Contacts of the strand formed by residues 238 - 246 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236K MSE 3.9 9.7 + - - +
237K THR* 1.3 78.7 - - - +
239K TRP* 1.3 66.9 + - - +
256K ALA* 3.5 5.4 - - - -
257K VAL* 2.8 31.8 + - - +
259K GLU 2.8 29.2 + - - +
260K ASP* 4.0 2.0 - - - +
261K LEU* 3.4 43.7 - - + +
318K ARG* 3.2 31.5 + - - +
320K PHE* 4.0 7.0 - - + -
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Residues in contact with TRP 239 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237K THR* 5.0 8.1 + - + +
238K ASN* 1.3 83.5 - - - +
240K LEU* 1.3 58.5 + - - +
254K ASP* 3.8 33.7 - - + -
255K ILE 3.4 7.4 - - - -
256K ALA* 3.7 34.1 - - + -
318K ARG* 2.8 31.0 + - + +
319K LEU* 3.4 16.0 - - + +
320K PHE* 3.1 29.6 + - - -
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Residues in contact with LEU 240 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239K TRP* 1.3 71.8 - - - +
241K ARG* 1.3 69.4 + - - +
242K VAL* 3.6 15.3 + - + +
253K LYS 3.5 1.0 - - - +
254K ASP* 3.5 3.0 - - - -
255K ILE* 2.8 35.2 + - + +
257K VAL* 3.6 17.9 - - + +
270K LEU* 4.3 6.5 - - + -
273K LEU* 4.0 24.2 - - + -
319K LEU* 4.6 0.7 - - - -
320K PHE* 4.1 10.5 - - + -
322K TRP* 3.5 49.8 - - + +
324K LEU* 4.0 26.0 - - + +
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Residues in contact with ARG 241 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240K LEU* 1.3 76.0 - - - +
242K VAL* 1.3 64.4 + - - +
243K TYR* 4.6 8.7 - - + -
252K ILE* 3.8 25.3 - - + +
254K ASP* 3.0 39.6 + - - +
316K GLN* 4.2 13.9 + - - +
319K LEU* 4.0 39.6 - - + +
320K PHE 5.5 0.8 + - - +
322K TRP 5.0 1.0 + - - -
323K LYS* 3.5 48.8 - - + +
324K LEU 3.3 18.7 + - - -
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Residues in contact with VAL 242 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240K LEU* 3.8 21.1 - - + +
241K ARG* 1.3 80.7 - - - +
243K TYR* 1.3 65.6 + - - +
244K TYR* 4.9 0.9 - - + +
251K THR 3.6 0.5 - - - +
252K ILE* 3.4 6.4 - - - +
253K LYS* 2.8 46.0 + - + +
255K ILE* 3.5 24.5 - - + -
274K THR* 5.3 0.2 - - + -
278K PHE* 3.6 33.4 - - + -
324K LEU* 3.1 18.4 - - + +
326K ILE* 3.8 13.0 - - + -
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Residues in contact with TYR 243 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241K ARG* 4.6 8.2 - - + -
242K VAL* 1.3 75.8 - - - +
244K TYR* 1.3 59.4 + - - +
245K TYR* 3.5 21.0 - - + -
250K SER* 3.8 16.2 - - - +
251K THR 3.5 2.7 - - - -
252K ILE* 3.6 36.8 - - + +
323K LYS* 3.2 49.3 + - + +
324K LEU 2.9 8.4 + - - +
325K HIS* 3.4 34.1 - + - +
326K ILE* 2.8 28.4 + - - +
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Residues in contact with TYR 244 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242K VAL* 4.0 1.5 - - + -
243K TYR* 1.3 71.6 - - - +
245K TYR* 1.3 67.2 + - - +
246K GLU* 3.6 33.0 + - + +
249K ILE 4.1 0.2 - - - +
250K SER* 3.2 1.9 - - - -
251K THR* 2.9 47.1 + - - +
253K LYS* 6.0 1.1 - - + +
278K PHE* 3.7 51.7 + + + +
280K ARG* 2.7 42.3 + - - -
283K ILE* 4.9 1.8 - - + -
326K ILE* 3.8 26.9 - - + -
327K THR* 6.3 0.2 - - - -
328K GLN 6.3 0.9 - - - -
282M ASP* 4.3 4.5 + - - -
328M GLN* 5.2 2.9 + - - -
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Residues in contact with TYR 245 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243K TYR* 3.5 19.5 - - + -
244K TYR* 1.3 82.3 - - - +
246K GLU* 1.3 64.2 + - - +
247K ASP 3.8 12.5 + - - +
248K THR 4.1 16.6 - - - -
249K ILE 3.5 3.1 - - - -
250K SER* 3.8 19.0 + - - -
280K ARG* 5.6 1.4 + - - -
288K ARG* 3.0 25.3 + - - -
294K LEU* 4.7 3.6 - - + -
325K HIS* 2.6 43.7 + - + -
326K ILE 2.9 26.6 + - - +
327K THR* 3.9 16.8 - - + -
328K GLN* 4.7 11.4 + - - +
331K ASN* 4.5 3.2 + - - +
334K VAL* 3.8 22.9 - - + -
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Residues in contact with GLU 246 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244K TYR* 3.6 28.9 + - + +
245K TYR* 1.3 77.6 - - - +
247K ASP* 1.3 70.8 + - - +
248K THR 3.3 1.4 + - - -
249K ILE* 3.0 21.2 + - - +
251K THR* 5.6 6.7 + - + -
280K ARG* 6.3 0.7 - - - +
328M GLN* 3.7 25.5 + - - +
330M ASP* 4.9 3.9 - - - +
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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