Contacts of the helix formed by residues 223 - 230 (chain D) in PDB entry 3B4M
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 LYS 223 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ASP 5.6 0.9 + - - -
207A LYS* 3.5 38.3 - - - +
171D ALA* 4.2 28.5 - - + +
172D ARG* 3.7 24.3 - - + +
222D ASP* 1.4 70.0 - - - +
224D GLU* 1.3 69.2 + - + +
226D VAL* 2.8 25.2 + - - +
227D ARG* 4.2 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D ASP* 3.3 14.8 - - + +
223D LYS* 1.3 75.5 - - + +
225D SER* 1.3 58.1 + - - +
226D VAL 3.0 6.1 + - - -
227D ARG* 3.4 19.7 + - - +
228D THR* 3.2 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D CYS* 3.2 25.7 + - - +
196D GLY* 4.0 8.7 - - - -
197D SER 4.7 1.0 + - - -
220D PHE* 3.4 38.7 - - - +
222D ASP* 3.5 13.2 + - - +
223D LYS 2.9 1.6 + - - -
224D GLU* 1.3 76.1 - - - +
226D VAL* 1.3 56.6 + - - +
228D THR* 3.6 6.4 - - - -
229D SER* 3.0 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D ALA 3.6 22.4 - - - +
172D ARG* 3.6 26.0 - - - +
173D SER 4.2 4.7 - - - +
174D ILE* 4.0 15.9 - - + -
220D PHE* 4.1 6.1 - - + -
222D ASP 4.8 0.2 - - - +
223D LYS* 2.8 23.2 + - - +
224D GLU 3.0 0.2 + - - -
225D SER* 1.3 68.7 - - - +
227D ARG* 1.4 68.2 + - + +
228D THR 3.1 0.9 - - - -
229D SER* 2.9 21.8 + - - -
230D LEU* 3.4 8.5 + - - +
246D PRO* 4.0 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D LYS 4.2 1.5 + - - +
224D GLU* 3.4 12.9 + - - +
226D VAL* 1.4 77.4 - - + +
228D THR* 1.4 63.8 + - - +
230D LEU* 3.4 23.4 - - - +
231D ALA 4.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D GLY 5.4 0.7 - - - +
195D CYS* 3.8 29.5 + - + +
224D GLU* 3.2 14.7 + - - +
225D SER* 3.6 13.0 - - - -
226D VAL 3.1 0.4 - - - -
227D ARG* 1.4 77.2 - - - +
229D SER* 1.3 58.3 + - - +
231D ALA* 2.9 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D ILE* 3.4 24.7 - - - +
192D PHE* 3.9 12.7 - - - -
195D CYS* 3.9 13.2 - - - -
220D PHE* 3.5 20.6 - - - -
225D SER 3.0 18.5 + - - -
226D VAL 2.9 15.6 + - - -
228D THR* 1.3 71.4 - - - +
230D LEU* 1.3 55.3 + - - +
231D ALA 3.1 1.6 - - - -
232D LEU* 3.0 24.0 + - - +
244D VAL* 3.5 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D ILE* 4.5 1.6 - - + -
226D VAL 3.5 15.9 - - - +
227D ARG* 3.4 16.8 - - + +
228D THR 2.9 0.8 + - - -
229D SER* 1.3 75.2 + - - +
231D ALA* 1.3 64.3 + - - +
232D LEU 3.1 0.2 - - - -
233D ASP* 3.0 21.8 + - + +
244D VAL* 3.4 36.3 - - + +
245D ILE* 4.2 0.7 - - - -
246D PRO* 3.7 35.2 - - + -
----------------------------------------------------------
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