Contacts of the strand formed by residues 238 - 246 (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 ASN 238 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237M THR* 1.3 79.6 + - - +
239M TRP* 1.3 66.5 + - - +
256M ALA* 3.5 5.9 - - - -
257M VAL* 2.9 33.9 + - - +
258M GLU 4.3 3.8 + - - -
259M GLU 2.9 24.5 + - - -
260M ASP* 4.0 2.6 + - - +
261M LEU* 3.6 41.3 - - + +
318M ARG* 3.6 31.3 - - - +
320M PHE* 4.1 6.5 - - + -
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Residues in contact with TRP 239 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C ARG* 3.0 35.9 - - - +
412C ASP* 5.6 5.8 - - - -
415C GLY* 5.7 10.8 - - - -
416C GLN* 6.0 2.0 - - - -
237M THR* 4.2 15.3 + - + -
238M ASN* 1.3 79.8 - - - +
240M LEU* 1.3 60.4 + - - +
254M ASP* 3.6 30.5 - - + -
255M ILE 3.3 6.3 - - - -
256M ALA* 3.5 39.3 - - + -
317M LYS 4.8 4.0 - - - -
318M ARG* 2.9 28.0 + - + +
319M LEU* 3.4 17.2 - - + +
320M PHE* 3.0 29.2 + - - -
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Residues in contact with LEU 240 (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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238M ASN 4.4 0.2 - - - -
239M TRP* 1.3 71.9 - - - +
241M ARG* 1.3 69.7 + - - +
242M VAL* 3.6 22.5 + - + +
253M LYS 3.6 0.3 - - - +
254M ASP* 3.4 1.8 - - - -
255M ILE* 2.8 37.1 + - + +
257M VAL* 4.0 17.2 - - + +
270M LEU* 4.3 8.7 - - + -
273M LEU* 4.3 16.2 - - + -
320M PHE* 4.0 12.0 - - + -
322M TRP* 3.5 57.0 - - + +
324M LEU* 4.1 17.7 - - + +
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Residues in contact with ARG 241 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239M TRP 4.0 3.0 + - - -
240M LEU* 1.3 76.2 - - - +
242M VAL* 1.3 66.5 + - - +
243M TYR* 4.6 7.4 - - + -
252M ILE* 3.9 25.6 - - + +
254M ASP* 2.8 41.5 + - - +
319M LEU* 3.7 41.5 - - + +
320M PHE* 5.5 0.8 + - - +
322M TRP 5.1 1.4 + - - -
323M LYS* 3.6 49.1 - - + +
324M LEU 3.3 19.2 + - - -
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Residues in contact with VAL 242 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240M LEU* 3.7 24.5 - - + +
241M ARG* 1.3 80.4 - - - +
243M TYR* 1.3 64.6 + - - +
244M TYR* 4.9 0.9 - - + +
251M THR 3.6 0.3 - - - +
252M ILE* 3.4 7.4 - - - +
253M LYS* 2.8 44.4 + - + +
255M ILE* 3.6 22.9 - - + -
273M LEU* 5.3 0.4 - - + -
278M PHE* 3.7 30.5 - - + -
324M LEU* 3.2 17.7 - - + +
326M ILE* 4.0 15.3 - - + -
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Residues in contact with TYR 243 (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* 4.6 5.6 - - + -
242M VAL* 1.3 75.2 - - - +
244M TYR* 1.3 59.0 + - - +
245M TYR* 3.6 16.6 - - + -
250M SER* 3.7 22.7 - - - +
251M THR 3.3 3.1 - - - -
252M ILE* 3.8 33.7 - - + +
323M LYS* 3.3 46.0 + - + +
324M LEU 3.0 8.4 + - - +
325M HIS* 3.3 38.8 - + - +
326M ILE* 2.9 28.9 + - - +
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Residues in contact with TYR 244 (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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280K ARG* 4.9 1.4 + - - -
282K ASP* 5.0 1.6 + - - -
242M VAL* 5.1 1.3 - - + -
243M TYR* 1.3 72.4 - - - +
245M TYR* 1.3 68.9 + - - +
246M GLU* 3.9 10.3 + - + +
250M SER* 3.1 0.9 - - - -
251M THR* 2.9 45.8 + - - +
253M LYS* 6.0 2.2 - - + -
278M PHE* 3.7 47.6 + + + +
280M ARG* 2.8 46.0 + - - -
283M ILE* 5.1 1.3 - - + -
326M ILE* 3.8 25.6 - - + -
327M THR* 6.4 0.4 - - - -
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Residues in contact with TYR 245 (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* 3.6 15.7 - - + +
244M TYR* 1.3 80.5 - - - +
246M GLU* 1.3 58.8 + - - +
247M ASP 3.8 12.6 + - - +
248M THR 4.2 16.4 - - - -
249M ILE 3.5 3.6 - - - -
250M SER* 3.7 17.7 + - - -
280M ARG* 5.4 3.3 + - - -
288M ARG* 2.9 30.6 + - - -
294M LEU* 4.3 3.1 - - + +
325M HIS* 2.9 40.0 + - + -
326M ILE 2.9 26.1 + - - +
327M THR* 3.9 17.2 - - + -
328M GLN* 4.7 11.3 + - - +
331M ASN* 4.5 2.8 + - - +
334M VAL* 3.8 25.4 - - + -
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Residues in contact with GLU 246 (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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244M TYR* 5.0 10.5 - - + +
245M TYR* 1.3 71.7 - - - +
247M ASP* 1.3 71.0 + - - +
248M THR 3.2 1.7 + - - -
249M ILE* 2.9 27.6 + - - +
251M THR* 4.9 15.6 - - + +
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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