Contacts of the helix formed by residues 223 - 237 (chain A) in PDB entry 3CNO
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 ASP 223 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ALA* 3.8 5.2 - - - +
215A LEU* 2.8 27.7 + - - +
216A LEU 4.3 5.3 - - - +
217A LYS* 3.9 33.5 + - + +
221A VAL 3.3 1.2 + - - -
222A PRO* 1.3 68.3 - - - +
224A ILE* 1.3 61.8 + - - +
225A GLU* 3.5 10.2 + - - +
226A ARG* 3.4 42.8 + - + +
227A ALA* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A PHE* 5.1 8.3 - - + -
203A SER 5.3 0.9 - - - +
206A PHE* 3.7 19.5 - - + +
207A GLU* 3.7 35.0 - - + +
210A ALA* 4.4 0.2 - - + -
222A PRO* 3.2 21.6 + - + +
223A ASP* 1.3 73.4 + - - +
225A GLU* 1.3 57.7 + - - +
227A ALA* 3.2 3.9 - - - +
228A LEU* 3.0 43.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A PHE* 6.4 0.9 - - + -
223A ASP* 3.3 7.5 + - - +
224A ILE* 1.3 76.8 - - - +
226A ARG* 1.3 65.7 + - - +
228A LEU* 3.3 12.4 + - + +
229A MET* 3.1 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A GLY 5.6 1.2 + - - -
215A LEU* 3.7 39.7 - - + +
216A LEU 5.2 6.7 + - - +
223A ASP* 3.4 34.3 + - + +
225A GLU* 1.3 73.6 - - - +
227A ALA* 1.3 57.6 + - - +
229A MET* 3.1 7.4 + - - +
230A LEU* 2.8 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A PHE* 4.0 25.8 - - + +
209A PHE* 3.5 14.6 - - + -
210A ALA* 4.0 6.3 - - + -
215A LEU* 3.5 12.0 - - - +
223A ASP 3.1 12.4 + - - +
224A ILE* 3.2 15.5 - - - +
226A ARG* 1.3 79.4 - - - +
228A LEU* 1.3 53.7 + - - +
230A LEU 3.3 0.2 + - - -
231A PHE* 2.8 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A VAL* 4.4 0.2 - - - +
182A GLN* 6.1 2.7 - - + -
185A PHE* 4.0 29.4 - - + -
202A PHE* 3.7 20.9 - - + -
206A PHE* 3.5 44.4 - - + -
224A ILE* 3.0 32.0 + - + +
225A GLU* 3.7 10.5 - - + +
227A ALA* 1.3 74.5 - - - +
229A MET* 1.3 72.2 + - + +
232A PHE* 3.1 41.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A VAL* 3.6 38.4 - - + +
177A GLU* 5.0 9.2 - - + +
179A ILE 5.8 0.4 - - - +
185A PHE* 3.4 33.9 - - + -
225A GLU* 3.1 33.7 + - + +
226A ARG* 3.4 11.4 - - - +
228A LEU* 1.3 79.0 - - + +
230A LEU* 1.3 57.5 + - - +
233A THR* 2.7 33.8 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
209A PHE* 4.1 13.7 - - + -
213A ARG* 4.0 26.0 - - + +
215A LEU* 4.2 20.9 - - + -
226A ARG 2.8 20.3 + - - +
227A ALA 3.9 2.2 - - - +
229A MET* 1.3 71.2 - - - +
231A PHE* 1.3 66.2 + - - +
233A THR* 3.4 10.6 + - + -
234A GLU* 2.9 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A PHE* 5.0 2.0 - + - -
192A PHE* 3.6 38.6 - + + -
205A PHE* 3.6 28.9 - + - -
206A PHE* 3.6 30.5 - + + -
209A PHE* 3.6 29.7 - + + -
227A ALA 2.8 21.5 + - - +
228A LEU 4.0 1.1 - - - +
230A LEU* 1.3 72.2 - - - +
232A PHE* 1.3 81.6 + + - +
234A GLU* 3.2 6.9 + - + +
235A VAL* 2.8 52.7 + - + +
240A ALA* 4.6 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU* 4.0 20.3 - - + +
170A LEU* 3.8 22.0 - - + -
176A VAL* 3.6 17.0 - - + -
185A PHE* 3.5 51.4 - + - -
188A ALA* 3.5 22.7 - - + -
189A PHE 3.7 5.4 - - - -
206A PHE* 3.9 19.5 - + - -
228A LEU* 3.1 31.0 + - + +
231A PHE* 1.3 97.6 - + - +
233A THR* 1.3 66.1 + - - +
235A VAL* 3.4 4.9 + - + +
236A ALA* 3.1 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A VAL* 3.6 18.8 - - - +
229A MET 2.7 24.4 + - - -
230A LEU* 3.4 11.9 - - + +
232A PHE* 1.3 75.9 - - - +
234A GLU* 1.3 63.0 + - + +
236A ALA* 3.5 4.9 + - - +
237A GLN* 3.1 47.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
209A PHE* 3.8 9.5 - - - -
213A ARG* 2.9 44.3 + - - -
230A LEU* 2.9 38.1 + - + +
231A PHE* 3.5 5.0 - - + +
233A THR* 1.3 74.4 - - + +
235A VAL* 1.3 64.3 + - - +
237A GLN* 3.3 6.4 + - - +
238A GLY 3.1 3.8 + - - -
239A LYS* 2.8 63.7 + - + +
240A ALA* 4.3 5.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ARG* 3.0 12.3 + - - -
170A LEU* 3.8 16.4 - - + +
192A PHE* 4.0 9.6 - - + -
231A PHE* 2.8 57.9 + - + +
232A PHE* 3.8 8.3 - - + +
234A GLU* 1.3 70.9 - - - +
236A ALA* 1.3 57.0 + - - +
238A GLY* 2.8 23.4 + - - -
240A ALA* 3.9 18.1 - - + +
241A GLY 5.5 0.3 - - - +
243A VAL* 5.9 0.9 - - + -
245A PHE* 3.5 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ARG* 3.1 21.1 + - - +
55A LYS* 4.8 6.1 + - - -
58A ILE* 3.9 3.1 - - - +
169A LEU 4.1 1.1 - - - +
170A LEU 3.2 14.4 + - - +
171A VAL 4.1 1.8 - - - +
172A GLY* 3.4 36.3 - - - +
232A PHE 3.1 17.0 + - - +
233A THR* 3.8 6.3 - - - +
235A VAL* 1.3 75.9 - - - +
237A GLN* 1.3 60.6 + - + +
238A GLY 3.2 0.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
58A ILE* 4.0 12.6 - - - +
233A THR* 3.1 36.7 + - + +
234A GLU* 3.8 5.9 - - - +
235A VAL 3.2 1.2 - - - -
236A ALA* 1.3 76.8 - - + +
238A GLY* 1.3 60.3 + - - +
239A LYS* 3.2 39.9 + - + +
501A GDP 4.7 10.3 + - - +
----------------------------------------------------------
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