Contacts of the helix formed by residues 265 - 274 (chain E) 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 VAL 265 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E ASP* 3.3 18.0 + - - +
228E LEU* 3.9 23.1 - - + -
229E ASP 5.6 0.9 - - - +
230E ALA* 5.6 0.7 - - - +
232E THR* 4.0 14.8 - - - +
233E GLY 3.5 28.7 - - - +
234E GLN* 4.3 7.9 - - - +
236E GLY* 4.3 4.9 - - - -
237E LEU* 3.8 22.4 - - + +
263E GLY* 3.1 6.5 + - - +
264E GLY* 1.3 74.1 - - - +
266E LEU* 1.3 66.1 + - - +
267E ILE 3.1 0.2 - - - -
268E PRO* 3.3 15.7 - - + +
269E ILE* 3.2 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 266 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E LEU* 5.0 0.4 - - - -
228E LEU* 4.0 14.4 - - + -
252E VAL* 3.9 24.2 - - + -
254E VAL* 3.9 27.4 - - + -
263E GLY 2.9 13.7 + - - +
265E VAL* 1.3 80.0 - - - +
267E ILE* 1.3 55.3 + - + +
269E ILE* 3.6 8.9 - - + +
270E VAL* 2.8 41.7 + - + +
277E ILE* 3.7 40.4 - - + -
292E PHE* 4.5 2.7 - - + -
297E PHE* 3.8 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 267 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E VAL* 4.0 25.6 - - + -
48E ALA* 4.2 3.1 - - + -
52E ILE* 4.3 12.6 - - + -
72E LEU* 4.5 18.2 - - + -
75E MET* 4.4 7.9 - - + +
76E LEU* 3.6 38.8 - - + -
264E GLY* 3.0 15.1 + - - +
266E LEU* 1.3 77.6 - - - +
268E PRO* 1.4 67.7 - - + +
270E VAL* 3.8 1.7 - - - +
271E ARG* 2.9 48.7 + - + +
297E PHE* 4.3 10.5 - - + -
298E VAL* 5.8 0.7 - - + -
301E LEU* 4.7 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 268 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E VAL 3.4 20.9 - - - +
47E SER* 5.0 7.0 - - - +
48E ALA* 4.0 16.6 - - + -
234E GLN* 5.0 4.9 - - - +
237E LEU* 3.8 18.7 - - + +
264E GLY 3.3 10.5 - - - +
265E VAL* 3.3 23.6 - - + +
267E ILE* 1.4 96.3 - - + +
269E ILE* 1.3 54.9 + - - -
271E ARG* 3.7 7.1 - - + +
272E THR* 2.8 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 269 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E LEU* 5.5 0.4 - - + -
228E LEU* 3.7 27.4 - - + -
236E GLY 3.5 25.4 - - - +
237E LEU* 3.7 26.5 - - + +
240E ALA* 3.8 22.2 - - + -
252E VAL* 4.8 16.8 - - + -
265E VAL* 3.2 20.5 + - + +
266E LEU* 3.6 8.7 - - + +
267E ILE 3.2 0.8 - - - -
268E PRO* 1.3 76.6 - - - +
270E VAL* 1.3 63.2 + - + +
272E THR* 3.4 0.3 + - - -
273E LEU* 2.9 36.5 + - + +
275E VAL* 4.9 5.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 270 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E MET* 3.9 26.3 - - + +
76E LEU* 4.2 18.6 - - + +
252E VAL* 6.4 0.4 - - + -
266E LEU* 2.8 23.5 + - + +
267E ILE 4.0 2.0 - - - +
269E ILE* 1.3 75.0 - - + +
271E ARG* 1.3 65.0 + - - +
274E LYS* 3.2 25.4 + - - +
275E VAL 3.5 27.6 - - - +
276E PRO* 5.9 0.7 - - + -
277E ILE* 3.5 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 271 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E ALA* 4.3 19.1 + - - +
51E GLU* 2.6 36.8 + - - +
52E ILE* 5.1 2.2 - - - +
55E GLU* 3.3 24.2 + - - -
71E LYS* 4.2 10.5 - - - +
75E MET* 3.6 38.3 - - + +
267E ILE* 2.9 32.1 + - - +
268E PRO* 3.8 5.8 - - + +
270E VAL* 1.3 77.1 - - - +
272E THR* 1.3 64.1 + - - +
274E LYS* 3.8 18.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 272 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237E LEU* 4.0 13.7 - - + +
241E LYS* 4.5 19.1 - - + -
268E PRO* 2.8 22.5 + - - +
269E ILE 4.0 1.3 - - - -
271E ARG* 1.3 81.0 - - - +
273E LEU* 1.3 75.1 + - + +
274E LYS* 3.6 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 273 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237E LEU* 4.7 4.7 - - + -
240E ALA* 3.6 42.6 - - + +
241E LYS* 3.7 20.2 - - + +
244E HIS* 3.6 35.2 + - + -
249E LEU* 5.6 0.9 - - + -
269E ILE* 2.9 17.2 + - + +
272E THR* 1.3 85.9 - - + +
274E LYS* 1.3 76.2 + - - +
275E VAL* 3.3 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 274 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269E ILE 3.9 0.4 + - - -
270E VAL* 3.2 22.5 + - - +
271E ARG 3.8 20.4 + - - +
272E THR 4.1 7.6 - - - +
273E LEU* 1.3 83.0 - - - +
275E VAL* 1.3 60.3 + - - +
276E PRO* 3.9 5.9 - - - +
----------------------------------------------------------
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