Contacts of the helix formed by residues 286 - 291 (chain B) in PDB entry 1U0O
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 ASP 286 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B PHE* 1.3 75.1 - - - +
287B TYR* 1.3 55.1 + - - +
288B ASP* 2.9 38.0 + - - +
289B ASP* 2.6 55.7 + - - +
290B TYR 4.0 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B CYS 4.1 5.4 - - - -
276B ARG* 3.0 34.7 - - + +
277B PHE* 3.1 42.6 + + - -
285B PHE* 3.7 25.5 + + - -
286B ASP* 1.3 72.8 + - - +
288B ASP* 1.3 58.3 + - - +
289B ASP 3.0 0.4 - - - -
290B TYR* 3.0 30.7 + + + +
291B TYR* 4.1 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ASP* 2.7 28.9 + - - +
287B TYR* 1.3 77.8 - - - +
289B ASP* 1.3 61.6 + - - +
290B TYR 3.2 1.2 + - - -
291B TYR* 4.1 10.1 + - - +
667C LYS* 3.4 12.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 3.5 35.9 - - + +
45A TYR* 4.0 8.1 + - - -
285B PHE* 5.4 1.0 - - + +
286B ASP* 2.6 43.1 + - - +
288B ASP* 1.3 76.6 - - - +
290B TYR* 1.3 69.7 + - + +
291B TYR 3.5 2.2 + - - -
293B ILE* 3.9 1.4 - - - +
667C LYS* 3.7 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE 4.1 1.2 + - - -
44A ILE* 3.5 29.6 + - + -
71A LEU* 4.4 12.6 - - + -
115A TRP* 3.7 8.9 - + - -
273B ASN* 4.8 2.3 - - - +
277B PHE* 4.3 18.4 - + + -
279B TRP* 3.3 28.1 + - - -
283B MET* 4.0 5.2 - - - +
285B PHE* 3.3 56.9 - + + +
286B ASP 4.8 1.3 - - - -
287B TYR* 3.0 18.2 + + + +
289B ASP* 1.3 92.5 - - + +
291B TYR* 1.3 64.0 + - - +
292B LEU 3.3 3.3 + - - -
293B ILE* 3.2 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 5.8 0.8 + - - -
273B ASN* 4.4 8.5 - - - +
287B TYR 4.1 2.7 + - - -
288B ASP* 4.1 9.8 + - - +
289B ASP 3.5 3.2 + - - -
290B TYR* 1.3 76.3 - - - +
292B LEU* 1.3 92.5 + - + +
293B ILE* 4.5 0.6 - - - +
625C GLN* 5.6 1.0 + - - -
628C PRO* 4.5 12.0 - - + +
658C SER* 4.8 0.5 + - - -
660C LYS* 3.9 44.2 - - + +
661C GLN* 3.2 42.6 + - + -
664C LEU* 4.0 20.0 - - + -
667C LYS* 5.5 3.8 - - - +
----------------------------------------------------------
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