Contacts of the strand formed by residues 238 - 246 (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 ASN 238 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236J MSE 3.6 4.1 + - - +
237J THR* 1.3 81.9 - - - +
239J TRP* 1.3 59.7 + - - +
240J LEU 4.3 0.2 - - - -
256J ALA* 3.5 0.7 - - - -
257J VAL* 2.9 41.2 + - - +
258J GLU 4.2 4.4 + - - -
259J GLU 2.8 27.6 + - - +
260J ASP* 4.0 2.0 + - - +
261J LEU* 3.6 30.8 - - + +
318J ARG* 2.6 39.6 + - - +
320J PHE* 4.2 4.5 - - + -
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Residues in contact with TRP 239 (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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235J HIS* 4.1 16.8 + + - -
237J THR* 3.4 47.6 + - + -
238J ASN* 1.3 75.6 - - - +
240J LEU* 1.3 58.8 + - - +
254J ASP* 3.8 32.3 - - + -
255J ILE 3.4 6.3 - - - -
256J ALA* 3.5 34.3 - - + -
317J LYS 3.8 17.7 - - - -
318J ARG 3.0 8.5 + - - +
319J LEU* 3.2 17.9 - - + +
320J PHE* 2.9 28.4 + - - -
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Residues in contact with LEU 240 (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* 1.3 72.3 - - - +
241J ARG* 1.3 69.1 + - - +
242J VAL* 3.6 22.2 + - + +
253J LYS 3.8 0.3 - - - +
254J ASP* 4.5 0.9 - - - -
255J ILE* 2.9 36.3 + - + +
257J VAL* 4.0 9.8 - - + +
270J LEU* 4.4 4.3 - - + -
273J LEU* 4.3 22.9 - - + -
319J LEU* 4.5 0.7 - - - -
320J PHE* 3.8 15.6 - - + -
322J TRP* 3.5 55.4 - - + +
324J LEU* 4.3 16.4 - - + +
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Residues in contact with ARG 241 (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* 1.3 74.8 - - - +
242J VAL* 1.3 64.2 + - - +
243J TYR* 4.7 3.1 - - + -
252J ILE* 3.5 26.0 - - + +
253J LYS 3.7 0.2 - - - -
254J ASP* 2.7 44.6 + - - +
319J LEU* 3.9 31.2 - - + +
320J PHE* 5.4 1.2 + - - +
322J TRP 5.2 1.4 + - - -
323J LYS* 3.5 34.3 - - + +
324J LEU 3.3 19.1 + - - -
259K GLU* 2.8 45.1 + - - -
266K LEU* 3.9 7.1 - - - +
268K LYS* 5.3 1.4 - - - +
269K ASP* 2.9 27.5 + - - -
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Residues in contact with VAL 242 (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 21.8 - - + +
241J ARG* 1.3 78.8 - - - +
243J TYR* 1.3 64.0 + - - +
244J TYR 5.0 0.2 - - - +
251J THR 3.6 0.7 - - - +
252J ILE* 3.5 6.8 - - - +
253J LYS* 2.9 35.9 + - + +
255J ILE* 3.7 20.9 - - + -
273J LEU* 5.0 0.2 - - + -
278J PHE* 3.5 36.3 - - + -
324J LEU* 3.2 25.4 - - + +
326J ILE* 4.1 10.1 - - + -
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Residues in contact with TYR 243 (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* 4.9 3.4 - - + -
242J VAL* 1.3 72.8 - - - +
244J TYR* 1.3 60.9 + - - +
245J TYR* 3.7 12.4 - - + -
250J SER* 3.7 24.9 - - - +
251J THR 3.5 2.5 - - - -
252J ILE* 3.8 21.3 - - + -
323J LYS* 3.3 33.4 + - + +
324J LEU 2.8 10.6 + - - +
325J HIS* 3.2 37.1 - + - +
326J ILE* 2.8 30.0 + - - +
259K GLU* 2.7 26.0 + - - -
260K ASP* 3.2 23.3 + - + -
263K SER* 3.6 21.3 - - - -
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Residues in contact with TYR 244 (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* 4.0 0.6 + - + -
243J TYR* 1.3 71.9 - - - +
245J TYR* 1.3 73.1 + - - +
246J GLU* 3.8 22.2 + - - -
250J SER* 3.2 3.5 - - - -
251J THR* 2.8 50.4 + - - +
253J LYS* 5.9 0.4 - - + -
278J PHE* 3.6 52.4 + + + +
280J ARG* 3.3 39.6 + - - -
283J ILE* 5.1 4.9 - - + +
326J ILE* 3.8 27.4 - - + -
327J THR* 6.2 0.7 - - - -
328J GLN 6.3 0.2 - - - -
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Residues in contact with TYR 245 (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 14.6 - - + +
244J TYR* 1.3 83.3 - - - +
246J GLU* 1.3 61.9 + - - +
247J ASP 3.7 12.9 + - - +
248J THR 3.9 19.5 - - - -
249J ILE 3.5 3.8 - - - -
250J SER* 3.9 16.4 - - - -
288J ARG* 3.1 20.7 + - - -
294J LEU* 4.3 4.7 - - + +
325J HIS* 2.7 45.9 + - + -
326J ILE 3.0 24.9 + - - +
327J THR* 3.8 17.7 - - + -
328J GLN* 4.8 10.2 + - - +
331J ASN* 4.5 3.1 + - - +
334J VAL* 3.9 22.7 - - + -
260K ASP* 3.9 5.0 + - - -
262K SER* 4.2 8.1 - - - -
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Residues in contact with GLU 246 (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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244J TYR* 3.8 23.2 + - + -
245J TYR* 1.3 72.1 - - - +
247J ASP* 1.3 71.1 + - - +
248J THR 3.2 1.4 + - - -
249J ILE* 3.0 21.1 + - - +
251J THR* 6.1 1.8 - - + +
280J ARG* 5.6 2.1 + - - -
308K ARG* 3.9 21.3 + - - +
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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