Contacts of the helix formed by residues 206 - 216 (chain D) in PDB entry 2UZ3
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 206 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PRO* 2.7 42.6 + - + +
78B LEU* 3.6 21.8 - - - +
79B ASN* 3.3 21.7 + - - +
82B MET* 4.7 1.3 - - + +
204D ASN* 3.1 15.0 + - - -
205D SER* 1.3 81.1 + - - +
207D SER* 1.3 61.9 + - - +
208D GLU 3.6 1.1 - - - -
209D GLU* 3.4 23.4 - - - +
210D PHE* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 207 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 4.4 6.7 - - - +
107B GLU* 2.7 29.4 + - - +
108B VAL 5.4 0.2 + - - -
111B ILE* 3.0 25.4 - - - +
202D TYR* 3.8 9.4 - - - -
204D ASN* 3.1 20.8 + - - +
205D SER 3.6 0.4 - - - -
206D ASN* 1.3 78.3 + - - +
208D GLU* 1.3 67.0 + - - +
210D PHE* 3.1 5.2 + - - +
211D ILE* 3.0 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 208 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D TYR* 3.2 48.5 + - + +
204D ASN 5.7 1.1 - - - +
205D SER 5.1 4.4 + - - +
207D SER* 1.3 74.8 - - - +
209D GLU* 1.3 63.3 + - - +
211D ILE* 3.3 11.3 + - - +
212D LYS* 3.0 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 209 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ASN* 5.0 3.4 + - - -
82B MET* 3.8 27.4 - - - +
205D SER 5.2 2.3 + - - +
206D ASN* 3.4 24.6 + - - +
208D GLU* 1.3 78.8 - - - +
210D PHE* 1.3 57.8 + - - +
212D LYS* 3.3 14.8 + - + +
213D PHE* 2.9 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 3.6 41.3 - - + -
81B ILE* 3.7 22.0 - - + -
82B MET* 3.7 26.5 - - + -
111B ILE* 3.6 27.8 - - + -
112B LEU* 3.9 22.0 - - + -
115B ASN* 4.1 15.7 - - + -
117B PHE* 4.5 1.6 - + - -
206D ASN 3.1 9.9 + - - +
207D SER 3.1 9.6 + - - +
209D GLU* 1.3 78.9 - - - +
211D ILE* 1.3 56.4 + - - +
213D PHE* 3.4 2.3 + - - +
214D PHE* 3.0 57.4 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ILE* 4.3 22.0 - - + -
114B GLU* 5.3 4.5 - - - +
115B ASN* 4.4 18.2 - - - +
200D ARG* 5.4 0.2 - - - +
202D TYR* 3.6 40.4 - - + +
207D SER 3.0 16.8 + - - +
208D GLU* 3.3 9.6 + - - +
210D PHE* 1.3 73.3 - - - +
212D LYS* 1.3 59.5 + - - +
214D PHE* 3.4 1.8 + - - +
215D LYS* 3.0 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D GLU* 3.0 22.8 + - + +
209D GLU* 3.3 15.5 - - - +
211D ILE* 1.3 71.7 - - - +
213D PHE* 1.3 67.4 + - - +
215D LYS* 3.0 35.6 + - - +
216D ASN* 3.2 15.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ILE 4.6 2.5 - - - -
82B MET* 3.4 62.4 - - + -
209D GLU* 2.9 17.1 + - + +
210D PHE 3.5 5.4 - - - +
212D LYS* 1.3 76.4 - - - +
214D PHE* 1.3 81.3 + + - +
216D ASN* 3.2 33.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ILE* 3.9 13.7 - - + -
86B PHE* 4.8 8.1 - + - -
115B ASN* 3.9 35.7 - - + +
117B PHE* 3.6 33.9 - + - -
210D PHE* 3.0 44.4 + + + +
211D ILE 4.1 1.3 - - - +
212D LYS 3.1 0.2 - - - -
213D PHE* 1.3 97.0 - + - +
215D LYS* 1.3 59.7 + - - +
216D ASN 3.0 13.4 + - - +
217D LYS* 3.7 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 215 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ASN* 5.2 0.8 + - - -
211D ILE* 3.0 19.3 + - + +
212D LYS* 3.0 26.2 + - - +
214D PHE* 1.3 75.0 - - - +
216D ASN* 1.3 63.6 + - - +
217D LYS* 3.3 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 216 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D LYS* 3.2 14.1 + - - +
213D PHE* 3.2 23.8 + - - +
214D PHE* 3.0 5.3 - - - +
215D LYS* 1.3 84.9 - - - +
217D LYS* 1.3 63.2 + - - +
----------------------------------------------------------
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