Contacts of the helix formed by residues 252 - 257 (chain J) in PDB entry 3LUE
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 ASN 252 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196J ARG* 5.2 1.0 - - - +
227J MET* 3.3 31.3 - - + +
230J ALA* 4.0 23.4 - - + +
237J GLU* 4.7 2.8 + - - -
251J GLY* 1.4 69.3 - - - +
253J GLU* 1.3 86.0 + - - +
254J ARG 3.3 0.7 + - - -
255J PHE* 3.5 17.9 + - - -
256J ARG* 2.8 58.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 253 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189J LEU* 4.6 4.2 - - + +
192J ILE* 3.9 25.2 - - + +
193J LEU* 3.9 19.5 - - + +
196J ARG* 3.2 41.8 + - - +
217J CYS* 4.4 0.8 - - - -
250J ILE* 3.6 14.3 - - + -
251J GLY 2.8 23.5 + - - -
252J ASN* 1.3 92.6 + - - +
254J ARG* 1.3 63.7 + - - +
256J ARG* 3.8 21.3 + - - +
257J CYS* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 254 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216J LEU* 2.8 45.0 + - + +
217J CYS* 3.0 38.1 - - - +
218J TYR* 3.1 43.8 + - + +
235J SER 4.7 0.2 + - - -
236J LEU* 3.2 36.3 + - - +
238J LYS* 3.7 35.9 - - - +
250J ILE* 3.7 24.0 - - + -
251J GLY 3.0 13.3 + - - +
253J GLU* 1.3 76.9 - - - +
255J PHE* 1.3 59.3 + - + +
258J PRO* 3.3 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 255 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218J TYR* 3.0 23.9 - - + +
219J VAL* 5.0 0.7 - - - -
220J ALA* 4.2 14.8 - - + +
223J PHE* 3.2 36.6 - + - -
226J GLU* 3.5 49.6 - - + -
227J MET* 3.2 27.6 - - + -
229J THR 4.7 2.0 - - - -
230J ALA* 4.2 6.3 - - + -
236J LEU* 5.3 7.4 - - + -
251J GLY 4.9 2.9 - - - -
252J ASN* 3.5 24.8 + - + -
253J GLU 3.3 0.2 - - - -
254J ARG* 1.3 76.7 - - + +
256J ARG* 1.4 64.3 + - - +
257J CYS 3.2 2.9 + - - -
258J PRO* 3.3 9.4 - - - +
259J GLU* 3.2 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 256 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188J TYR* 3.3 24.3 + - - +
192J ILE* 3.8 34.5 + - + +
195J GLU* 5.4 3.2 + - - +
223J PHE* 3.9 20.0 - - + -
227J MET* 3.9 22.0 - - - -
252J ASN* 2.8 56.5 + - - +
253J GLU* 3.8 22.9 + - - +
255J PHE* 1.4 74.7 - - - +
257J CYS* 1.3 66.7 + - - +
259J GLU* 3.8 9.5 - - - +
266J PHE* 3.9 7.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 257 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185J LEU* 3.2 38.4 - - - +
188J TYR* 4.2 9.6 - - - -
189J LEU* 3.6 24.7 - - + -
192J ILE* 4.3 2.7 - - + +
213J LYS* 4.0 16.8 - - - -
217J CYS* 3.7 9.6 - - - -
253J GLU 3.0 16.0 + - - +
255J PHE 3.2 0.4 - - - -
256J ARG* 1.3 77.7 - - - +
258J PRO* 1.4 73.5 - - + +
259J GLU 2.9 2.1 + - - -
260J ALA* 3.0 17.8 + - - +
306J TYR* 5.0 0.7 - - - -
----------------------------------------------------------
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