Contacts of the helix formed by residues 204 - 214 (chain J) in PDB entry 4ZZ7
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 ASP 204 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ARG* 3.1 22.9 + - - +
204G ASP* 3.8 6.9 - - - +
206G GLU* 5.4 3.9 - - - +
18J ARG* 2.9 40.5 + - - -
36J LEU* 4.3 11.6 - - + +
37J ALA 4.6 1.7 - - - +
172J LYS* 4.7 2.0 - - - +
175J GLU* 3.7 20.6 - - - +
203J GLY* 1.3 77.5 - - - -
205J LYS* 1.3 71.5 + - - +
206J GLU* 3.2 7.6 + - - +
207J ALA* 2.9 14.3 + - - +
208J VAL* 3.2 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 205 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204G ASP* 6.1 1.1 - - - +
205G LYS* 3.6 35.2 - - + +
206G GLU* 5.5 17.9 + - + +
209G ASP* 3.8 11.3 + - - +
204J ASP* 1.3 78.8 - - - +
206J GLU* 1.3 57.3 + - - +
208J VAL* 3.1 13.0 + - + +
209J ASP* 2.8 49.6 + - - +
228J ILE* 6.4 0.4 - - - +
231J TYR* 3.6 36.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 206 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204G ASP* 5.3 6.3 + - - +
205G LYS* 6.6 0.2 - - - -
18J ARG* 2.9 32.8 + - - +
37J ALA 4.9 1.6 - - - +
38J SER* 3.5 14.5 - - - -
39J THR* 3.4 38.8 + - + +
204J ASP* 3.2 5.2 + - - +
205J LYS* 1.3 78.1 - - - +
207J ALA* 1.3 62.2 + - - +
209J ASP* 3.5 7.5 + - + +
210J ALA* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J ALA 4.0 17.8 + - - +
38J SER 5.7 0.2 - - - -
42J VAL* 3.9 20.7 - - + +
172J LYS* 3.9 21.5 - - + -
201J VAL* 4.7 3.8 - - + -
202J ASN 4.7 1.3 - - - +
203J GLY* 4.1 5.4 - - - -
204J ASP* 2.9 17.9 + - - +
206J GLU* 1.3 76.5 - - - +
208J VAL* 1.3 64.7 + - - +
210J ALA* 3.2 12.5 + - - +
211J LEU* 3.2 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 208 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145J ILE* 3.7 25.4 - - + -
172J LYS* 3.6 26.2 - - + +
204J ASP 3.2 7.8 + - - +
205J LYS* 3.1 14.5 + - + +
207J ALA* 1.3 75.8 - - - +
209J ASP* 1.3 65.4 + - - +
211J LEU* 3.0 22.7 + - - +
212J LEU* 3.1 16.9 + - + +
231J TYR* 5.3 1.3 - - + -
232J ILE* 3.4 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 209 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205G LYS* 4.0 14.7 + - - +
39J THR* 6.4 0.4 - - + -
205J LYS* 2.8 37.8 + - - +
206J GLU* 3.9 7.4 - - + +
208J VAL* 1.3 72.0 - - - +
210J ALA* 1.3 62.1 + - - +
212J LEU* 3.3 6.7 + - - +
213J HIS* 3.0 43.9 + - + +
231J TYR* 2.6 38.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39J THR* 4.0 25.0 - - - +
42J VAL* 3.7 28.0 - - + -
43J GLU* 6.0 1.6 - - + +
46J ILE* 4.6 0.6 - - - +
206J GLU 3.0 14.4 + - - +
207J ALA 3.2 11.0 + - - +
209J ASP* 1.3 77.2 - - - +
211J LEU* 1.3 61.4 + - - +
213J HIS* 4.0 2.4 - - - +
214J ASP* 3.2 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J VAL* 3.9 14.8 - - + -
46J ILE* 4.3 10.3 - - + -
143J ALA* 4.1 22.4 - - + -
145J ILE* 4.3 15.9 - - + -
170J VAL* 3.7 38.8 - - + +
172J LYS* 3.9 29.4 - - + -
201J VAL* 5.0 2.2 - - + -
207J ALA 3.2 12.5 + - - +
208J VAL* 3.0 8.1 + - - +
210J ALA* 1.3 77.5 - - - +
212J LEU* 1.3 67.8 + - + +
213J HIS 3.2 0.7 + - - -
214J ASP 3.7 1.7 + - - -
217J VAL* 3.5 32.2 - - + +
241J LYS* 3.7 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145J ILE* 4.7 4.5 - - + -
208J VAL* 3.1 19.4 + - + +
209J ASP* 3.3 14.3 + - - +
211J LEU* 1.3 76.5 - - + +
213J HIS* 1.3 60.2 + - - +
220J VAL* 3.8 37.2 - - + -
231J TYR* 4.3 1.8 - - + -
232J ILE* 3.7 35.2 - - + -
235J THR* 3.7 35.8 - - + +
236J ALA* 4.4 9.6 - - + +
239J ASN* 3.6 18.5 + - - +
241J LYS* 3.4 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 213 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209J ASP* 3.0 43.2 + - + +
210J ALA* 4.3 2.0 - - - +
211J LEU 3.2 0.2 - - - -
212J LEU* 1.3 80.3 - - - +
214J ASP* 1.3 62.8 + - - +
215J ASP* 3.6 9.4 + - - +
231J TYR* 4.7 2.5 - - - -
235J THR* 3.8 23.6 - - + +
239J ASN* 3.7 28.9 + - - +
241J LYS* 4.4 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 214 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43J GLU* 3.9 11.6 - - + +
46J ILE* 3.3 25.8 - - + +
210J ALA 3.2 16.1 + - - +
211J LEU 3.7 2.9 + - - +
213J HIS* 1.3 75.6 - - - +
215J ASP* 1.3 58.9 + - - +
216J ARG* 2.8 67.3 + - - +
217J VAL* 3.2 8.5 + - + +
241J LYS* 2.6 25.8 + - - -
----------------------------------------------------------
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