Contacts of the helix formed by residues 252 - 263 (chain D) in PDB entry 1ZKK
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 ILE 252 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C LEU* 3.6 31.0 - - + +
223C ILE 3.7 2.9 - - - -
224C ASP* 3.4 52.7 - - + +
251D GLU* 1.3 83.1 - - + +
253D THR* 1.3 75.1 + - + +
255D ALA* 3.3 7.4 + - + +
256D LYS* 3.0 38.6 + - + +
274D TYR* 5.7 0.7 - - + -
280D LYS* 5.4 2.0 - - - +
281D THR* 3.5 28.7 + - + +
282D TYR* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D GLU* 2.8 36.1 + - - +
252D ILE* 1.3 81.3 - - + +
254D ASP* 1.3 61.4 + - - +
256D LYS* 3.4 9.2 + - + +
257D LYS* 3.1 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D ILE* 3.6 15.1 - - + +
251D GLU* 2.9 20.9 + - - +
253D THR* 1.3 75.6 + - - +
255D ALA* 1.3 59.0 + - - +
257D LYS* 3.2 11.5 + - - +
258D ARG* 2.8 71.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D ILE* 3.6 20.1 - - + +
251D GLU 3.0 17.5 + - - +
252D ILE* 3.3 8.5 + - + +
254D ASP* 1.3 76.5 - - - +
256D LYS* 1.3 57.3 + - + +
258D ARG 3.3 0.9 + - - -
259D GLU* 2.8 35.2 + - - +
272D MET* 3.6 5.2 - - + +
274D TYR* 3.8 29.6 - - + +
283D CYS* 4.0 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ASP* 2.8 35.2 + - - -
222C LEU* 2.8 39.0 + - + +
223C ILE* 5.4 0.2 - - - +
252D ILE* 3.0 40.9 + - + +
253D THR* 3.7 7.9 - - + +
255D ALA* 1.3 74.8 - - + +
257D LYS* 1.3 66.4 + - - +
259D GLU* 3.4 10.6 + - - +
260D ALA* 3.2 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D THR* 3.1 19.2 + - - +
254D ASP* 3.2 17.7 + - - +
256D LYS* 1.3 80.1 - - - +
258D ARG* 1.3 61.4 + - + +
260D ALA* 3.3 15.3 + - - +
261D LEU* 3.2 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248D ASP* 3.2 32.7 + - - +
250D ILE* 3.7 22.8 - - - +
254D ASP* 2.8 44.3 + - - +
255D ALA 3.7 3.1 - - - +
257D LYS* 1.3 73.9 - - + +
259D GLU* 1.3 59.2 + - - +
261D LEU* 3.1 12.6 + - + +
262D TYR* 2.8 57.8 + - + +
272D MET* 4.2 3.6 - - + -
285D ASP* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C LEU* 4.4 3.5 - - - +
255D ALA 2.8 20.1 + - - +
256D LYS* 3.6 9.9 - - - +
258D ARG* 1.3 73.2 - - - +
260D ALA* 1.3 57.4 + - - +
262D TYR* 3.3 8.9 + - - +
263D ALA* 2.9 31.9 + - - +
272D MET* 3.6 13.2 - - - +
274D TYR* 2.5 34.7 + - - +
17H ARG* 4.4 13.2 + - - +
19H ARG* 2.9 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D LYS 3.2 10.1 + - - +
257D LYS* 3.7 20.2 - - - +
258D ARG 3.2 0.2 - - - -
259D GLU* 1.3 80.4 - - - +
261D LEU* 1.3 62.1 + - + +
263D ALA* 3.8 10.4 + - - +
264D GLN* 3.2 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D LYS* 3.2 23.1 + - + +
258D ARG* 3.1 13.3 + - + +
260D ALA* 1.3 76.3 - - + +
262D TYR* 1.3 70.3 + - + +
264D GLN* 3.1 36.5 + - - +
265D ASP* 4.0 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D ARG* 2.8 41.4 + - + +
259D GLU 3.8 1.8 - - - +
261D LEU* 1.3 76.3 - - + +
263D ALA* 1.3 57.5 + - - +
264D GLN 3.0 0.2 - - - -
265D ASP* 2.9 32.9 + - - +
268D THR* 3.4 20.3 + - + -
272D MET* 3.7 24.5 - - - -
285D ASP* 2.6 29.0 + - - -
287D THR* 3.3 32.8 - - + -
17H ARG* 3.5 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259D GLU 2.9 18.3 + - - +
260D ALA* 3.9 9.9 - - - +
261D LEU 3.2 0.6 - - - -
262D TYR* 1.3 76.6 - - - +
264D GLN* 1.3 59.5 + - + +
265D ASP 3.2 3.0 + - - -
266D PRO* 5.1 1.0 - - - +
17H ARG* 3.8 20.8 - - + +
----------------------------------------------------------
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