Contacts of the helix formed by residues 252 - 257 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ARG* 5.2 0.8 - - - +
227A MET* 3.3 30.9 - - + +
230A ALA* 4.0 23.9 - - + +
237A GLU* 4.7 2.4 + - - -
251A GLY* 1.4 69.5 - - - +
253A GLU* 1.3 85.3 + - - +
254A ARG 3.3 0.6 + - - -
255A PHE* 3.5 17.8 + - - -
256A ARG* 2.8 59.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 4.6 4.2 - - + +
192A ILE* 3.9 23.9 - - + +
193A LEU* 3.9 21.0 - - + +
196A ARG* 3.2 41.0 + - - +
217A CYS* 5.0 0.4 - - - -
250A ILE* 3.6 14.2 - - + -
251A GLY 2.8 24.5 + - - -
252A ASN* 1.3 92.2 + - - +
254A ARG* 1.3 64.7 + - - +
256A ARG* 3.8 21.7 + - - +
257A CYS* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A LEU* 2.8 44.7 + - + +
217A CYS* 3.0 37.3 - - - +
218A TYR* 3.1 43.2 + - + +
235A SER 4.7 0.2 + - - -
236A LEU* 3.2 36.1 + - - +
238A LYS* 3.7 35.9 - - - +
250A ILE* 3.7 24.9 - - + -
251A GLY 3.0 15.2 + - - +
253A GLU* 1.3 76.3 - - - +
255A PHE* 1.3 59.4 + - + +
258A PRO* 3.3 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A TYR* 3.0 24.3 - - + +
219A VAL* 5.0 0.9 - - - -
220A ALA* 4.2 14.4 - - + +
223A PHE* 3.2 36.8 - + - -
226A GLU* 3.5 48.9 - - + -
227A MET* 3.2 28.7 - - + -
229A THR 4.7 1.8 - - - -
230A ALA* 4.2 7.0 - - + -
236A LEU* 5.3 7.4 - - + -
251A GLY 4.9 2.2 - - - -
252A ASN* 3.5 24.0 + - + -
254A ARG* 1.3 77.4 - - + +
256A ARG* 1.4 65.0 + - - +
257A CYS 3.2 3.3 + - - -
258A PRO* 3.3 9.2 - - - +
259A GLU* 3.2 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A TYR* 3.3 23.8 + - - +
192A ILE* 3.8 34.2 + - + +
195A GLU* 5.4 3.2 + - - +
223A PHE* 3.9 21.5 - - + -
227A MET* 3.9 22.0 - - - -
252A ASN* 2.8 56.9 + - - +
253A GLU* 3.8 23.4 + - - +
255A PHE* 1.4 73.4 - - - +
257A CYS* 1.3 67.1 + - - +
259A GLU* 3.8 8.7 - - - +
266A PHE* 3.9 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 3.2 39.6 - - - +
188A TYR* 4.2 9.6 - - - -
189A LEU* 3.6 24.2 - - + -
192A ILE* 4.3 2.7 - - + +
213A LYS* 4.0 16.6 - - - -
217A CYS* 3.7 9.4 - - - -
253A GLU 3.0 15.8 + - - +
255A PHE 3.2 0.4 - - - -
256A ARG* 1.3 77.2 - - - +
258A PRO* 1.4 73.0 - - + +
259A GLU 2.9 2.3 + - - -
260A ALA* 3.0 18.0 + - - +
306A 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