Contacts of the helix formed by residues 204 - 214 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ARG* 3.3 39.2 + - - -
20D GLN* 5.2 3.6 - - - +
36D LEU* 4.6 10.1 - - + +
37D ALA 4.9 0.9 - - - +
172D LYS* 4.4 1.5 - - - +
175D GLU* 3.7 21.3 - - - +
203D GLY* 1.3 74.5 - - - -
205D LYS* 1.3 69.5 + - + +
206D GLU* 3.3 13.6 + - - +
207D ALA* 3.1 12.5 + - - +
208D VAL* 3.3 16.9 + - - +
501D NAD 4.8 2.5 - - - -
234E ARG* 5.2 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 205 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D ASP* 1.3 81.9 - - - +
206D GLU* 1.3 57.3 + - - +
208D VAL* 3.4 1.2 + - - +
209D ASP* 2.9 55.0 + - - +
231D TYR* 3.4 22.2 + - - -
501D NAD 3.1 53.3 + - + +
205E LYS* 3.2 43.5 - - - +
209E ASP* 4.1 0.9 - - - -
231E TYR* 4.0 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ARG* 2.8 31.3 + - - +
37D ALA 4.6 1.3 - - - +
38D SER* 3.5 29.8 - - - -
39D THR* 3.7 24.9 + - + +
204D ASP* 3.2 13.8 + - - +
205D LYS* 1.3 80.0 - - - +
207D ALA* 1.3 56.4 + - - +
209D ASP* 3.7 6.1 + - - +
210D ALA* 3.1 24.4 + - - +
234E ARG* 5.1 4.9 - - - +
238E ALA* 5.3 6.2 - - - +
234F ARG* 5.7 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ALA* 4.0 15.4 + - + +
38D SER 5.6 0.7 - - - -
42D VAL* 3.8 24.2 - - + +
172D LYS* 4.3 12.1 - - + -
201D VAL* 4.5 4.9 - - + -
203D GLY* 4.2 15.7 - - - -
204D ASP* 3.1 9.9 + - - +
206D GLU* 1.3 75.2 - - - +
208D VAL* 1.3 65.6 + - - +
210D ALA* 3.3 4.3 + - - +
211D LEU* 3.2 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 208 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D ILE* 3.9 21.5 - - + -
172D LYS* 3.6 25.5 - - + +
204D ASP 3.3 7.8 + - - +
205D LYS 3.6 7.6 - - - +
207D ALA* 1.3 75.0 - - - +
209D ASP* 1.3 61.3 + - - +
211D LEU* 3.1 14.9 + - - +
212D LEU* 3.0 32.0 + - + +
232D ILE* 3.4 32.8 - - + -
501D NAD 3.8 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 209 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D THR* 5.9 0.9 - - + -
205D LYS* 2.9 46.9 + - - +
206D GLU* 3.9 6.6 - - - +
208D VAL* 1.3 73.8 - - - +
210D ALA* 1.3 67.1 + - - +
212D LEU* 3.2 5.0 + - - +
213D HIS* 3.0 43.0 + - + +
231D TYR* 2.8 31.9 + - - -
209E ASP* 4.4 5.0 - - - +
213E HIS* 5.5 6.1 - - - -
231E TYR* 5.0 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D THR* 3.9 24.8 - - - +
42D VAL* 3.7 28.0 - - + -
43D GLU* 5.7 4.1 - - + +
46D ILE* 4.6 0.2 - - - +
206D GLU 3.1 16.1 + - - +
207D ALA 3.4 9.9 - - - +
208D VAL 3.2 0.6 - - - -
209D ASP* 1.3 74.6 - - - +
211D LEU* 1.3 62.4 + - - +
213D HIS* 3.4 2.8 + - - +
214D ASP* 3.1 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D VAL* 3.9 14.8 - - + -
46D ILE* 4.0 12.3 - - + -
143D ALA* 4.1 24.9 - - + -
144D GLY 5.2 0.2 - - - +
145D ILE* 4.6 9.2 - - + -
170D VAL* 3.8 35.9 - - + +
172D LYS* 3.9 28.7 - - + -
201D VAL* 5.1 2.0 - - + -
207D ALA 3.2 15.0 + - - +
208D VAL* 3.1 12.4 + - - +
210D ALA* 1.3 79.1 - - - +
212D LEU* 1.3 63.0 + - + +
213D HIS 3.5 0.2 + - - -
214D ASP 3.7 2.3 + - - -
217D VAL* 3.6 22.2 - - + +
220D VAL* 5.5 0.4 - - + -
241D LYS* 3.5 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D ILE* 4.9 3.1 - - + -
208D VAL* 3.0 23.7 + - + +
209D ASP* 3.2 9.2 + - - +
211D LEU* 1.3 77.5 - - + +
213D HIS* 1.3 61.5 + - - +
214D ASP 3.5 0.2 - - - -
220D VAL* 3.9 34.5 - - + -
231D TYR* 4.2 8.1 - - + -
232D ILE* 4.0 32.3 - - + -
235D THR* 3.7 37.7 - - + -
236D ALA* 4.3 12.6 - - + +
239D ASN* 3.5 13.0 - - - +
241D LYS* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D ASP* 3.0 42.0 + - + +
210D ALA* 3.8 3.1 - - - +
212D LEU* 1.3 78.8 - - + +
214D ASP* 1.3 61.3 + - - +
215D ASP* 3.6 10.7 + - - +
231D TYR* 5.0 1.8 - - - -
235D THR* 4.0 24.4 - - + +
239D ASN* 3.5 27.5 + - - +
241D LYS* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D GLU* 3.9 12.0 - - - +
46D ILE* 3.5 27.2 - - + +
210D ALA 3.1 17.4 + - - +
211D LEU 3.7 3.5 + - - +
212D LEU 3.5 0.4 - - - -
213D HIS* 1.3 77.2 - - - +
215D ASP* 1.3 59.8 + - - +
216D ARG* 2.8 64.7 + - - +
217D VAL* 3.3 7.3 + - + +
241D LYS* 2.6 27.0 + - - -
----------------------------------------------------------
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