Contacts of the helix formed by residues 254 - 264 (chain A) in PDB entry 2CNW
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 GLY 254 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ALA 3.0 23.8 + - - -
42A ASP* 3.8 7.9 - - - +
43A VAL* 3.7 19.1 - - - +
252A ARG 3.6 1.0 - - - -
253A GLY* 1.3 72.7 - - - +
255A ALA* 1.3 60.6 + - - +
256A ALA 3.1 5.6 - - - -
257A LEU* 3.1 16.2 + - - +
258A SER* 3.4 12.1 + - - -
291A ILE* 4.1 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASP* 3.8 5.8 + - - +
218A LEU* 3.6 11.3 - - + +
219A ASP 4.7 3.8 - - - +
220A ALA 4.8 4.3 - - - +
222A THR* 3.4 33.9 + - - +
223A GLY 4.4 0.4 - - - +
226A ALA* 3.5 25.4 - - + +
244A LEU* 5.6 1.3 - - + -
253A GLY 3.1 1.0 - - - +
254A GLY* 1.3 73.1 - - - +
256A ALA* 1.3 59.1 + - - +
257A LEU 3.3 0.2 - - - -
258A SER* 3.6 6.2 - - - -
259A ALA* 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 4.0 2.9 - - + +
218A LEU* 4.3 9.1 - - - +
242A LEU* 5.4 1.3 - - + -
244A LEU* 3.8 20.1 - - + +
253A GLY 3.1 14.4 + - - +
254A GLY 3.1 0.4 - - - -
255A ALA* 1.3 77.9 - - - +
257A LEU* 1.3 57.9 + - - +
259A ALA* 3.9 2.5 - - - +
260A ARG* 3.1 32.6 + - - +
267A ILE* 3.9 15.8 - - + +
287A LEU* 3.6 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 5.2 3.1 - - + -
43A VAL* 3.9 27.1 - - + -
47A VAL* 3.9 13.2 - - + -
51A PHE* 4.4 19.3 - - + -
82A LEU* 3.8 24.5 - - + -
85A ALA* 3.6 40.6 - - + +
86A LEU* 3.8 13.7 - - + +
253A GLY 4.4 0.4 + - - -
254A GLY 3.1 10.5 + - - +
256A ALA* 1.3 77.4 - - - +
258A SER* 1.3 54.7 + - - +
260A ARG* 3.3 1.4 + - - -
261A HIS* 2.7 43.7 + - + +
291A ILE* 5.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASP 4.3 0.5 + - - -
43A VAL* 4.0 0.9 - - - +
44A ASN* 3.0 36.6 + - - +
47A VAL* 3.9 14.5 - - - +
223A GLY 5.4 0.3 + - - -
226A ALA* 4.1 4.7 - - - +
227A LEU* 3.8 25.3 - - - -
254A GLY 3.4 7.9 + - - -
255A ALA* 3.6 10.1 - - - -
257A LEU* 1.3 78.4 - - - +
259A ALA* 1.3 62.2 + - - +
261A HIS* 3.4 1.7 + - - +
262A VAL* 3.3 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A LEU* 5.1 0.2 - - + -
218A LEU* 4.0 9.0 - - + -
226A ALA 4.9 2.6 + - - +
230A ALA* 3.8 25.1 - - + -
242A LEU* 3.6 30.5 - - + -
255A ALA 3.0 17.6 + - - +
256A ALA 3.9 2.2 - - - +
258A SER* 1.3 76.7 - - - +
260A ARG* 1.3 53.4 + - - +
262A VAL* 3.7 0.2 - - - +
263A THR* 2.7 41.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU 4.7 3.4 + - - -
85A ALA* 3.1 28.9 + - - +
86A LEU* 3.4 18.4 - - - +
87A GLY* 3.6 23.1 - - - +
91A ARG* 4.7 4.8 - - - +
242A LEU* 5.6 1.1 - - + -
256A ALA 3.1 14.1 + - - +
257A LEU* 3.8 2.2 - - - +
259A ALA* 1.3 75.6 - - - +
261A HIS* 1.3 60.5 + - - +
263A THR* 4.0 4.9 - - - -
264A GLY* 2.6 50.8 + - - +
265A LYS 2.7 46.1 + - - +
266A PRO* 3.3 12.3 - - - +
267A ILE* 3.7 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLU 5.7 0.2 - - - -
47A VAL* 3.7 36.4 - - + +
50A ASP* 3.5 39.3 + - + +
51A PHE* 5.4 1.1 - - - +
85A ALA 5.3 0.4 + - - -
227A LEU* 5.4 2.2 - - + -
257A LEU* 2.7 27.4 + - + +
258A SER 3.7 4.7 - - - +
259A ALA 3.4 0.2 - - - -
260A ARG* 1.3 75.0 - - - +
262A VAL* 1.3 64.8 + - + +
264A GLY* 4.5 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU* 3.8 28.5 - - + +
230A ALA* 4.0 2.9 - - + -
231A ARG* 3.8 48.1 - - + +
234A ASP* 4.9 2.4 - - - +
258A SER 3.3 15.4 + - - +
259A ALA 3.7 5.2 - - - +
261A HIS* 1.3 84.0 - - + +
263A THR* 1.3 72.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A LEU* 5.8 0.9 - - + -
230A ALA* 3.8 26.7 - - + +
231A ARG* 4.5 1.1 - - - +
234A ASP* 4.1 20.5 - - + +
239A VAL* 5.7 3.1 - - + -
242A LEU* 4.2 6.9 - - + +
259A ALA 2.7 24.2 + - - +
260A ARG* 4.0 0.3 - - - -
262A VAL* 1.3 92.9 - - + +
264A GLY* 1.3 60.9 + - - +
265A LYS* 3.2 43.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ARG* 2.6 43.1 + - - -
261A HIS 4.5 1.4 + - - -
262A VAL 3.8 0.4 - - - -
263A THR* 1.3 69.9 + - - +
265A LYS* 1.3 62.2 + - - +
266A PRO* 4.0 1.9 - - - +
----------------------------------------------------------
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