Contacts of the strand formed by residues 319 - 321 (chain D) in PDB entry 4OBZ
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 TRP 319 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D LEU* 4.0 14.1 - - + -
213D VAL* 4.3 29.4 - - + -
221D LEU* 4.5 13.7 - - + -
222D CYS* 4.8 1.1 - - + -
226D CYS* 3.5 39.5 - - + -
227D GLU 3.1 6.6 + - - +
228D ALA* 3.9 17.7 - - + -
229D ILE* 2.9 26.2 + - - +
237D MET* 5.7 1.3 - - + -
238D VAL 3.3 21.8 - - - -
239D GLY* 3.8 11.0 - - - -
240D PRO* 3.4 26.0 - - + +
243D GLU* 3.6 23.6 + - + -
244D VAL* 4.4 9.6 - - + -
247D LEU* 4.8 2.5 - - + -
276D LEU* 5.6 4.3 - - + -
306D PHE* 4.1 27.4 - + - -
317D PRO 6.2 0.2 - - - -
318D LEU* 1.3 76.0 - - - +
320D ILE* 1.3 66.3 + - - +
321D LEU* 5.3 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 320 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D ILE* 3.6 22.9 - - + +
231D ASP* 3.5 31.4 - - + +
234D THR* 3.8 25.4 - - + +
237D MET* 3.3 9.4 - - - +
238D VAL* 2.8 59.9 + - + +
309D MET* 6.0 2.7 - - - -
311D ILE* 4.1 23.8 - - + -
318D LEU* 4.8 1.3 - - + +
319D TRP* 1.3 76.1 - - - +
321D LEU* 1.3 65.6 + - - +
322D GLY 3.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 321 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D VAL* 4.9 0.7 - - + -
210D LEU* 5.0 2.7 - - + -
228D ALA* 4.3 18.8 - - + -
229D ILE 3.0 14.2 + - - +
230D VAL* 3.8 12.8 - - + -
231D ASP 3.1 21.8 + - - +
237D MET* 3.8 16.4 - - + -
276D LEU* 3.4 29.8 - - + -
278D LEU* 4.0 31.9 - - + -
319D TRP* 5.3 4.5 - - + -
320D ILE* 1.3 72.8 - - - +
322D GLY* 1.3 64.3 + - - +
325D PHE* 4.0 25.1 - - + -
326D ILE* 3.7 6.2 - - - +
342D PHE* 4.5 9.4 - - + -
----------------------------------------------------------
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