Contacts of the helix formed by residues 270 - 276 (chain D) in PDB entry 2BS3
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 GLU 270 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D ASP* 4.5 2.3 - - - +
141D PHE* 3.6 35.6 - - + -
142D GLY* 3.2 28.4 + - - -
143D GLY 4.4 3.4 + - - -
257D HIS* 4.6 0.2 - - - -
269D THR* 1.3 69.6 + - - +
271D GLY* 1.3 58.5 - - - +
272D CYS 2.9 11.8 + - - -
273D ARG* 3.2 12.4 + - - +
274D GLY* 3.1 18.7 + - - +
301D ARG* 2.8 62.7 + - - +
406D GLY* 5.7 0.2 - - - -
1657D CIT 3.8 10.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 271 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D ARG* 3.9 20.7 - - - +
269D THR* 3.0 15.0 + - - -
270D GLU* 1.3 77.8 - - - +
272D CYS* 1.3 55.3 + - - +
273D ARG 3.5 0.2 - - - -
274D GLY* 3.6 5.4 - - - -
275D ASP* 2.6 43.8 + - - +
342D LEU* 4.9 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 272 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259D THR* 5.8 0.9 - - - +
268D LEU* 4.4 10.1 - - - +
269D THR* 3.1 27.7 + - - +
270D GLU 2.9 2.0 + - - -
271D GLY* 1.3 77.8 - - - +
273D ARG* 1.3 53.9 + - + +
275D ASP* 3.7 2.9 - - - +
276D GLY 3.1 9.0 + - - -
277D GLY* 2.6 28.6 + - - -
328D LEU* 4.3 12.6 - - + -
330D ILE* 4.1 19.3 - - + -
333D LEU* 4.1 2.3 - - - +
342D LEU* 4.2 17.9 - - - -
345D VAL* 3.8 29.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 273 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D ASN* 5.2 0.2 - - - +
258D PRO* 4.4 2.8 - - - +
259D THR* 3.9 19.6 - - + +
270D GLU* 3.2 10.4 + - - +
272D CYS* 1.3 74.9 - - + +
274D GLY* 1.3 65.6 + - - +
276D GLY* 3.3 10.2 + - - -
277D GLY 3.5 21.7 + - - +
279D LEU* 4.4 19.1 - - + -
297D GLU* 2.5 40.4 + - + +
298D LEU* 3.4 22.5 - - - +
299D ALA 4.5 7.3 + - - -
301D ARG* 2.6 60.9 - - - +
304D VAL* 4.4 8.1 - - - +
328D LEU* 4.3 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 274 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D ILE* 3.9 5.4 - - - +
120D ASN* 2.9 26.7 + - - +
140D ASP* 5.5 3.9 - - - +
270D GLU* 3.1 15.8 + - - +
271D GLY* 3.6 5.4 - - - -
273D ARG* 1.3 79.9 - - - +
275D ASP* 1.3 61.2 + - - +
298D LEU* 3.9 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 275 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D ILE* 4.1 27.7 - - + +
120D ASN* 4.8 0.8 - - - +
123D LYS* 6.0 0.2 + - - -
139D ARG* 5.6 2.8 + - - -
271D GLY* 2.6 33.7 + - - +
272D CYS 3.7 3.6 - - - +
274D GLY* 1.3 82.3 - - - +
276D GLY* 1.3 55.9 - - - +
333D LEU* 3.5 16.6 - - + +
337D HIS* 2.8 39.0 + - - +
341D ASN* 4.3 2.9 - - - +
342D LEU* 3.3 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 276 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D ASN* 5.5 2.7 - - - -
272D CYS 3.1 0.6 + - - -
273D ARG 3.3 7.7 + - - -
275D ASP* 1.3 80.0 - - - +
277D GLY* 1.3 70.5 + - - +
278D ILE* 3.4 12.0 + - - +
332D ILE* 3.1 18.5 - - - +
333D LEU* 3.5 13.4 - - - +
----------------------------------------------------------
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