Contacts of the helix formed by residues 253 - 259 (chain C) in PDB entry 2PK9
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 ASP 253 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C PRO 3.7 1.6 + - - -
252C ARG* 1.3 70.8 - - - +
254C LEU* 1.3 64.7 + - - +
255C ARG* 3.2 23.0 + - - +
256C GLN* 3.0 51.6 + - + +
257C VAL* 3.6 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 254 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C LEU* 5.7 3.1 - - + -
224C ILE* 4.5 12.1 - - + +
225C MET* 3.6 39.3 - - + -
252C ARG 2.8 10.9 + - - +
253C ASP* 1.3 72.7 + - - +
255C ARG* 1.3 63.3 + - + +
257C VAL* 3.5 20.6 + - + +
258C LEU* 3.7 30.5 + - + +
271C MET* 5.2 4.3 - - - -
274C LEU* 4.4 14.1 - - + +
275C HIS* 3.5 43.1 - - + +
278C LEU* 5.1 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 255 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C ASP* 3.1 14.5 + - - +
254C LEU* 1.3 78.4 - - + +
256C GLN* 1.3 74.6 + - - +
258C LEU* 3.7 1.8 + - - +
259C GLN* 3.3 36.1 + - + +
266C LEU* 3.3 25.5 + - - +
267C ASP* 4.7 1.4 - - - +
268C GLY* 3.7 27.1 - - - +
271C MET* 3.9 32.5 - - + +
275C HIS* 6.1 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 256 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C ASP* 3.0 42.6 + - + +
255C ARG* 1.3 85.4 - - - +
257C VAL* 1.3 64.0 + - + +
259C GLN* 4.9 2.9 - - - -
260C PRO* 3.4 17.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 257 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C THR* 6.4 0.2 - - + -
208C LEU* 4.5 22.2 - - + -
224C ILE* 4.5 22.2 - - + -
252C ARG* 3.9 31.0 - - + +
253C ASP 3.7 14.8 - - - +
254C LEU* 3.7 12.3 - - + +
255C ARG 3.2 0.8 - - - -
256C GLN* 1.3 81.8 - - + +
258C LEU* 1.3 62.9 + - + +
260C PRO* 3.5 3.3 - - - +
261C HIS* 3.3 27.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C ALA* 3.9 23.3 - - + +
203C ILE* 5.0 5.8 - - + -
204C THR* 3.6 32.8 - - + +
208C LEU* 4.0 20.6 - - + -
254C LEU* 3.7 27.8 + - + +
255C ARG* 3.7 2.9 + - - +
256C GLN 3.5 0.2 - - - -
257C VAL* 1.3 78.2 - - + +
259C GLN* 1.3 67.5 + - - +
260C PRO* 3.3 2.7 - - - -
261C HIS* 3.3 10.4 + - - -
262C THR* 3.5 10.7 - - - +
266C LEU* 4.3 10.3 - - + -
271C MET* 4.5 10.5 - - + -
274C LEU* 3.5 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 259 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C ARG* 3.3 26.2 + - + +
256C GLN* 4.8 2.7 - - - +
258C LEU* 1.3 76.8 - - - +
260C PRO* 1.4 69.8 - - + +
261C HIS 3.3 0.3 + - - -
262C THR* 3.2 21.3 + - - +
264C GLU 3.3 22.1 - - - +
265C PRO* 4.2 6.5 - - - +
266C LEU* 3.5 36.7 + - + +
----------------------------------------------------------
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