Contacts of the helix formed by residues 202 - 206 (chain D) 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 THR 202 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D THR* 1.3 30.9 - - - +
203D THR 1.3 20.4 - - - -
204D ALA 2.7 0.2 + - - -
205D GLU* 3.1 2.0 - - - +
285F CYS 2.6 2.1 + - - +
286F ASP 1.6 48.2 - - - +
287F VAL* 0.7 370.3 - - - +
288F ASP 2.0 0.5 + - - -
290F ARG* 1.5 84.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D GLN 3.4 11.9 - - - +
62D ARG* 4.2 16.6 - - + -
63D GLY* 5.7 0.2 - - - -
201D THR 3.8 0.2 + - - -
202D THR* 1.3 57.9 - - - +
204D ALA* 1.4 55.5 - - - +
205D GLU 3.2 0.2 - - - -
206D ARG* 2.9 21.7 + - - +
207D GLU* 3.7 1.2 + - - +
270E GLU* 4.1 3.6 + - - -
286F ASP* 0.6 147.0 + - - +
287F VAL* 1.5 16.7 - - - +
288F ASP* 1.9 49.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 204 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D SER* 3.6 0.9 - - - +
203D THR 1.4 58.4 - - - -
205D GLU* 1.3 52.0 + - - +
207D GLU* 2.6 35.0 + - - +
208D ILE* 3.5 6.3 + - + -
288F ASP* 1.4 102.0 - - + +
291F LYS* 3.0 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 205 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D SER 2.8 26.7 - - - +
200D PHE* 3.2 24.0 - - - +
201D THR 3.6 3.6 - - - -
202D THR* 2.8 10.0 + - - +
204D ALA* 1.3 72.5 - - - +
206D ARG* 1.3 54.7 + - - -
207D GLU 3.2 0.4 - - - -
208D ILE* 3.1 40.9 + - + +
209D VAL* 3.9 1.7 + - - +
242D LEU* 4.4 13.0 - - + +
243D PRO* 5.3 4.6 - - + +
244D ASP* 5.4 8.5 - - - +
287F VAL* 2.0 45.1 - - + +
290F ARG* 3.4 27.4 + - - +
291F LYS* 4.7 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D GLU* 4.0 22.9 + - - +
183D ARG* 5.0 8.5 - - - +
186D THR* 3.7 23.4 - - - +
187D ASP* 3.1 25.4 + - - -
190D MET* 3.7 31.6 - - - +
200D PHE 4.8 5.8 - - - +
203D THR* 2.9 18.1 + - - +
204D ALA 2.7 3.0 + - - -
205D GLU* 1.3 71.1 - - - +
207D GLU* 1.3 69.4 + - - +
208D ILE 3.2 0.9 - - - -
209D VAL* 2.9 19.2 - - - +
210D ARG 4.5 0.3 + - - -
287F VAL* 3.3 4.7 - - + +
----------------------------------------------------------
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