Contacts of the helix formed by residues 246 - 255 (chain B) in PDB entry 1KKQ
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 246 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B PHE* 4.2 6.6 - - + -
240B VAL 3.8 18.4 - - - +
241B ILE* 3.4 3.3 - - - -
242B HIS* 2.8 50.5 + - + +
243B ASP* 2.8 26.6 + - - +
245B GLU* 1.3 75.3 - - + +
247B LEU* 1.3 64.0 + - - +
248B CYS 2.7 13.6 + - - -
249B MET* 2.7 31.3 + - - +
250B ALA* 3.0 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ILE* 3.4 25.3 - - + +
243B ASP 2.8 10.2 + - - +
244B MET* 3.5 15.3 - - + -
246B THR* 1.3 81.6 + - - +
248B CYS* 1.3 56.6 + - - +
250B ALA* 3.9 2.0 - - - +
251B GLU* 2.8 30.8 + - + +
268B ALA 4.5 1.3 - - - +
271B ARG* 4.3 12.3 - - - +
272B ILE* 3.4 41.7 - - + +
339B ILE* 5.8 0.4 - - + -
343B PHE* 3.2 26.0 - - + -
776B 471 4.4 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B MET 3.0 10.7 + - - +
245B GLU* 2.7 14.0 + - - +
246B THR 2.7 2.0 + - - -
247B LEU* 1.3 78.4 - - - +
249B MET* 1.3 54.9 + - - -
251B GLU* 2.6 29.3 - - - +
252B LYS* 3.0 14.9 - - - +
264B GLN 4.2 11.7 - - - -
271B ARG* 3.0 41.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B PHE* 3.9 30.1 - - + -
245B GLU* 3.0 20.0 + - + +
246B THR* 2.7 24.3 + - - +
248B CYS* 1.3 72.5 - - - +
250B ALA* 1.3 69.8 + - - +
251B GLU* 3.3 0.2 - - - -
252B LYS* 3.0 21.9 - - + +
253B THR* 3.4 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B PHE* 4.1 13.2 - - + -
241B ILE* 3.6 33.0 - - + -
246B THR 3.0 10.6 + - - +
247B LEU 3.9 4.0 - - - +
249B MET* 1.3 74.5 - - - +
251B GLU* 1.3 58.3 + - - +
252B LYS 2.6 15.5 + - - -
253B THR* 2.7 19.2 + - - -
254B LEU* 2.9 12.4 + - - +
776B 471 4.5 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LEU* 2.8 26.7 - - + +
248B CYS* 2.6 45.6 - - - +
250B ALA* 1.3 75.4 - - - +
252B LYS* 1.3 90.3 + - - +
254B LEU* 3.7 15.2 - - - +
255B VAL* 3.5 15.4 + - - +
258B LEU* 4.1 16.4 - - + +
264B GLN* 5.9 2.3 - - - -
271B ARG* 3.8 34.3 - - + +
275B CYS* 5.0 13.9 - - + -
776B 471 4.6 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B CYS 3.0 22.7 - - - +
249B MET* 3.0 18.6 - - + +
250B ALA 2.6 2.8 + - - -
251B GLU* 1.3 93.8 + - - +
253B THR* 1.3 65.5 + - + +
255B VAL 3.5 9.0 - - - +
258B LEU* 3.1 33.2 + - - +
259B VAL* 4.7 20.5 - - + +
264B GLN* 4.8 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B MET 3.8 11.2 + - - +
250B ALA* 2.7 15.0 + - - -
252B LYS* 1.3 78.8 - - + +
254B LEU* 1.3 68.9 + - - +
255B VAL 3.0 12.6 + - - -
256B ALA* 3.6 4.9 + - - -
259B VAL* 5.9 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ALA* 2.9 8.3 + - + +
251B GLU* 3.5 16.1 + - - +
253B THR* 1.3 79.2 + - - +
255B VAL* 1.3 60.4 + - + +
256B ALA 3.4 2.8 + - - -
275B CYS* 4.3 19.1 - - + +
278B CYS* 5.5 3.8 - - - -
279B THR* 5.8 0.9 - - - +
333B ALA* 4.6 17.7 - - + -
776B 471 3.1 43.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B GLU 3.5 3.5 + - - +
252B LYS 3.5 7.6 - - - +
253B THR* 3.1 5.9 - - - +
254B LEU* 1.3 76.2 - - + +
256B ALA* 1.3 64.7 + - - +
257B LYS* 2.8 25.7 + - + +
258B LEU* 2.9 48.7 + - + -
259B VAL* 5.6 0.5 - - - +
274B HIS* 5.1 6.3 - - + -
275B CYS* 3.7 29.6 - - - -
278B CYS* 5.6 1.3 - - - -
----------------------------------------------------------
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