Contacts of the helix formed by residues 252 - 257 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196F ARG* 5.2 1.2 - - - +
227F MET* 3.3 31.5 - - + +
230F ALA* 4.0 23.7 - - + +
237F GLU* 4.7 2.6 + - - -
251F GLY* 1.4 69.7 - - - +
253F GLU* 1.3 85.6 + - - +
254F ARG 3.3 0.6 + - - -
255F PHE* 3.5 18.2 + - - -
256F ARG* 2.8 58.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 253 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189F LEU* 4.6 4.4 - - + +
192F ILE* 3.9 23.8 - - + +
193F LEU* 3.9 20.9 - - + +
196F ARG* 3.2 42.6 + - - +
217F CYS* 4.4 0.8 - - - -
250F ILE* 3.6 13.3 - - + -
251F GLY 2.8 23.4 + - - -
252F ASN* 1.3 93.2 + - - +
254F ARG* 1.3 63.3 + - - +
256F ARG* 3.8 20.5 + - - +
257F CYS* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 254 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216F LEU* 2.8 44.3 + - + +
217F CYS* 3.0 37.7 - - - +
218F TYR* 3.1 42.7 + - + +
235F SER 4.7 0.2 + - - -
236F LEU* 3.2 36.3 + - - +
238F LYS* 3.7 35.7 - - - +
250F ILE* 3.7 24.4 - - + +
251F GLY 3.0 14.4 + - - +
253F GLU* 1.3 76.3 - - - +
255F PHE* 1.3 60.0 + - + +
258F PRO* 3.3 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 255 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218F TYR* 3.0 23.7 - - + +
219F VAL* 5.0 0.7 - - - -
220F ALA* 4.2 14.6 - - + +
223F PHE* 3.2 36.3 - + - -
226F GLU* 3.5 49.1 - - + -
227F MET* 3.2 28.5 - - + -
229F THR 4.7 1.8 - - - -
230F ALA* 4.2 6.7 - - + -
236F LEU* 5.3 6.7 - - + -
251F GLY 4.9 2.7 - - - -
252F ASN* 3.5 24.9 + - + -
253F GLU 3.3 0.2 - - - -
254F ARG* 1.3 76.3 - - + +
256F ARG* 1.4 64.7 + - - +
257F CYS 3.2 2.7 + - - -
258F PRO* 3.3 9.4 - - - +
259F GLU* 3.2 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 256 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188F TYR* 3.3 24.6 + - - +
192F ILE* 3.8 35.1 + - + +
195F GLU* 5.4 3.2 + - - +
223F PHE* 3.9 20.4 - - + -
227F MET* 3.9 21.3 - - - -
252F ASN* 2.8 57.3 + - - +
253F GLU* 3.8 22.3 + - - +
255F PHE* 1.4 74.1 - - - +
257F CYS* 1.3 66.1 + - - +
259F GLU* 3.8 9.1 - - - +
266F PHE* 3.9 7.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 257 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185F LEU* 3.2 38.3 - - - +
188F TYR* 4.2 9.6 - - - -
189F LEU* 3.6 25.4 - - + -
192F ILE* 4.3 2.7 - - + +
213F LYS* 4.0 16.6 - - - -
217F CYS* 3.7 9.4 - - - -
253F GLU 3.0 16.0 + - - +
255F PHE 3.2 0.2 - - - -
256F ARG* 1.3 77.5 - - - +
258F PRO* 1.4 73.3 - - + +
259F GLU 2.9 2.1 + - - -
260F ALA* 3.0 17.7 + - - +
306F TYR* 5.0 0.4 - - - -
----------------------------------------------------------
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