Contacts of the helix formed by residues 252 - 257 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196I ARG* 5.2 1.0 - - - +
227I MET* 3.3 31.1 - - + +
230I ALA* 4.0 23.0 - - + +
237I GLU* 4.7 2.6 + - - -
251I GLY* 1.4 70.6 - - - +
253I GLU* 1.3 85.2 + - - +
254I ARG 3.4 0.3 + - - -
255I PHE* 3.5 18.1 + - - -
256I ARG* 2.8 59.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 253 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189I LEU* 4.6 4.8 - - + +
192I ILE* 3.9 25.3 - - + +
193I LEU* 3.9 20.5 - - + +
196I ARG* 3.2 41.9 + - - +
217I CYS* 5.0 0.4 - - - -
250I ILE* 3.6 14.1 - - + -
251I GLY 2.8 23.8 + - - -
252I ASN* 1.3 92.8 + - - +
254I ARG* 1.3 63.8 + - - +
256I ARG* 3.8 21.5 + - - +
257I CYS* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 254 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216I LEU* 2.8 44.1 + - + +
217I CYS* 3.0 38.4 - - - +
218I TYR* 3.1 42.1 + - + +
235I SER 4.7 0.2 + - - -
236I LEU* 3.2 35.6 + - - +
238I LYS* 3.7 36.5 - - - +
250I ILE* 3.7 25.3 - - + +
251I GLY 3.0 14.5 + - - +
253I GLU* 1.3 76.8 - - - +
255I PHE* 1.3 59.8 + - + +
258I PRO* 3.3 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 255 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218I TYR* 3.0 24.4 - - + +
219I VAL* 5.0 0.7 - - - -
220I ALA* 4.2 14.4 - - + +
223I PHE* 3.2 37.0 - + - -
226I GLU* 3.5 47.3 - - + -
227I MET* 3.2 28.9 - - + -
229I THR 4.7 2.0 - - - -
230I ALA* 4.2 6.5 - - + -
236I LEU* 5.3 7.6 - - + -
251I GLY 4.9 2.5 - - - -
252I ASN* 3.5 24.4 + - + -
254I ARG* 1.3 77.6 - - + +
256I ARG* 1.4 63.9 + - - +
257I CYS 3.2 3.5 + - - -
258I PRO* 3.3 9.2 - - - +
259I GLU* 3.2 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 256 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188I TYR* 3.3 24.0 + - - +
192I ILE* 3.8 35.1 + - + +
195I GLU* 5.4 3.0 + - - +
223I PHE* 3.9 20.6 - - + -
227I MET* 3.9 22.2 - - - -
252I ASN* 2.8 57.3 + - - +
253I GLU* 3.3 23.9 + - - +
255I PHE* 1.4 72.8 - - - +
257I CYS* 1.3 66.3 + - - +
259I GLU* 3.8 9.5 - - - +
266I PHE* 3.9 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 257 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185I LEU* 3.2 37.8 - - - +
188I TYR* 4.2 9.6 - - - -
189I LEU* 3.6 26.0 - - + -
192I ILE* 4.3 2.4 - - + +
213I LYS* 4.0 16.6 - - - -
217I CYS* 3.7 8.7 - - - -
253I GLU 3.0 16.4 + - - +
255I PHE 3.2 0.4 - - - -
256I ARG* 1.3 76.3 - - - +
258I PRO* 1.4 73.4 - - + +
259I GLU 2.9 2.3 + - - -
260I ALA* 3.0 17.7 + - - +
306I 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