Contacts of the helix formed by residues 256 - 261 (chain C) in PDB entry 4PE5
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 GLY 256 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C GLU* 5.9 0.2 - - - -
255C SER* 1.3 71.4 - - - +
257C ASN* 1.3 64.3 + - - -
259C LEU* 3.0 24.5 + - - +
260C ARG* 3.8 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 257 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C GLU* 5.1 9.5 - - + +
226C ASP* 6.1 1.8 - - - -
229C ALA* 4.5 10.7 - - + +
255C SER 3.2 1.0 + - - -
256C GLY* 1.3 72.8 - - - -
258C ALA* 1.3 58.1 + - - +
259C LEU 3.0 0.4 - - - -
260C ARG* 2.9 31.2 + - + +
261C TYR* 3.9 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 258 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C GLU* 3.3 32.4 + - - +
228C ALA* 3.8 16.8 - - + -
229C ALA* 4.3 7.7 - - - +
232C TYR* 3.6 8.3 - - - -
252C ARG 4.0 3.6 - - - +
253C GLU 3.9 12.8 - - - +
255C SER 3.0 14.0 + - - +
257C ASN* 1.3 78.4 - - - +
259C LEU* 1.3 57.4 + - - +
261C TYR 3.8 1.1 + - - -
262C ALA* 3.2 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 259 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C ILE* 3.6 40.8 - - + +
255C SER* 3.8 4.1 + - - +
256C GLY 3.0 15.3 + - - +
258C ALA* 1.3 78.3 - - - +
260C ARG* 1.3 62.8 + - - +
261C TYR 3.1 4.1 + - - -
262C ALA* 3.2 25.0 + - + +
266C ILE* 6.1 0.4 - - + -
356C LEU* 5.7 5.2 - - + -
359C ARG* 4.9 3.3 + - - -
361C LEU* 4.0 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 260 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C GLY 3.8 1.4 + - - +
257C ASN* 2.9 22.1 + - + +
259C LEU* 1.3 78.3 - - - +
261C TYR* 1.3 57.6 + - + +
359C ARG* 3.7 20.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C ALA* 4.5 22.9 - - + +
232C TYR* 3.4 19.2 - - + +
233C ARG* 4.5 17.1 + - + +
257C ASN 3.9 2.2 + - - +
258C ALA 3.8 3.2 + - - -
259C LEU 3.1 0.2 - - - -
260C ARG* 1.3 80.1 - - + +
262C ALA* 1.3 65.1 + - - +
263C PRO* 3.5 1.4 - - - +
359C ARG* 4.4 5.8 + - - +
----------------------------------------------------------
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