Contacts of the helix formed by residues 226 - 238 (chain A) in PDB entry 1X1O
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 PRO 226 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ASN 3.7 6.3 - - - +
225A PHE* 1.3 84.7 - - + +
227A LEU* 1.3 67.8 + - - +
228A GLU* 4.0 12.8 - - + +
229A ALA* 3.0 24.7 + - + +
230A LEU* 2.9 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A PHE 3.6 1.6 + - - -
226A PRO* 1.3 71.7 - - - +
228A GLU* 1.3 75.8 + - - +
230A LEU* 3.1 12.6 + - + +
231A ARG* 3.0 61.2 + - - +
256A ALA* 4.0 41.3 - - + +
260A ALA* 4.4 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A PRO* 3.2 12.7 + - + +
227A LEU* 1.3 92.4 + - - +
229A ALA* 1.3 63.0 + - - +
231A ARG* 3.4 17.8 + - - +
232A GLU* 3.2 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU* 3.9 15.3 - - + +
225A PHE* 3.6 20.6 - - + -
226A PRO* 3.0 27.6 + - + +
228A GLU* 1.3 76.8 - - - +
230A LEU* 1.3 61.1 + - - +
232A GLU* 3.1 8.3 + - - +
233A ALA* 2.8 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LEU* 3.4 33.0 - - + +
225A PHE* 3.6 37.2 - - + +
226A PRO 2.9 7.0 + - - +
227A LEU* 3.1 18.6 + - + +
229A ALA* 1.3 75.9 - - - +
231A ARG* 1.3 63.8 + - - +
233A ALA* 3.1 5.0 + - - +
234A VAL* 3.0 27.1 + - - +
245A ALA* 4.4 7.4 - - + -
249A MET* 5.9 2.2 - - + -
253A ARG 5.5 0.4 - - - +
256A ALA* 6.0 0.2 - - + -
257A ALA* 3.6 36.3 - - + +
260A ALA* 4.5 7.0 - - + -
262A VAL* 4.3 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU* 3.0 59.3 + - + +
228A GLU* 3.6 18.5 + - - +
230A LEU* 1.3 76.6 - - - +
232A GLU* 1.3 62.9 - - - +
234A VAL* 3.3 6.9 + - - +
235A ARG* 3.0 23.1 + - - +
260A ALA* 4.1 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU* 3.6 27.8 - - + -
228A GLU 3.2 10.5 + - - +
229A ALA* 3.1 8.9 + - - +
231A ARG* 1.3 75.9 - - - +
233A ALA* 1.3 64.9 + - - +
235A ARG* 2.7 43.0 + - - +
236A ARG* 3.0 52.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU* 4.0 5.8 - - + +
209A LEU* 3.7 25.8 - - + -
222A LEU* 3.8 25.6 - - + -
225A PHE* 4.2 5.6 - - + -
229A ALA 2.8 16.8 + - - +
230A LEU 3.4 8.5 - - - +
232A GLU* 1.3 74.6 - - - +
234A VAL* 1.3 63.8 + - - +
236A ARG* 3.4 0.9 + - - +
237A VAL* 3.0 31.0 + - - +
243A LEU* 4.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LEU* 5.4 0.2 - - + -
230A LEU 3.0 13.4 + - - +
231A ARG 3.3 6.9 + - - +
233A ALA* 1.3 77.9 - - + +
235A ARG* 1.3 64.4 + - - +
237A VAL* 4.0 1.6 - - - +
238A GLY* 3.0 20.3 + - - -
239A GLY 4.6 1.6 + - - +
243A LEU* 3.8 16.1 - - + +
260A ALA* 3.6 26.5 - - + +
261A GLY* 3.8 28.5 - - - +
262A VAL* 3.9 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ARG 3.0 13.6 + - - +
232A GLU* 2.7 42.8 + - - +
234A VAL* 1.3 78.4 - - - +
236A ARG* 1.3 76.3 - - - +
238A GLY* 3.2 14.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU* 3.6 40.6 + - - +
207A GLU* 5.1 4.9 + - - -
209A LEU* 4.6 11.0 - - + -
210A GLU* 3.1 40.5 + - - +
213A LEU* 5.3 0.9 - - + -
232A GLU* 3.0 46.3 + - - +
233A ALA* 3.7 3.6 - - - +
235A ARG* 1.3 89.8 - - - +
237A VAL* 1.3 64.4 + - + +
238A GLY* 3.1 1.6 + - - -
240A ARG* 3.0 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 4.0 20.0 - - + -
213A LEU* 4.1 11.2 - - + -
233A ALA 3.0 17.3 + - - +
234A VAL 4.0 1.3 - - - +
236A ARG* 1.3 75.3 - - - +
238A GLY* 1.3 63.4 + - - +
239A GLY* 3.8 4.0 - - - +
240A ARG* 2.9 47.2 + - + +
241A VAL* 3.4 35.4 - - + +
243A LEU* 3.6 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A VAL 3.0 13.3 + - - -
235A ARG 3.2 10.5 + - - -
236A ARG 3.1 3.7 - - - -
237A VAL* 1.3 76.8 - - - +
239A GLY* 1.3 59.2 + - - +
240A ARG* 3.3 4.3 + - - +
----------------------------------------------------------
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