Contacts of the helix formed by residues 194 - 213 (chain B) in PDB entry 1ZKK
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 194 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LYS* 1.3 75.8 - - - +
195B LYS* 1.3 64.5 + - - +
196B ALA* 3.4 9.6 + - - +
197B GLU* 3.0 39.9 + - - +
198B LEU* 3.0 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LYS 4.0 0.6 + - - -
194B SER* 1.3 72.1 - - - +
196B ALA* 1.3 57.4 + - - +
198B LEU* 3.2 11.5 + - - +
199B GLN* 2.9 66.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B SER* 3.2 9.5 + - - +
195B LYS* 1.3 78.6 - - - +
197B GLU* 1.3 57.3 + - + +
199B GLN* 3.4 11.5 + - - +
200B SER* 3.0 30.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ARG 4.9 0.3 - - - +
193B LYS* 3.5 21.0 - - + +
194B SER* 3.0 40.5 + - - +
196B ALA* 1.3 75.3 - - + +
198B LEU* 1.3 58.0 + - - +
200B SER* 3.4 5.8 + - - -
201B GLU* 3.0 44.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LYS* 3.9 41.3 - - + +
194B SER 3.0 20.2 + - - +
195B LYS* 3.6 10.1 - - - +
197B GLU* 1.3 76.2 - - - +
199B GLN* 1.3 58.3 + - + +
201B GLU* 3.6 6.5 + - + +
202B GLU* 3.0 29.3 + - - +
205B ARG* 4.6 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B LYS* 2.9 53.4 + - + +
196B ALA* 3.8 9.7 - - - +
198B LEU* 1.3 77.4 - - + +
200B SER* 1.3 57.8 + - - +
202B GLU* 3.3 6.8 + - - +
203B ARG* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ALA 3.0 18.8 + - - -
197B GLU* 3.6 7.0 - - - -
199B GLN* 1.3 77.2 - - - +
201B GLU* 1.3 58.5 + - - +
203B ARG* 3.3 6.6 + - - +
204B LYS* 3.0 51.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LYS* 2.8 43.0 + - - +
197B GLU* 3.0 23.0 + - - +
198B LEU* 4.0 5.9 - - + +
200B SER* 1.3 74.6 - - - +
202B GLU* 1.3 64.4 + - - +
204B LYS* 3.5 13.1 + - + +
205B ARG* 3.2 44.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU 3.0 19.2 + - - +
199B GLN* 3.6 6.7 - - - +
201B GLU* 1.3 74.3 - - - +
203B ARG* 1.3 64.4 + - - +
205B ARG* 2.9 44.5 + - - +
206B ILE* 3.2 38.4 + - + +
239B GLY 4.9 7.3 - - - +
240B ASP* 5.8 1.4 - - - -
241B PHE 5.7 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B GLN 2.9 20.3 + - - +
200B SER* 3.3 7.4 + - - +
202B GLU* 1.3 73.8 - - - +
204B LYS* 1.3 58.7 + - + +
206B ILE* 3.2 10.2 + - - +
207B ASP* 2.9 41.0 + - - +
310B HIS* 3.8 29.3 + - + +
311B ASP* 2.9 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B SER* 3.0 37.9 + - - +
201B GLU* 3.8 11.9 - - + +
202B GLU 3.2 0.2 - - - -
203B ARG* 1.3 79.0 - - + +
205B ARG* 1.3 61.3 + - - +
207B ASP* 3.4 12.6 + - - +
208B GLU* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 4.6 4.0 + - - +
201B GLU* 3.2 31.9 + - - +
202B GLU* 2.9 48.5 + - - +
204B LYS* 1.3 76.1 - - + +
206B ILE* 1.3 64.2 + - + +
208B GLU* 3.3 7.3 + - - +
209B LEU* 3.1 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLU* 3.2 40.9 + - + +
203B ARG* 3.6 7.6 - - - +
205B ARG* 1.3 75.6 - - + +
207B ASP* 1.3 66.3 + - - +
209B LEU* 3.2 10.3 + - + +
210B ILE* 3.0 32.4 + - + +
239B GLY 5.9 1.6 - - - +
241B PHE* 4.1 21.3 - - + +
310B HIS* 3.5 32.3 - - + +
319B ILE* 4.0 15.3 - - + -
321B ILE* 5.4 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ARG* 2.9 29.7 + - - +
204B LYS* 3.6 14.4 - - - +
206B ILE* 1.3 76.8 - - - +
208B GLU* 1.3 57.3 + - - +
210B ILE* 3.4 1.7 + - - +
211B GLU* 3.0 39.4 + - + +
310B HIS* 2.7 33.9 + - - -
311B ASP 4.7 0.5 - - - +
312B ILE* 3.6 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LYS 3.0 16.7 + - - +
205B ARG* 3.7 6.5 - - - +
206B ILE 3.2 0.2 - - - -
207B ASP* 1.3 74.5 - - - +
209B LEU* 1.3 61.2 + - + +
211B GLU* 3.8 9.8 - - - +
212B SER* 2.9 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ARG* 3.1 25.5 + - + +
206B ILE* 3.2 9.2 + - + +
208B GLU* 1.3 73.0 - - + +
210B ILE* 1.3 66.0 + - - +
212B SER* 3.4 4.6 + - - +
213B GLY* 3.1 22.0 + - - -
214B LYS* 3.8 43.7 + - + +
241B PHE* 3.7 47.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ILE* 3.0 21.7 + - + +
207B ASP 3.7 6.3 - - - +
209B LEU* 1.3 78.2 - - - +
211B GLU* 1.3 65.8 + - + +
213B GLY* 3.4 9.0 + - - -
241B PHE* 4.1 11.7 - - + -
244B GLU* 3.5 25.6 - - - +
246B HIS* 5.7 0.5 - - - -
292B ARG* 4.9 4.0 + - - -
310B HIS* 3.4 33.9 - - + -
312B ILE* 3.8 13.2 - - + -
317B HIS* 3.6 28.7 - - + +
319B ILE* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ASP* 3.0 23.0 + - - +
208B GLU* 4.0 13.2 - - - +
210B ILE* 1.3 79.0 - - + +
212B SER* 1.3 62.0 + - - +
292B ARG* 5.9 0.3 + - - -
312B ILE* 4.1 27.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B GLU* 2.9 33.8 + - - +
209B LEU* 3.4 6.6 + - - +
211B GLU* 1.3 77.6 - - - +
213B GLY* 1.3 62.4 + - - +
214B LYS* 3.1 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU 3.1 11.7 + - - -
210B ILE 3.4 3.5 + - - -
211B GLU 3.3 3.2 + - - -
212B SER* 1.3 77.3 - - - +
214B LYS* 1.3 64.7 + - - +
215B GLU* 3.3 16.4 + - - +
292B ARG* 3.6 34.8 + - - -
----------------------------------------------------------
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