Contacts of the helix formed by residues 280 - 284 (chain D) in PDB entry 1KOH
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 LEU 280 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D MET* 5.4 0.4 - - + -
277D LEU* 5.0 6.7 - - + -
279D ARG* 1.3 78.6 - - - +
281D ASP* 1.3 55.3 + - - +
282D ASP 2.7 15.5 + - - +
283D MET* 2.8 48.2 + - + -
284D SER* 3.4 9.2 + - - -
298D LEU* 4.4 18.4 - - + -
303D LEU* 3.9 22.4 - - + -
308D GLU* 2.8 43.8 + - - +
309D LEU* 4.3 3.8 - - + +
311D LYS* 3.9 10.6 - - + +
312D ILE* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C ALA* 4.1 15.1 - - - +
258C ARG* 5.5 4.5 - - - +
289C LYS* 3.5 25.6 + - - -
250D ARG* 2.5 37.6 + - - +
279D ARG* 3.6 10.8 - - + +
280D LEU* 1.3 77.4 - - - +
282D ASP* 1.3 63.1 + - - +
283D MET 3.4 0.2 - - - -
284D SER* 3.1 18.3 + - - -
307D ARG* 5.7 2.5 - - - +
308D GLU* 4.9 0.8 + - - -
311D LYS* 3.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 282 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D LEU 5.3 0.4 - - - +
248D ASN 5.0 1.6 - - - -
249D ARG* 3.4 4.2 + - - +
250D ARG* 2.8 55.7 + - - +
253D MET* 4.1 27.2 - - + +
254D ALA* 5.1 4.5 - - - +
257D LEU* 4.6 1.0 - - - +
279D ARG* 2.9 51.0 + - - +
280D LEU 2.7 1.4 - - - -
281D ASP* 1.3 80.3 - - - +
283D MET* 1.3 57.5 + - - +
284D SER 3.6 0.9 - - - -
285D SER* 4.5 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 283 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D MET* 3.2 34.3 - - + -
257D LEU* 3.8 20.4 - - + -
272D LEU* 4.3 10.5 - - - -
280D LEU* 2.8 33.5 + - + +
282D ASP* 1.3 78.5 - - + +
284D SER* 1.3 57.2 + - - +
285D SER 2.9 11.6 + - - +
286D ILE* 3.0 35.5 + - + +
296D LEU* 3.9 18.8 - - + -
298D LEU* 4.3 4.7 - - + -
312D ILE* 3.4 44.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 284 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C SER* 3.4 29.4 + - - -
288C GLN* 4.0 16.5 + - - +
289C LYS* 4.3 14.3 - - - -
280D LEU 3.4 4.5 + - - -
281D ASP* 3.1 24.6 + - - -
282D ASP 3.6 0.6 - - - -
283D MET* 1.3 75.6 - - - +
285D SER* 1.3 57.3 + - - +
286D ILE 3.5 0.2 - - - -
287D VAL* 3.7 17.5 - - - +
288D GLN* 5.2 2.1 + - - +
311D LYS* 3.2 23.8 - - - -
312D ILE* 4.5 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