Contacts of the helix formed by residues 226 - 237 (chain A) in PDB entry 1TKK
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 226 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A PRO* 3.7 18.4 - - - +
222A VAL* 3.6 12.1 - - + +
223A HIS* 3.2 27.3 + - + +
224A LYS 4.8 0.2 - - - -
225A ASP* 1.3 74.4 - - - +
227A LEU* 1.3 57.8 + - - +
228A ALA* 3.9 2.3 + - - +
229A GLY* 3.1 23.5 + - - -
230A LEU* 3.0 23.8 + - - +
246A SER* 5.7 0.2 - - - -
260E ARG* 3.5 17.9 + - - -
288E CYS 5.1 8.9 - - - +
251F ARG* 5.2 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LYS 3.8 20.2 - - - +
225A ASP* 3.2 10.6 + - - +
226A ASP* 1.3 71.9 - - - +
228A ALA* 1.3 66.4 + - - +
230A LEU* 3.1 8.5 + - + +
231A LYS* 3.0 19.8 + - - +
246A SER* 4.2 18.6 - - - +
255A GLU* 4.1 31.6 - - + +
256A VAL* 4.6 15.9 - - + -
259A THR* 5.3 5.2 - - + +
261A SER* 3.5 21.1 + - - +
251F ARG* 5.3 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ASP* 3.3 1.5 + - - +
227A LEU* 1.3 77.7 - - - +
229A GLY* 1.3 56.8 + - - +
231A LYS* 3.4 10.6 - - - +
232A LYS* 3.1 23.2 + - - +
260E ARG* 3.4 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A PRO* 3.9 8.8 - - - +
222A VAL* 4.1 5.8 - - - -
226A ASP* 3.1 23.0 + - - -
227A LEU 3.1 0.6 - - - -
228A ALA* 1.3 76.0 - - - +
230A LEU* 1.3 62.5 + - - +
231A LYS 3.3 0.4 - - - -
232A LYS* 3.2 5.1 + - - +
233A VAL* 3.2 29.0 + - - +
260E ARG* 3.4 16.1 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
220A GLN* 4.1 13.2 - - - +
221A PRO* 3.6 33.0 - - + -
222A VAL* 3.6 8.4 - - + +
226A ASP 3.0 13.5 + - - +
227A LEU* 3.1 12.1 + - + +
229A GLY* 1.3 72.7 - - - +
231A LYS* 1.3 65.1 + - - +
232A LYS 3.4 0.2 + - - -
233A VAL* 3.5 4.7 + - - +
234A THR* 3.0 25.6 + - - -
241A ILE* 3.8 13.7 - - + -
243A ALA* 4.0 25.4 - - + -
246A SER* 3.9 22.7 - - - +
256A VAL* 5.1 3.1 - - + -
261A SER* 3.3 21.3 - - - +
262A ALA* 4.3 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU 3.0 11.5 + - - +
228A ALA* 3.4 14.6 - - - +
230A LEU* 1.3 76.9 - - - +
232A LYS* 1.3 51.9 + - - +
234A THR* 3.2 2.5 + - - -
235A ASP* 2.7 61.0 + - - +
259A THR* 2.9 32.5 + - - +
260A ARG* 3.2 21.3 + - - +
261A SER* 3.4 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A PRO* 3.4 28.5 - - + +
199A LYS* 4.8 14.1 - - + +
202A VAL* 4.9 7.6 - - + -
228A ALA 3.1 12.1 + - - +
229A GLY 3.2 8.0 + - - +
231A LYS* 1.3 75.8 - - - +
233A VAL* 1.3 65.4 + - - +
235A ASP* 3.9 4.6 - - - +
236A ALA* 3.0 32.0 + - + +
234E THR* 5.8 3.5 - - - +
235E ASP* 4.3 20.5 + - - +
260E ARG* 3.2 33.1 + - - +
263E ASP* 4.7 10.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A PRO* 3.9 17.9 - - + +
201A ALA* 3.9 11.2 - - + -
202A VAL* 3.8 10.8 - - + -
205A ILE* 3.8 29.6 - - + -
221A PRO* 4.0 15.9 - - + -
222A VAL* 3.8 22.7 - - + -
229A GLY 3.2 15.6 + - - +
230A LEU 3.9 4.3 - - - +
232A LYS* 1.3 73.8 - - - +
234A THR* 1.3 58.1 + - - +
236A ALA 3.2 1.4 + - - -
237A THR* 2.8 40.3 + - + +
241A ILE* 4.1 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LEU 3.0 14.7 + - - -
231A LYS 3.3 4.7 - - - -
233A VAL* 1.3 76.5 - - - +
235A ASP* 1.3 69.5 + - - +
236A ALA 3.6 0.2 + - - -
237A THR 3.8 1.0 - - - +
241A ILE* 3.2 23.1 - - - +
260A ARG 4.2 6.3 - - - +
261A SER 2.9 25.1 + - - +
262A ALA* 3.5 9.6 - - - -
263A ASP* 3.7 22.9 - - - +
199G LYS* 2.7 35.7 + - + +
232G LYS* 4.5 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LYS* 2.7 53.3 + - - +
232A LYS* 4.0 4.9 - - - +
234A THR* 1.3 80.7 - - - +
236A ALA* 1.3 60.4 + - + +
237A THR 3.7 4.0 + - - +
260A ARG 4.4 1.6 - - - +
199G LYS* 5.8 0.2 - - - +
206G ARG* 5.9 1.9 + - - -
232G LYS* 3.1 34.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
202A VAL* 3.9 22.7 - - + -
206A ARG* 3.2 31.2 + - - +
232A LYS* 3.0 21.6 + - + +
235A ASP* 1.3 76.4 - - + +
237A THR* 1.3 61.9 + - - +
206G ARG* 5.9 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A VAL* 4.2 15.7 - - + +
205A ILE* 3.8 26.7 - - + -
206A ARG* 4.8 2.5 - - + +
209A GLU* 3.6 12.1 - - - +
233A VAL* 2.8 33.3 + - + +
234A THR 3.8 1.2 - - - +
235A ASP 3.4 4.2 - - - +
236A ALA* 1.3 83.9 - - - +
238A ASP* 1.3 67.4 + - - +
239A THR 3.4 7.2 + - - -
241A ILE* 4.1 4.2 - - - +
199G LYS* 3.3 32.7 + - - +
206G ARG* 5.9 0.2 + - - -
----------------------------------------------------------
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