Contacts of the helix formed by residues 273 - 278 (chain D) in PDB entry 6BAA
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 SER 273 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D ALA* 3.1 2.0 - - - +
272D PRO* 1.3 81.7 - - - +
274D ASP* 1.3 80.0 + - - +
275D LEU 3.4 1.8 - - - -
276D HIS* 3.8 17.8 + - - +
277D HIS* 4.3 10.6 - - - +
278D HIS* 5.4 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 274 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D ALA* 3.9 14.2 + - + +
273D SER* 1.3 84.9 + - - +
275D LEU* 1.3 65.2 + - - +
276D HIS 3.1 3.6 + - - -
277D HIS 4.0 0.2 - - - -
278D HIS* 3.2 51.1 + - + +
279D GLN* 3.2 14.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 275 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D ILE* 6.4 0.7 - - + -
270D LEU* 3.9 17.9 - - + -
271D ALA* 2.9 35.0 + - - +
274D ASP* 1.3 78.5 - - - +
276D HIS* 1.3 64.4 + - + +
279D GLN* 3.5 30.8 - - - +
281D LEU* 5.5 2.1 + - - +
306D ALA* 2.9 20.1 - - - +
311D TRP* 5.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 276 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D ARG* 4.9 2.1 + - - -
189D ILE* 5.2 1.6 - - + -
271D ALA 4.9 1.3 + - - -
272D PRO 3.2 28.6 + - - -
273D SER* 3.9 7.2 - - - +
274D ASP 3.1 0.6 - - - -
275D LEU* 1.3 82.7 - - + +
277D HIS* 1.3 81.6 + - + +
279D GLN 4.2 0.2 - - - +
306D ALA* 2.8 43.4 + - - +
307D ASP* 3.1 14.6 + - - +
309D ILE* 3.0 40.5 + - + +
311D TRP* 3.5 28.8 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 277 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D ARG* 2.7 35.9 + - - +
273D SER 4.3 9.2 + - - -
274D ASP 3.4 2.6 + - - -
276D HIS* 1.3 96.5 + - + +
278D HIS* 1.3 75.8 + + + +
279D GLN 3.4 2.9 - - - +
307D ASP* 3.8 25.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 278 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D ARG* 5.0 1.1 + - - -
273D SER 5.4 0.4 - - - -
274D ASP* 3.2 40.2 + - + +
277D HIS* 1.3 83.5 - - + +
279D GLN* 1.3 63.8 + - + +
280D ASP* 4.0 1.9 + - - +
----------------------------------------------------------
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