Contacts of the strand formed by residues 208 - 219 (chain P) in PDB entry 2AAZ
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 LYS 208 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194P PHE* 3.5 2.1 - - - +
195P VAL* 3.3 7.4 - - - -
196P SER* 2.9 50.2 + - - +
199P PRO* 6.3 4.9 - - - -
206P LYS 4.3 7.0 + - - +
207P PRO* 1.3 75.4 - - - +
209P LEU* 1.3 59.9 + - - +
210P SER* 5.1 0.9 + - - -
245P GLU* 3.3 23.7 - - + +
246P PRO 5.9 0.2 + - - -
247P HIS* 3.8 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160P ILE* 3.9 24.2 - - + -
193P PHE* 4.1 11.2 - - + -
194P PHE 3.5 11.7 - - - +
195P VAL* 4.0 10.5 - - + +
207P PRO 3.9 0.2 + - - -
208P LYS* 1.3 72.7 - - - +
210P SER* 1.3 68.7 + - - +
235P THR* 3.7 38.4 - - + +
238P ILE* 3.8 15.5 - - + -
239P ALA* 3.8 9.2 - - - +
244P THR* 3.7 25.6 - - + +
245P GLU 2.8 15.4 + - - +
246P PRO* 3.6 2.5 - - + +
247P HIS 2.7 29.0 + - - -
248P GLU 3.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 210 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49O PHE* 3.8 25.7 - - - -
193P PHE* 3.3 11.5 - - - +
194P PHE* 2.9 36.3 + - - -
196P SER* 5.6 1.2 + - - -
208P LYS 4.1 0.9 + - - -
209P LEU* 1.3 73.2 - - - +
211P CYS* 1.3 63.0 + - - +
235P THR* 4.9 1.1 - - - -
247P HIS* 3.5 27.5 - - - +
248P GLU* 3.2 19.6 + - - +
250P ILE* 4.8 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 211 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49O PHE* 4.3 1.1 - - - -
191P CYS* 4.0 23.6 - - - -
192P GLN 3.4 5.4 - - - -
193P PHE* 3.8 23.8 - - + -
210P SER* 1.3 77.5 - - - +
212P LEU* 1.3 57.6 + - - +
231P TYR* 4.2 11.7 - - - -
235P THR* 3.3 23.6 - - - +
248P GLU 2.9 8.5 + - - +
249P PHE* 3.3 18.8 - - + -
250P ILE* 2.7 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49O PHE* 3.8 17.5 - - + -
50O ALA* 3.5 25.8 - - + -
214O TYR* 3.5 45.1 - - + +
252O GLN* 3.7 14.6 - - + +
253O MET 3.9 2.2 - - - +
190P PHE* 4.9 1.5 - - + -
191P CYS* 3.0 4.3 - - - -
192P GLN 2.8 35.9 + - - +
211P CYS* 1.3 73.0 - - - +
213P MET* 1.3 76.5 + - - +
214P TYR* 4.3 3.1 - - + +
250P ILE* 3.3 21.3 - - + +
252P GLN* 4.7 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 213 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188P HIS* 3.5 20.4 - - + -
190P PHE 3.5 12.8 - - - +
191P CYS* 3.9 5.8 - - + -
211P CYS* 4.1 0.4 - - - -
212P LEU* 1.3 79.9 - - - +
214P TYR* 1.3 80.6 + - - +
215P GLN* 3.4 18.2 - - - +
227P ASN* 4.0 10.8 - - + +
231P TYR* 3.7 39.0 - - + -
249P PHE* 3.8 18.8 - - + -
250P ILE 2.8 6.7 + - - -
251P LEU* 3.4 28.6 - - + +
252P GLN 2.9 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 214 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190O PHE* 3.2 33.9 - + - -
192O GLN* 2.5 37.9 + - - +
212O LEU* 3.6 34.2 - - + +
214O TYR* 5.3 5.8 - + + -
189P MET* 3.3 30.8 + - + +
190P PHE* 3.0 32.5 + - + +
212P LEU* 4.3 3.1 - - + +
213P MET* 1.3 79.1 - - - +
215P GLN* 1.3 59.8 + - - +
216P ARG* 3.9 12.1 - - - -
252P GLN* 3.4 33.4 - - + -
253P MET 4.3 2.0 - - - -
254P GLY* 3.4 13.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 215 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187P CYS 3.3 18.4 - - - +
188P HIS* 3.9 3.1 - - - +
213P MET* 3.4 14.5 - - - +
214P TYR* 1.3 74.4 - - - +
216P ARG* 1.3 62.4 + - - +
217P SER 3.0 16.5 + - - +
218P CYS* 3.4 24.4 - - - +
219P ASP 4.5 0.2 - - - +
224P VAL* 4.5 5.4 - - - +
227P ASN* 2.9 44.3 + - - +
251P LEU* 4.1 9.7 - - + +
252P GLN 2.9 11.3 + - - +
253P MET* 3.5 0.5 - - - -
254P GLY 2.8 25.3 + - - -
700P UMP 3.0 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 216 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167O ARG 2.9 24.4 + - - +
168O ARG* 3.7 9.3 - - - +
170O ILE* 4.3 2.2 - - + -
192O GLN* 3.1 35.0 + - - +
174P TRP* 3.7 24.1 - - - -
185P PRO* 3.0 30.5 + - - +
186P PRO 2.7 20.1 + - - +
187P CYS* 3.0 21.9 + - - +
189P MET* 3.7 17.5 - - - +
214P TYR* 3.9 5.6 + - - -
215P GLN* 1.3 71.5 - - - +
217P SER* 1.3 65.0 + - - +
255P ASP* 2.7 29.7 + - - +
700P UMP 2.6 46.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 217 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167O ARG* 3.3 9.5 + - - -
187P CYS* 3.8 3.3 - - - +
215P GLN* 3.0 18.7 + - - +
216P ARG* 1.3 93.6 - - - +
218P CYS* 1.3 61.9 + - - +
255P ASP* 3.5 4.5 - - - -
257P HIS* 3.1 21.3 - - - -
700P UMP 3.0 49.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 218 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215P GLN* 3.4 41.3 - - - +
217P SER* 1.3 77.6 - - - +
219P ASP* 1.3 59.1 + - - +
220P LEU* 3.1 3.2 + - + +
224P VAL* 3.8 13.9 - - + -
253P MET* 3.4 39.9 - - - -
254P GLY 4.3 0.2 - - - -
255P ASP 2.8 15.3 + - - +
256P ALA* 4.2 1.8 - - - -
257P HIS* 3.0 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 219 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218P CYS* 1.3 68.5 - - - +
220P LEU* 1.3 58.4 + - - +
221P GLY 3.2 5.9 + - - -
222P LEU* 3.2 31.5 + - - +
223P GLY* 2.8 32.4 + - - +
224P VAL* 3.0 6.7 + - - +
257P HIS* 3.9 7.4 - - - +
259P TYR* 3.4 24.5 + - + -
262P HIS* 3.7 14.3 + - - -
315P MET* 5.1 6.8 - - - +
316P SER 5.5 0.7 + - - -
700P UMP 3.0 38.0 + - - +
----------------------------------------------------------
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