Contacts of the helix formed by residues 222 - 230 (chain D) in PDB entry 2P2N
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 222 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B PRO* 5.4 5.9 - - - +
220D GLY 3.4 6.0 + - - -
221D ILE* 1.3 77.9 - - - +
223D ALA* 1.3 63.5 + - - +
224D ASP* 3.7 23.8 + - - +
225D VAL* 3.3 28.0 + - - +
226D VAL 4.2 0.3 + - - -
253D PHE* 3.9 12.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D SER* 1.3 72.2 - - - +
224D ASP* 1.3 64.6 + - - +
225D VAL 3.1 3.3 + - - -
226D VAL* 3.4 3.2 + - - +
227D ARG* 3.2 17.8 + - - +
250D ASN* 5.1 1.5 + - - +
252D ALA* 3.6 43.7 - - + +
253D PHE* 3.7 16.1 - - + +
256D GLU* 3.3 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B PRO* 5.4 12.6 - - + +
222D SER* 3.1 16.1 + - - +
223D ALA* 1.3 79.1 - - - +
225D VAL* 1.3 58.7 + - - +
227D ARG* 3.8 19.6 + - + +
228D ASN* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B PHE* 5.4 13.0 - - + -
233B PRO* 5.7 10.3 - - + -
215D VAL* 3.7 28.9 - - + -
218D TYR* 4.8 7.6 - - - +
221D ILE* 3.7 23.6 - - + -
222D SER* 3.3 21.7 + - - +
223D ALA 3.1 0.4 - - - -
224D ASP* 1.3 76.4 - - - +
226D VAL* 1.3 67.5 + - + +
228D ASN* 3.0 15.1 + - - +
229D PHE* 3.1 34.8 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
215D VAL* 5.7 4.7 - - + -
223D ALA 3.4 3.2 + - - +
225D VAL* 1.3 79.6 - - + +
227D ARG* 1.3 62.6 + - - +
229D PHE* 3.5 7.3 + - - +
230D LEU* 3.3 28.2 + - + +
237D LEU* 4.2 16.6 - - + -
239D LEU* 5.6 3.6 - - + -
253D PHE* 4.1 27.6 - - + -
256D GLU* 3.6 42.0 - - + +
257D LEU* 3.9 27.4 - - + -
260D ALA* 4.6 0.7 - - + -
----------------------------------------------------------
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 ALA 3.2 12.0 + - - +
224D ASP* 3.8 19.0 + - - +
225D VAL 3.2 0.2 - - - -
226D VAL* 1.3 78.9 - - - +
228D ASN* 1.3 62.1 + - - +
230D LEU* 3.3 20.9 + - + +
231D ARG* 4.1 1.7 + - - +
256D GLU* 2.9 43.0 + - - +
259D GLU* 4.0 13.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ASN* 3.0 73.4 + - - +
229B PHE* 4.0 10.3 - - - +
231B ARG* 5.6 2.3 - - - +
233B PRO* 4.7 13.0 - - + +
224D ASP 3.0 19.9 + - - +
225D VAL* 3.0 9.4 + - - +
227D ARG* 1.3 74.1 - - - +
229D PHE* 1.3 66.8 + - + +
230D LEU 3.3 0.3 + - - -
231D ARG* 3.4 13.5 - - - +
233D PRO* 4.9 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B TYR* 5.6 0.4 - - - -
225B VAL* 5.4 14.6 - - + -
229B PHE* 4.7 23.6 - + - -
213D GLY* 3.7 31.9 - - - -
214D VAL 4.1 18.2 - - - -
215D VAL* 4.6 9.9 - - + -
225D VAL* 3.1 46.7 + - + -
226D VAL* 3.8 8.7 - - - +
227D ARG 3.4 0.2 - - - -
228D ASN* 1.3 80.4 - - + +
230D LEU* 1.3 57.6 + - + +
231D ARG 3.1 5.6 + - - -
233D PRO* 3.8 11.9 - - + +
234D VAL* 3.3 29.2 + - + +
237D LEU* 3.7 25.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
226D VAL* 3.3 20.4 - - + +
227D ARG* 3.3 17.2 + - + +
228D ASN 3.2 1.0 - - - -
229D PHE* 1.3 76.7 - - - +
231D ARG* 1.3 56.5 + - - +
232D GLN 4.0 0.2 - - - -
234D VAL* 5.1 0.9 - - + -
237D LEU* 4.4 10.1 - - + -
256D GLU* 4.5 9.0 - - - +
259D GLU* 4.3 3.8 - - + +
260D ALA* 3.4 47.1 - - + +
263D ARG* 3.0 54.7 + - - +
265D ILE* 3.6 20.6 - - + -
----------------------------------------------------------
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