Contacts of the strand formed by residues 283 - 288 (chain L) 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 L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244L TYR* 5.2 0.7 - - + -
271L LEU* 3.8 30.7 - - + +
274L THR* 3.9 22.7 - - + -
280L ARG* 4.0 37.5 - - + +
281L GLU* 3.2 8.6 - - - +
282L ASP* 1.3 92.7 - - - +
284L ALA* 1.3 61.1 + - - +
285L LEU* 3.9 17.0 - - + -
326L ILE* 3.9 17.3 - - + -
327L THR 3.2 18.4 - - - +
329L LYS* 4.1 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 284 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271L LEU* 6.0 0.7 - - - -
283L ILE* 1.3 74.5 - - - +
285L LEU* 1.3 65.8 + - - +
286L ASN* 3.4 5.5 + - - +
296L ARG* 3.6 42.4 - - + +
326L ILE* 3.6 3.6 - - - -
327L THR* 2.6 45.0 + - - +
329L LYS* 4.5 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 285 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267L LEU* 4.1 10.8 - - + -
270L LEU* 3.4 44.2 - - + -
271L LEU* 3.9 19.5 - - + +
274L THR* 3.7 18.4 - - - +
283L ILE* 3.9 11.9 - - + -
284L ALA* 1.3 79.2 - - - +
286L ASN* 1.3 68.0 + - - +
296L ARG* 3.7 2.9 - - - +
297L LEU* 2.8 44.7 + - + +
324L LEU* 4.1 11.9 - - + -
325L HIS 3.7 1.6 - - - -
326L ILE* 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 286 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284L ALA 3.4 4.6 + - - -
285L LEU* 1.3 77.7 - - - +
287L TYR* 1.3 63.2 + - - +
294L LEU* 3.7 23.6 - - + -
295L VAL 3.1 10.5 - - - +
296L ARG* 3.2 16.3 - - - +
297L LEU* 4.2 5.6 - - - +
324L LEU* 3.9 9.4 - - - +
325L HIS* 2.8 47.9 + - - +
327L THR* 2.9 31.5 + - - +
335L TYR* 2.5 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 287 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C VAL* 4.0 9.0 - - - +
286L ASN* 1.3 73.1 - - - +
288L ARG* 1.3 73.2 + - - +
289L ASP* 4.2 14.3 - - + +
294L LEU* 3.5 8.0 - - - -
295L VAL* 2.8 63.4 + - + +
297L LEU* 3.7 29.6 - - + -
302L ASP* 4.4 5.0 + - + -
305L LEU* 4.0 23.4 - - - +
306L MSE 3.7 40.6 - - + -
309L GLN* 3.8 25.0 - - + -
322L TRP* 6.1 0.2 - - + -
323L LYS 4.1 10.8 - - - +
325L HIS* 4.2 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 288 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245L TYR* 2.9 32.1 + - - -
287L TYR* 1.3 81.1 - - - +
289L ASP* 1.3 64.5 + - - +
292L GLY* 3.0 37.6 + - - +
293L ASP* 3.5 6.0 - - - +
294L LEU* 3.6 28.7 - - + +
309L GLN* 4.1 5.2 + - - -
323L LYS 4.9 0.6 + - - -
325L HIS* 3.8 28.1 + - + +
334L VAL* 4.7 7.7 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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