Contacts of the strand formed by residues 226 - 230 (chain D) in PDB entry 3OMA
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 VAL 226 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C ARG* 4.4 4.7 - - - +
50D VAL* 5.4 2.9 - - + -
219D TRP* 4.1 21.3 - - + -
220D THR* 2.6 26.9 + - - -
221D VAL* 3.2 32.3 + - + +
222D PRO* 5.2 0.4 - - - +
224D PHE* 3.8 22.2 - - + +
225D GLY* 1.3 82.7 - - - +
227D LYS* 1.3 55.3 + - - +
238D LEU* 4.0 22.2 - - + -
239D TRP 3.4 25.8 - - - +
240D PHE* 4.2 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C THR* 4.0 24.0 - - + -
408C ARG* 3.1 45.6 + - + +
409C TYR* 2.8 25.7 + - - +
411C HIS* 2.8 37.3 + - + +
413C THR* 4.1 5.8 - - - +
218D SER* 3.7 16.2 - - - +
219D TRP 3.3 7.9 - - - -
220D THR* 3.6 22.3 + - - +
226D VAL* 1.3 78.2 - - - +
228D GLN* 1.3 69.6 + - - +
238D LEU* 4.7 3.2 - - - +
253D SER* 4.0 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C TYR 5.4 0.2 - - - +
337C THR* 3.0 29.9 - - - +
338C ALA 4.4 0.3 - - - -
339C GLY* 3.8 12.2 + - - -
408C ARG* 5.8 2.6 - - - +
127D GLN* 4.8 12.3 + - - +
210D VAL* 3.8 17.3 - - + +
218D SER* 3.7 4.3 - - - -
219D TRP 3.0 26.8 + - - +
227D LYS* 1.3 80.9 + - - +
229D ASP* 1.3 70.3 + - - +
230D ALA 3.5 0.3 + - - -
236D ALA* 3.6 30.3 - - + +
237D GLN 3.1 25.7 + - - +
238D LEU* 3.8 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C MG 4.2 7.6 - - - -
175C TYR* 5.8 0.5 - - - -
276C GLN* 5.0 5.0 + - - +
337C THR* 3.0 39.1 + - - +
338C ALA* 3.4 22.0 - - - +
411C HIS* 4.7 2.9 + - - -
210D VAL* 4.0 7.6 - - - +
216D ILE* 4.1 8.6 - - + +
217D HIS 3.4 7.4 - - - +
218D SER* 2.9 22.9 + - - -
228D GLN* 1.3 82.8 + - - +
230D ALA* 1.3 60.0 + - - +
231D VAL* 3.5 23.9 + - + +
236D ALA* 4.6 4.7 - - - +
254D GLU* 4.2 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D GLY 4.5 0.2 - - - +
145D TRP* 4.1 8.5 - - + -
210D VAL* 3.6 16.4 - - + -
211D THR* 3.3 26.0 - - - +
212D GLY* 3.3 13.6 - - - +
216D ILE* 3.3 6.3 - - - -
217D HIS* 2.5 48.2 + - + +
218D SER* 4.8 0.2 - - - -
228D GLN 3.5 0.6 + - - -
229D ASP* 1.3 68.4 - - - +
231D VAL* 1.3 60.3 + - - +
----------------------------------------------------------
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