Contacts of the helix formed by residues 227 - 243 (chain A) in PDB entry 3P2Y
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 SER 227 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A GLU* 1.3 61.6 + - - +
229A ALA 3.8 0.4 - - - -
230A GLU* 4.0 16.5 - - - +
231A ARG* 2.9 35.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
227A SER* 1.3 80.9 - - - +
229A ALA* 1.3 62.3 + - + +
231A ARG* 3.4 10.7 + - - +
232A ALA* 3.5 10.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
228A GLU* 1.3 75.1 - - - +
230A GLU* 1.3 63.7 + - - +
232A ALA* 3.7 9.3 + - - +
233A GLN* 3.3 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A SER* 4.0 21.0 - - - +
228A GLU 3.2 0.4 - - - -
229A ALA* 1.3 76.4 - - - +
231A ARG* 1.3 58.9 + - - +
232A ALA 3.2 0.2 - - - -
233A GLN* 3.1 8.2 + - - +
234A GLN* 3.0 29.1 + - - +
----------------------------------------------------------
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 SER 2.9 21.2 + - - +
228A GLU* 3.4 7.1 + - - +
230A GLU* 1.3 75.2 - - - +
232A ALA* 1.3 57.3 + - - +
234A GLN* 3.4 13.3 + - - +
235A GLN* 3.0 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A GLU 3.5 9.3 + - - +
229A ALA* 3.9 11.0 - - - +
230A GLU 3.2 0.6 - - - -
231A ARG* 1.3 75.8 - - - +
233A GLN* 1.3 60.7 + - - +
235A GLN* 3.8 12.2 - - - +
236A GLN* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ALA 3.3 12.0 + - - +
230A GLU* 3.1 12.2 + - - +
232A ALA* 1.3 78.6 - - - +
234A GLN* 1.3 53.7 + - - +
236A GLN* 3.5 6.5 + - - +
237A ALA* 2.8 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A TYR* 4.5 11.2 + - - -
194A VAL* 6.1 1.4 - - - +
212A LEU* 3.8 28.3 - - + +
213A GLY 5.8 0.2 - - - +
230A GLU 3.0 12.2 + - - +
231A ARG* 3.4 16.0 + - - +
233A GLN* 1.3 74.4 - - - +
235A GLN* 1.3 55.9 + - + +
237A ALA* 3.0 8.4 + - - +
238A LEU* 2.8 34.5 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
231A ARG* 3.0 30.2 + - - +
232A ALA* 3.5 10.6 + - - +
234A GLN* 1.3 76.8 - - + +
236A GLN* 1.3 58.5 + - - +
238A LEU* 3.3 8.8 + - - +
239A GLU* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ALA 2.9 18.7 + - - +
233A GLN* 3.7 6.7 - - - +
235A GLN* 1.3 74.7 - - - +
237A ALA* 1.3 58.8 + - - +
239A GLU* 3.4 27.7 + - - +
240A ASP* 2.9 64.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A LEU* 3.9 31.0 - - + +
233A GLN 2.8 19.7 + - - +
234A GLN* 3.0 8.7 + - - +
236A GLN* 1.3 73.5 - - - +
238A LEU* 1.3 60.8 + - - +
240A ASP* 3.4 8.6 + - - +
241A ALA* 2.9 28.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
169A LEU* 4.0 24.9 - - + -
192A TYR* 4.4 23.1 - - + +
210A LEU* 4.1 18.4 - - + -
212A LEU* 3.9 16.5 - - + +
234A GLN 2.8 16.0 + - - +
235A GLN* 3.6 10.5 - - + +
237A ALA* 1.3 69.5 - - - +
239A GLU* 1.3 65.9 + - - +
241A ALA* 3.1 2.4 + - - +
242A ILE* 3.0 40.8 + - + +
262A LEU* 3.7 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A GLN 2.9 18.6 + - - +
236A GLN* 3.4 31.5 + - - +
238A LEU* 1.3 78.6 - - - +
240A ASP* 1.3 63.3 + - - +
242A ILE* 3.3 12.1 + - - +
243A THR* 3.4 18.4 + - + +
264A THR* 2.7 30.9 + - + +
266A ALA* 3.7 21.2 - - - +
267A ALA* 3.7 28.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A GLN* 2.9 48.7 + - - +
237A ALA* 3.7 7.5 - - - +
239A GLU* 1.3 73.6 - - - +
241A ALA* 1.3 65.5 + - - +
243A THR* 2.7 29.6 + - - +
244A LYS* 3.8 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LEU* 5.4 0.4 - - + -
210A LEU* 4.2 34.3 - - + -
212A LEU* 5.0 0.7 - - + -
237A ALA 2.9 18.2 + - - +
238A LEU* 3.1 5.8 + - + +
240A ASP* 1.3 76.1 - - - +
242A ILE* 1.3 65.5 + - + +
244A LYS* 3.0 19.5 + - - +
245A PHE* 3.2 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LEU* 3.8 24.0 - - + -
169A LEU* 4.0 9.4 - - + -
238A LEU* 3.0 28.4 + - + +
239A GLU* 3.7 7.2 - - - +
240A ASP 3.3 0.2 - - - -
241A ALA* 1.3 76.4 - - - +
243A THR* 1.3 63.0 + - - +
244A LYS 2.9 1.9 + - - -
245A PHE* 3.1 16.2 + - - +
248A VAL* 4.1 10.5 - - + +
262A LEU 3.5 24.9 - - - +
263A VAL* 3.9 18.8 - - + -
267A ALA* 4.0 25.6 - - + +
271A MET* 3.6 28.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLU* 3.4 18.2 - - + +
240A ASP* 2.7 21.8 + - - +
241A ALA 3.2 0.2 - - - -
242A ILE* 1.3 76.6 - - - +
244A LYS* 1.3 71.1 + - - +
245A PHE 3.3 1.6 + - - +
266A ALA 4.7 1.1 - - - +
267A ALA* 3.7 19.1 - - - +
270A GLY* 3.4 25.6 - - - +
271A MET* 3.6 24.3 - - - -
272A GLN* 4.2 9.0 + - - +
----------------------------------------------------------
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