Contacts of the helix formed by residues 237 - 241 (chain N) in PDB entry 5DST
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 HIS 237 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229N ARG 5.7 0.2 - - - -
232N LYS* 3.2 37.8 + - + +
233N ASP* 3.7 31.9 - - - +
236N ILE* 1.3 94.6 - - + +
238N TRP* 1.3 61.2 + - - +
240N GLU* 2.7 62.0 + - - +
241N ASN 4.3 0.3 + - - -
251N ARG* 5.2 3.1 - - - -
255N MET* 5.3 1.6 - - + -
343N GLU 5.1 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 238 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87M GLU* 4.2 7.6 - - + -
90M LEU* 3.7 33.2 - - + -
91M LYS* 3.5 43.5 - - + +
233N ASP 2.9 11.1 + - - +
234N PHE* 3.2 28.9 - + - +
236N ILE 4.7 1.8 - - - +
237N HIS* 1.3 75.0 - - - +
239N TRP* 1.3 118.5 + + - +
240N GLU 3.1 1.4 + - - -
241N ASN* 3.2 25.7 + - - +
242N VAL* 3.9 19.7 - - + +
243N TYR* 5.5 2.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 239 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83M PHE* 3.6 26.0 - + + -
86M HIS* 4.8 1.1 - - + -
87M GLU* 3.6 33.0 + - + -
90M LEU* 4.3 7.9 - - + -
122M THR* 5.0 0.4 - - + -
235N LYS 3.4 22.7 + - - -
236N ILE* 3.4 22.9 - - - +
237N HIS 3.0 0.8 - - - -
238N TRP* 1.3 110.1 - + - +
240N GLU* 1.3 57.9 + - - +
241N ASN 3.2 0.7 + - - -
242N VAL* 3.8 4.8 - - - +
247N MET* 3.0 54.8 + - + +
250N ILE* 3.5 42.4 - - + -
251N ARG* 3.6 26.5 - - + -
254N ALA* 4.3 8.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 240 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237N HIS* 2.7 51.3 + - - +
239N TRP* 1.3 78.2 - - - +
241N ASN* 1.3 61.0 + - + +
245N PHE 4.1 1.1 - - - -
246N ASP* 3.5 24.0 + - - +
248N THR* 3.7 26.2 - - + -
251N ARG* 3.3 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 241 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237N HIS 4.3 0.4 + - - -
238N TRP* 3.2 16.2 + - - +
239N TRP 3.2 1.4 - - - -
240N GLU* 1.3 81.9 - - + +
242N VAL* 1.3 58.6 + - - +
243N TYR 3.7 2.6 + - - -
244N GLY* 2.9 34.1 + - - -
245N PHE 3.4 3.8 - - - -
----------------------------------------------------------
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