - -
245M TYR* 3.7 32.8 + - - -
248M THR 4.3 0.6 + - - -
249M ILE* 1.3 84.7 - - - +
251M THR* 1.3 64.9 + - - +
252M ILE* 5.5 1.2 - - - +
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Residues in contact with THR 251 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242M VAL 3.6 0.7 - - - +
243M TYR* 3.3 5.2 - - - -
244M TYR* 2.9 51.6 + - - +
246M GLU* 4.9 14.7 - - + +
249M ILE* 5.8 2.2 - - + +
250M SER* 1.3 78.2 - - - +
252M ILE* 1.3 67.4 + - - +
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Residues in contact with ILE 252 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241M ARG* 3.9 36.3 - - + +
242M VAL 3.4 2.7 - - - -
243M TYR* 3.8 26.2 - - + +
250M SER* 5.5 1.6 - - - +
251M THR* 1.3 81.5 - - - +
253M LYS* 1.3 66.2 + - - +
254M ASP* 4.3 3.4 - - - +
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Residues in contact with LYS 253 (chain M).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240M LEU 3.6 0.9 - - - +
242M VAL* 2.8 47.4 + - + +
244M TYR* 6.0 2.0 - - + -
251M THR 4.0 0.6 + - - -
252M ILE* 1.3 74.8 - - - +
254M ASP* 1.3 76.2 + - - +
255M ILE* 3.9 8.5 + - + -
277M GLU* 3.0 44.2 + - - +
278M PHE* 4.6 15.8 - - + -
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Residues in contact with ASP 254 (chain M).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397C ARG* 3.7 21.7 + - - +
239M TRP* 3.6 30.5 - - + -
240M LEU 3.4 4.9 - - - +
241M ARG* 2.8 55.1 + - - +
252M ILE* 4.3 3.7 - - - +
253M LYS* 1.3 82.2 - - - +
255M ILE* 1.3 61.8 + - - +
277M GLU* 5.4 0.3 - - - +
319M LEU* 4.8 5.3 - - - +
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Residues in contact with ILE 255 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239M TRP* 3.3 4.5 - - - -
240M LEU* 2.8 38.6 + - + +
242M VAL* 3.6 25.4 - - + -
253M LYS* 4.2 10.8 - - + +
254M ASP* 1.3 77.0 - - - +
256M ALA* 1.3 76.3 + - - +
257M VAL* 3.8 1.7 - - - +
273M LEU* 3.7 33.2 - - + -
277M GLU* 3.5 36.1 - - + +
278M PHE* 3.7 27.6 - - + -
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Residues in contact with ALA 256 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411C LYS* 3.8 34.2 + - + +
237M THR* 4.0 18.2 - - + -
238M ASN 3.5 7.0 - - - -
239M TRP* 3.5 22.5 - - + -
255M ILE* 1.3 82.3 - - - +
257M VAL* 1.3 64.0 + - - +
273M LEU* 4.9 1.4 - - - +
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Residues in contact with VAL 257 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411C LYS* 5.8 0.2 - - - +
237M THR* 4.0 0.6 - - - +
238M ASN* 2.9 31.7 + - - +
240M LEU* 4.0 16.8 - - + -
255M ILE 3.8 9.4 - - - +
256M ALA* 1.3 79.8 - - - +
258M GLU* 1.3 67.4 + - - +
259M GLU* 3.4 25.1 + - + +
273M LEU* 3.7 26.5 - - + -
320M PHE* 3.9 24.9 - - + -
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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