Contacts of the helix formed by residues 222 - 232 (chain D) in PDB entry 1KQN
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 SER 222 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D MET* 3.9 9.4 - - - -
220D ASP* 3.0 15.1 + - - -
221D ILE* 1.3 78.9 - - - +
223D SER* 1.3 64.1 + - - +
224D THR* 3.6 8.0 + - - -
225D LYS* 2.9 37.9 + - - +
226D ILE* 3.1 18.9 + - - +
780D NAD 5.3 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ASN* 3.3 27.5 + - - -
19D PRO* 2.7 25.1 + - - -
21D THR* 4.1 1.1 - - - +
23D MET* 4.9 1.6 - - - +
24D HIS* 3.5 14.9 + - - -
221D ILE 3.9 0.8 + - - -
222D SER* 1.3 74.4 - - - +
224D THR* 1.3 59.6 + - - +
226D ILE* 2.9 10.8 + - - +
227D ARG* 2.8 38.0 + - - +
780D NAD 4.7 9.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D SER* 3.9 8.6 - - - -
223D SER* 1.3 78.6 - - - +
225D LYS* 1.3 57.5 + - + +
227D ARG* 3.2 29.5 + - - +
228D ARG* 2.9 53.6 + - + +
231D ARG* 5.1 0.7 + - - +
259D GLU* 5.7 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TYR* 3.4 27.5 + - - +
199A GLU* 6.0 1.3 - - - -
216C TRP 3.1 16.6 + - - +
217C ILE* 3.8 34.4 - - + +
220D ASP* 2.7 35.1 + - - +
222D SER* 2.9 25.6 + - - +
224D THR* 1.3 75.2 - - - +
226D ILE* 1.3 62.7 + - - +
228D ARG* 3.7 18.8 - - - +
229D ALA* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C ILE* 5.3 2.2 - - + -
19D PRO* 3.8 23.3 - - + -
21D THR* 3.8 12.6 - - + -
221D ILE* 3.6 27.1 - - + -
222D SER 3.1 14.2 + - - +
223D SER* 2.9 11.0 + - - +
225D LYS* 1.3 78.4 - - + +
227D ARG* 1.3 56.9 - - - +
229D ALA* 3.1 6.0 + - - +
230D LEU* 2.8 46.3 + - + +
236D ILE* 3.9 22.0 - - + -
239D LEU* 3.7 28.9 - - + -
240D VAL* 4.3 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ASN* 3.0 39.8 + - - +
19D PRO* 4.1 4.0 - - + -
57D LYS* 5.9 5.5 - - - +
58D LYS 5.0 6.9 + - - -
59D GLY 4.6 2.8 + - - -
223D SER* 2.8 28.1 + - - +
224D THR* 3.4 30.8 + - - +
226D ILE* 1.3 76.1 - - - +
228D ARG* 1.3 56.8 + - - +
230D LEU* 3.1 10.9 + - - +
231D ARG* 2.9 43.4 + - - +
254D TYR* 3.5 39.6 - - + +
259D GLU* 2.9 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TYR* 3.1 42.6 + - + +
199A GLU* 4.3 26.6 + - - +
224D THR* 2.9 37.3 + - - +
225D LYS* 3.7 21.6 - - - +
227D ARG* 1.3 73.0 - - - +
229D ALA* 1.3 64.8 + - - +
231D ARG* 3.3 30.7 + - - +
232D ARG* 2.9 71.2 + - - +
234D GLN* 5.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C ILE* 5.3 8.7 - - + -
225D LYS 2.9 19.5 + - - +
226D ILE* 3.1 4.9 + - - +
228D ARG* 1.3 77.6 - - - +
230D LEU* 1.3 61.2 + - - +
232D ARG* 3.3 2.1 + - - -
233D GLY 3.1 3.6 + - - -
234D GLN* 2.8 56.5 + - + +
235D SER 4.9 2.0 - - - +
236D ILE* 3.9 18.4 - - + -
239D LEU* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D ILE* 2.8 35.1 + - + +
227D ARG* 3.1 6.3 + - - +
229D ALA* 1.3 74.4 - - - +
231D ARG* 1.3 68.0 + - - +
233D GLY* 3.0 14.4 + - - +
234D GLN 4.7 5.4 - - - +
236D ILE* 3.8 29.4 - - + -
248D ILE* 4.0 21.1 - - + -
249D GLU* 6.1 2.7 - - + -
254D TYR* 3.5 48.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ASP* 2.7 39.9 + - - +
224D THR* 5.1 1.4 + - - +
227D ARG* 2.9 17.6 + - - +
228D ARG* 3.3 51.6 + - - +
230D LEU* 1.3 73.0 - - - +
232D ARG* 1.3 62.7 + - + +
233D GLY 3.5 0.7 + - - -
254D TYR* 4.5 4.9 + - + -
255D SER* 3.6 27.1 + - - +
256D SER* 3.6 29.8 - - - +
259D GLU* 3.4 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TYR* 2.7 49.4 + - - -
199A GLU 4.1 0.8 + - - -
200A SER 3.8 3.0 - - - +
201A ASP* 2.9 43.1 + - - +
204A TRP* 3.3 50.5 - - + +
228D ARG* 2.9 37.2 + - - +
229D ALA 3.3 0.2 + - - -
230D LEU 3.1 0.8 - - - -
231D ARG* 1.3 79.1 - - + +
233D GLY* 1.3 63.3 + - - +
234D GLN* 3.3 22.9 + - + +
----------------------------------------------------------
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