Contacts of the helix formed by residues 249 - 259 (chain D) 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 THR 249 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D MET* 4.2 21.3 - - + -
247D VAL* 4.1 0.9 - - - +
248D PHE* 1.3 89.2 - - + +
250D PRO* 1.3 75.7 - - + +
251D ARG* 3.6 10.4 + - - +
252D GLN* 3.1 31.8 + - - +
253D ALA* 3.0 21.8 + - - +
272D ALA* 5.1 0.9 - - - +
281D ILE* 3.8 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C ALA* 4.2 11.0 - - + -
248D PHE 4.6 0.2 - - - +
249D THR* 1.3 85.8 - - + +
251D ARG* 1.3 56.9 + - - +
253D ALA* 3.0 4.8 + - + +
254D PHE* 2.8 26.2 + - - +
272D ALA 5.4 2.9 - - - +
277D GLY* 3.8 23.3 - - - +
280D LYS* 3.8 32.1 - - + -
281D ILE* 3.6 12.1 - - + -
284D MET* 3.5 27.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C ARG* 4.5 18.4 - - - +
287C ALA* 3.7 27.8 - - + +
288C CYS* 5.6 4.9 - - - +
249D THR* 3.3 8.8 + - - +
250D PRO* 1.3 77.0 - - - +
252D GLN* 1.3 64.3 + - + +
254D PHE* 3.3 23.7 + - - +
255D GLU* 3.3 34.5 + - - +
223E HIS* 5.5 5.7 - - - +
225E ASP* 3.5 48.8 + - + +
226E ASP* 4.6 4.6 - - - +
227E LEU 5.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D GLU 5.5 0.8 + - - -
246D SER 3.9 20.3 + - - +
247D VAL* 4.2 5.4 - - - -
248D PHE* 2.9 39.4 + - - +
249D THR* 3.1 25.1 + - - +
251D ARG* 1.3 75.6 - - + +
253D ALA* 1.3 64.9 + - - +
255D GLU* 3.5 6.5 + - - +
256D VAL* 3.2 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D VAL* 3.7 23.4 - - + +
249D THR 3.0 13.1 + - - +
250D PRO 3.4 7.4 - - - +
252D GLN* 1.3 73.7 - - - +
254D PHE* 1.3 67.7 + - - +
256D VAL* 3.0 2.8 + - - +
257D LEU* 2.9 32.3 + - + +
265D ILE* 4.3 9.2 - - + -
281D ILE* 3.9 22.7 - - + -
284D MET* 4.3 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C PHE* 3.3 47.0 - + - -
257C LEU* 3.9 13.0 - - + -
258C GLN* 3.6 38.4 - - + -
284C MET* 5.0 3.1 - - + -
287C ALA* 6.0 0.2 - - + -
288C CYS* 3.8 31.9 - - - -
250D PRO 2.8 12.7 + - - +
251D ARG* 3.5 25.1 - - - +
252D GLN 3.3 0.2 - - - -
253D ALA* 1.3 77.7 - - - +
255D GLU* 1.3 61.6 + - - +
257D LEU 3.4 0.2 + - - -
258D GLN* 2.8 39.5 + - + +
284D MET* 3.7 22.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D LEU* 3.4 31.1 - - + +
251D ARG* 3.3 28.7 + - - +
252D GLN* 3.8 9.0 - - - +
253D ALA 3.2 0.4 - - - -
254D PHE* 1.3 79.2 - - - +
256D VAL* 1.3 63.6 + - - +
258D GLN* 3.2 23.7 - - - +
259D THR* 3.0 33.7 + - + +
255E GLU* 5.2 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D LEU* 3.3 28.3 - - + -
230D LEU* 4.9 1.1 - - + -
243D ALA* 4.6 4.0 - - + -
246D SER* 4.9 7.6 - - - +
247D VAL* 3.6 24.5 - - + -
252D GLN 3.2 15.2 + - - +
253D ALA* 3.0 8.5 + - - +
255D GLU* 1.3 76.2 - - - +
257D LEU* 1.3 60.9 + - + +
259D THR* 3.5 4.0 + - - -
260D ARG* 3.0 23.0 + - - -
261D SER* 3.0 13.4 + - - -
262D ALA* 3.9 32.2 + - + +
265D ILE* 4.9 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C PHE* 3.9 6.7 - - + -
253D ALA* 2.9 26.3 + - + +
254D PHE 3.8 2.5 - - - +
256D VAL* 1.3 78.2 - - + +
258D GLN* 1.3 64.9 + - - +
260D ARG* 3.1 24.2 + - - +
262D ALA 5.6 3.6 - - - +
265D ILE* 4.0 22.9 - - + -
281D ILE 5.0 0.4 - - - +
284D MET* 3.8 19.7 - - + +
285D ALA* 3.8 27.6 - - + +
288D CYS* 3.8 24.0 - - + +
290D VAL* 3.8 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C PHE* 3.8 14.6 - - + -
258C GLN* 3.1 60.1 + - + +
260C ARG* 5.4 6.3 + - - +
251D ARG* 5.9 0.2 + - - -
254D PHE* 2.8 27.3 + - + +
255D GLU* 3.2 29.7 - - - +
257D LEU* 1.3 77.8 - - - +
259D THR* 1.3 70.1 + - + +
260D ARG* 3.7 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D LEU* 4.4 7.0 - - + +
231D LYS* 2.7 39.1 + - - +
255D GLU* 3.0 27.4 + - + +
256D VAL* 3.5 3.6 + - - -
258D GLN* 1.3 91.3 - - + +
260D ARG* 1.3 55.3 + - - +
261D SER* 2.6 25.8 + - - -
----------------------------------------------------------
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