Contacts of the helix formed by residues 221 - 229 (chain D) 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 ASN 221 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D TYR* 3.7 17.5 - - + +
215D LEU* 3.9 24.4 - - - +
218D PHE* 4.9 6.0 + - + +
219D ASN 4.0 0.4 + - - -
220D MET* 1.3 74.8 - - - +
222D LYS* 1.3 64.5 + - - +
223D VAL* 3.7 15.7 - - - +
224D LYS* 2.9 39.0 + - - +
225D ALA* 3.2 21.1 + - - +
323D SER* 4.8 4.9 - - - -
324D VAL* 6.0 0.2 - - - -
372D ASP* 3.4 16.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D TYR* 4.1 1.2 + - - -
221D ASN* 1.3 68.9 - - - +
223D VAL* 1.3 69.2 + - - +
225D ALA* 3.1 4.9 + - - +
226D ARG* 2.8 42.9 + - + +
323D SER* 4.0 29.6 - - - +
365D PHE* 5.5 3.2 + - - -
366D ASN* 3.9 29.0 + - - +
369D GLU* 4.3 5.1 - - - +
370D LEU* 2.6 47.1 + - - +
371D ASP* 4.5 3.4 - - - -
372D ASP* 2.7 28.2 + - - +
375D ILE* 4.0 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D TYR* 5.9 1.8 - - - +
215D LEU* 5.9 1.3 - - + -
221D ASN* 3.7 15.3 - - - +
222D LYS* 1.3 70.1 - - - +
224D LYS* 1.3 57.0 + - + +
226D ARG* 2.7 30.5 + - - +
227D VAL* 3.0 21.4 + - + +
372D ASP* 2.7 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D ASN* 3.1 36.5 + - - +
220D MET* 4.3 12.4 - - - +
221D ASN* 2.9 30.0 + - - +
223D VAL* 1.3 79.6 - - + +
225D ALA* 1.3 62.0 + - - +
227D VAL* 3.1 16.1 + - - +
228D ILE* 3.1 27.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D MET* 4.1 7.8 - - + -
221D ASN 3.2 18.4 + - - +
222D LYS 3.1 3.2 + - - +
224D LYS* 1.3 79.0 - - - +
226D ARG* 1.3 58.0 + - - +
228D ILE* 3.5 3.0 + - - +
229D LEU* 3.1 34.8 + - - +
323D SER 3.3 27.1 - - - +
324D VAL* 4.2 16.8 - - + -
331D LEU* 4.0 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D LYS* 2.8 30.0 + - + +
223D VAL* 2.7 18.7 + - - +
225D ALA* 1.3 70.1 - - - +
227D VAL* 1.3 58.2 + - - -
229D LEU* 3.0 28.3 - - - +
230D SER* 3.3 24.7 + - - -
231D GLY* 3.1 19.1 + - - -
322D SER 4.0 4.2 + - - -
323D SER* 2.9 26.9 + - - +
325D MET 2.7 23.1 + - - -
326D ASN* 4.8 4.2 - - - +
363D MET* 5.3 0.4 - - - +
366D ASN* 3.7 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D VAL* 3.0 25.4 + - + +
224D LYS* 3.1 10.9 + - - +
226D ARG* 1.3 79.3 - - + +
228D ILE* 1.3 63.8 + - + +
231D GLY* 3.8 9.0 - - - -
232D LYS 2.9 27.2 + - - -
233D ALA* 3.7 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D MET* 4.3 12.6 - - + -
224D LYS* 3.1 21.0 + - + +
225D ALA 3.8 4.0 - - - +
226D ARG 3.4 0.2 - - - -
227D VAL* 1.3 80.4 - - + +
229D LEU* 1.3 70.0 + - - +
232D LYS* 4.2 8.5 + - - +
238D PRO* 3.5 37.4 - - + +
331D LEU* 4.4 10.5 - - + -
334D TYR 5.0 0.7 - - - +
335D GLY* 3.7 30.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D ALA 3.1 14.6 + - - +
226D ARG* 3.0 35.4 - - - +
228D ILE* 1.3 85.2 - - - +
230D SER* 1.3 64.3 + - - +
232D LYS* 3.0 24.3 - - - +
238D PRO* 6.2 0.4 - - - -
324D VAL 4.4 13.2 - - - +
325D MET 4.3 9.2 - - - +
326D ASN* 4.2 19.5 - - + +
329D GLY 5.6 0.2 - - - +
331D LEU* 3.5 19.3 - - + -
338D PHE* 3.2 35.9 - - + -
----------------------------------------------------------
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