Contacts of the helix formed by residues 233 - 245 (chain A) in PDB entry 3LQ5
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 233 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 3.7 12.6 - - - -
231A GLY 3.5 0.4 - - - -
232A ASN* 1.3 90.9 - - + +
234A GLU* 1.3 68.3 + - - +
235A GLN* 4.3 8.8 + - - +
236A HIS* 2.8 15.0 + - - +
237A GLN* 2.7 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ASN* 5.3 4.9 - - - +
192A LEU* 4.1 11.1 - - + +
195A ARG* 4.7 10.7 + - - +
200A LEU* 4.1 36.1 - - + +
233A THR* 1.3 73.1 - - - +
235A GLN* 1.3 65.4 + - - +
237A GLN* 4.2 6.3 - - - -
238A LEU* 2.8 31.4 + - + +
265A LEU* 5.6 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A THR* 3.3 9.1 + - - +
234A GLU* 1.3 79.6 - - - +
236A HIS* 1.3 63.2 + - - +
238A LEU* 3.7 3.3 + - - +
239A ALA* 3.2 20.8 + - - +
265A LEU* 3.6 34.1 - - + +
266A GLU* 3.7 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A GLN 3.8 9.2 - - - -
231A GLY* 3.2 13.8 - - - -
232A ASN* 2.8 35.1 + - + +
233A THR* 2.8 25.6 + - - +
235A GLN* 1.3 73.9 - - - +
237A GLN* 1.3 67.8 + - - +
239A ALA* 3.2 10.2 + - + +
240A LEU* 3.1 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 2.9 47.9 + - + +
193A TRP* 3.3 22.2 + - - +
195A ARG 4.4 6.9 + - - -
200A LEU* 4.0 15.0 - - + -
213A TRP* 6.0 0.2 - - - +
229A MET* 3.1 30.0 + - - +
231A GLY* 3.2 20.4 + - - -
233A THR 2.7 14.3 + - - +
234A GLU* 3.5 6.5 - - - +
236A HIS* 1.3 72.1 - - - +
238A LEU* 1.3 55.2 + - - +
240A LEU* 2.5 32.8 + - - +
241A ILE* 3.2 15.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PRO* 5.0 9.0 - - + -
200A LEU* 3.8 32.2 - - + +
201A LEU* 3.4 32.8 - - + -
234A GLU* 2.8 19.6 + - + +
235A GLN 4.0 3.8 - - - +
237A GLN* 1.3 73.2 - - - +
239A ALA* 1.3 50.3 + - - +
241A ILE* 3.4 12.6 + - + +
242A SER* 2.7 35.5 + - - +
248A ILE* 4.1 23.3 - - + -
265A LEU* 3.9 35.0 - - + -
266A GLU 5.8 0.2 - - - +
267A LEU* 6.1 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A GLN 3.2 11.7 + - - +
236A HIS* 3.2 13.9 + - + +
237A GLN 2.6 4.8 + - - -
238A LEU* 1.3 74.4 - - - +
240A LEU* 1.3 65.4 + - + +
242A SER* 3.3 9.5 + - - -
243A GLN* 3.1 26.7 + - - +
266A GLU 5.5 5.6 - - - +
267A LEU* 6.3 1.8 - - - +
268A VAL* 5.5 11.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ILE 4.9 1.8 - - - +
229A MET* 3.6 24.6 - - + +
230A GLN 3.6 37.0 - - - +
231A GLY* 4.4 1.8 - - - +
236A HIS* 3.1 48.6 + - + +
237A GLN* 2.5 16.0 + - - +
239A ALA* 1.3 74.4 - - + +
241A ILE* 1.3 58.8 + - - +
243A GLN* 3.2 17.7 - - - +
244A LEU* 3.2 22.5 + - - +
278A ARG* 4.9 6.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ARG 4.3 12.8 - - - +
197A PRO* 4.2 12.1 - - + -
200A LEU* 3.8 28.9 - - + -
213A TRP* 3.9 24.7 - - + +
229A MET* 3.6 24.2 - - - -
237A GLN* 3.7 16.8 - - + +
238A LEU* 3.5 12.8 - - + +
240A LEU* 1.3 72.5 - - - +
242A SER* 1.3 57.3 + - - +
243A GLN 2.9 5.0 + - - -
244A LEU* 3.1 1.2 + - - -
245A CYS* 2.8 32.5 + - - +
248A ILE* 5.7 0.4 - - + -
298A LEU* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A LEU* 2.7 24.9 + - - +
239A ALA* 3.3 13.4 + - - -
241A ILE* 1.3 75.1 - - - +
243A GLN* 1.3 56.9 + - - +
244A LEU 3.5 0.2 - - - -
246A GLY 2.7 41.3 + - - +
247A SER* 4.3 5.8 - - - -
248A ILE* 3.9 20.5 - - - +
267A LEU* 5.1 7.3 - - - +
268A VAL* 5.0 13.9 + - - +
271A GLN* 3.1 17.6 - - - +
298A LEU* 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ALA* 3.1 15.2 + - - +
240A LEU* 3.2 25.5 - - - +
241A ILE 2.9 0.4 - - - -
242A SER* 1.3 80.4 - - - +
244A LEU* 1.3 57.2 + - - +
246A GLY 4.5 0.4 - - - -
268A VAL* 6.4 1.1 - - + -
271A GLN* 3.4 26.6 + - + +
272A LYS 4.4 0.3 - - - +
274A LYS* 4.3 12.5 - - - +
278A ARG* 4.7 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ILE* 4.7 7.4 - - + -
229A MET* 3.4 30.5 - - + -
240A LEU 3.2 11.8 + - - +
241A ILE 3.1 3.4 + - - +
243A GLN* 1.3 79.2 - - - +
245A CYS* 1.3 65.7 + - - +
246A GLY 3.6 1.1 - - - -
274A LYS* 3.0 29.4 + - - +
275A VAL* 3.1 32.8 + - + +
278A ARG* 3.4 54.3 - - + +
279A LEU* 5.6 7.6 - - + -
296A LEU* 4.7 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A TRP* 4.3 18.4 - - - -
229A MET* 4.7 1.8 - - - -
241A ILE* 2.8 16.9 + - - +
244A LEU* 1.3 97.0 - - - +
246A GLY* 1.3 59.6 + - - +
273A ARG* 3.1 22.0 + - + +
275A VAL* 4.1 12.6 - - + -
296A LEU* 3.8 24.7 - - - +
298A LEU* 3.2 35.7 - - + +
----------------------------------------------------------
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