Contacts of the strand formed by residues 283 - 288 (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 283 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244J TYR* 5.1 3.8 - - + -
271J LEU* 3.8 18.7 - - + +
274J THR* 3.8 16.8 - - - +
280J ARG* 3.8 38.1 - - + +
281J GLU* 3.1 10.5 + - - +
282J ASP* 1.3 91.1 - - - +
284J ALA* 1.3 59.8 + - - +
285J LEU* 3.6 29.8 - - + -
326J ILE* 4.0 17.9 - - + -
327J THR 3.1 17.7 - - - +
328J GLN* 4.4 2.7 - - - +
329J LYS* 3.9 9.4 - - - +
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Residues in contact with ALA 284 (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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271J LEU* 5.9 0.7 - - - -
283J ILE* 1.3 74.8 - - - +
285J LEU* 1.3 64.6 + - - +
286J ASN* 3.4 1.9 + - - -
296J ARG* 3.6 43.7 - - + +
326J ILE* 3.6 4.7 - - - +
327J THR* 2.7 45.1 + - - +
329J LYS* 4.2 4.9 - - + +
335J TYR* 4.3 1.3 - - - +
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Residues in contact with LEU 285 (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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267J LEU* 4.1 13.2 - - + -
270J LEU* 3.6 33.4 - - + +
271J LEU* 3.9 27.3 - - + +
274J THR* 3.7 17.9 - - + -
283J ILE* 3.6 22.4 - - + -
284J ALA* 1.3 75.0 - - - +
286J ASN* 1.3 67.6 + - - +
296J ARG* 3.6 3.1 - - - +
297J LEU* 2.9 42.8 + - + +
324J LEU* 4.1 11.4 - - + -
325J HIS 3.5 1.8 - - - -
326J ILE* 3.9 12.8 - - + -
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Residues in contact with ASN 286 (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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284J ALA 3.4 3.8 + - - -
285J LEU* 1.3 80.8 - - - +
287J TYR* 1.3 64.8 + - - +
294J LEU* 3.6 23.8 - - + -
295J VAL 3.0 11.2 - - - +
296J ARG* 3.2 16.3 - - - +
297J LEU* 3.9 6.5 - - - +
324J LEU* 3.8 8.5 - - - +
325J HIS* 2.7 40.9 + - + +
327J THR* 3.0 30.5 + - - +
335J TYR* 2.4 29.1 + - - -
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Residues in contact with TYR 287 (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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363A VAL* 4.1 8.5 + - - +
286J ASN* 1.3 74.7 - - - +
288J ARG* 1.3 70.2 + - - +
289J ASP* 4.1 10.8 - - + +
294J LEU* 3.5 6.8 - - - -
295J VAL* 2.8 65.2 + - + +
296J ARG 5.3 0.4 - - - -
297J LEU* 3.6 30.3 - - + -
302J ASP* 4.3 5.2 + - + -
305J LEU* 4.0 22.4 - - + +
306J MSE 3.7 37.7 - - + -
309J GLN* 3.6 31.6 - - + -
323J LYS 4.4 4.9 - - - +
325J HIS* 3.8 7.4 - - - -
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Residues in contact with ARG 288 (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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245J TYR* 3.1 28.9 + - - -
287J TYR* 1.3 76.3 - - - +
289J ASP* 1.3 62.3 + - - +
292J GLY* 3.1 43.8 + - - +
293J ASP* 3.5 2.9 - - - +
294J LEU* 3.8 27.5 - - + +
309J GLN* 3.0 15.6 + - - -
323J LYS 5.2 0.2 + - - -
325J HIS* 3.9 17.5 + - + +
334J VAL* 4.8 7.7 + - - +
260K ASP* 2.6 32.9 + - - +
261K LEU* 6.0 1.1 - - - +
262K SER* 4.2 10.3 + - - -
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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