Contacts of the strand formed by residues 208 - 219 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194E PHE* 3.5 1.4 - - - +
195E VAL* 3.2 6.7 - - - -
196E SER* 2.8 51.5 + - - +
199E PRO* 6.3 4.7 - - - -
206E LYS 4.3 7.5 + - - +
207E PRO* 1.3 74.5 - - - +
209E LEU* 1.3 59.5 + - - +
210E SER* 4.1 1.1 + - - -
245E GLU* 3.3 23.6 - - + +
246E PRO 5.8 0.4 + - - -
247E HIS* 3.8 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160E ILE* 3.8 24.7 - - + -
193E PHE* 4.1 10.8 - - + -
194E PHE 3.5 12.8 - - - +
195E VAL* 4.0 11.2 - - + -
207E PRO 3.9 0.4 + - - -
208E LYS* 1.3 72.3 - - - +
210E SER* 1.3 68.9 + - - +
235E THR* 3.6 38.4 - - + +
238E ILE* 3.8 14.8 - - + -
239E ALA* 3.8 10.1 - - + +
244E THR* 3.7 24.9 - - - +
245E GLU 2.8 15.4 + - - +
246E PRO* 3.6 3.1 - - + +
247E HIS 2.7 29.0 + - - -
248E GLU 3.7 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 210 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193E PHE* 3.2 10.4 - - - +
194E PHE* 2.8 37.6 + - - +
196E SER* 5.6 1.0 + - - -
208E LYS 5.1 1.0 + - - -
209E LEU* 1.3 75.0 - - - +
211E CYS* 1.3 62.3 + - - +
235E THR* 4.9 0.9 - - - -
247E HIS* 3.5 28.2 - - - +
248E GLU* 3.1 20.1 + - - +
250E ILE* 4.8 1.6 - - - -
49F PHE* 3.9 24.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 211 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E CYS* 4.0 23.3 - - - -
192E GLN 3.4 4.9 - - - -
193E PHE* 3.7 24.9 - - + -
210E SER* 1.3 75.9 - - - +
212E LEU* 1.3 58.3 + - - +
231E TYR* 4.2 11.4 - - - -
235E THR* 3.3 24.9 - - - +
248E GLU 2.9 7.9 + - - +
249E PHE* 3.3 19.2 - - + -
250E ILE* 2.7 33.1 + - - +
49F PHE* 4.2 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190E PHE* 4.8 1.6 - - + -
191E CYS* 2.9 6.0 - - - -
192E GLN 2.7 37.4 + - - +
211E CYS* 1.3 74.9 - - - +
213E MET* 1.3 77.3 + - - +
214E TYR* 4.2 2.5 - - + +
250E ILE* 3.3 20.4 - - + +
252E GLN* 4.7 9.9 - - + -
49F PHE* 3.7 18.6 - - + -
50F ALA* 3.4 26.5 - - + -
214F TYR* 3.6 39.3 - - + +
252F GLN* 3.6 19.5 - - - +
253F MET 3.9 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 213 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188E HIS* 3.4 23.8 - - + -
190E PHE 3.5 11.9 - - - +
191E CYS* 3.8 4.9 - - + -
211E CYS 4.1 0.6 - - - -
212E LEU* 1.3 79.1 - - - +
214E TYR* 1.3 78.1 + - - +
215E GLN* 3.4 19.7 - - - +
227E ASN* 4.0 10.5 - - + +
231E TYR* 3.7 39.3 - - + -
249E PHE* 3.8 19.1 - - + -
250E ILE 2.8 6.7 + - - -
251E LEU* 3.4 27.8 - - + +
252E GLN 2.9 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 214 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E MET* 3.2 29.9 + - + +
190E PHE* 3.0 34.1 + - + +
212E LEU* 4.2 4.0 - - + +
213E MET* 1.3 79.2 - - - +
215E GLN* 1.3 58.6 + - - +
216E ARG* 3.9 13.7 - - + -
252E GLN* 3.3 32.3 - - + -
253E MET 4.3 2.2 - - - -
254E GLY* 3.3 14.9 - - - -
190F PHE* 3.2 33.9 - + - -
192F GLN* 2.5 36.7 + - - +
212F LEU* 3.6 32.9 - - + +
214F TYR* 5.1 6.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 215 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187E CYS 3.2 19.7 - - - +
188E HIS* 3.9 3.1 - - - +
213E MET* 3.4 14.9 - - - +
214E TYR* 1.3 74.1 - - - +
216E ARG* 1.3 56.9 + - - +
217E SER 3.1 22.8 + - - +
218E CYS* 3.4 24.2 - - - +
224E VAL* 4.4 5.1 - - - +
227E ASN* 2.9 44.3 + - - +
251E LEU* 4.0 14.7 - - + +
252E GLN 2.9 8.2 + - - +
253E MET* 3.5 0.7 - - - -
254E GLY 2.8 31.4 + - - -
550E UMP 3.3 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 216 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174E TRP* 3.8 23.7 - - - -
185E PRO* 2.9 30.1 + - - +
186E PRO 2.6 18.6 + - - +
187E CYS* 2.9 25.4 + - - +
189E MET* 3.7 18.1 - - - +
214E TYR* 3.9 5.4 - - - -
215E GLN* 1.3 72.1 - - - +
217E SER* 1.3 65.0 + - - +
255E ASP* 2.8 28.7 + - - +
550E UMP 2.8 43.6 + - - -
167F ARG* 3.0 27.3 + - - +
168F ARG* 3.7 10.6 - - - +
170F ILE* 4.4 2.2 - - + -
192F GLN* 3.1 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 217 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187E CYS* 3.7 5.7 - - - +
215E GLN* 3.1 18.0 + - - +
216E ARG* 1.3 97.0 - - - +
218E CYS* 1.3 61.1 + - - +
255E ASP* 3.5 5.2 - - - -
257E HIS* 3.1 20.1 - - - -
550E UMP 2.7 43.9 + - - +
167F ARG* 3.2 9.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 218 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E GLN* 3.4 44.4 - - - +
217E SER* 1.3 78.3 - - - +
219E ASP* 1.3 59.4 + - - +
220E LEU* 3.1 2.4 + - + +
224E VAL* 3.8 14.8 - - + -
253E MET* 3.5 37.0 - - - -
255E ASP 2.8 16.1 + - - +
256E ALA* 4.3 1.8 - - - -
257E HIS* 3.0 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 219 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218E CYS* 1.3 70.2 - - - +
220E LEU* 1.3 61.9 + - - +
221E GLY 3.2 5.4 + - - -
222E LEU* 3.1 25.7 + - - +
223E GLY 2.9 17.2 + - - -
224E VAL* 3.0 7.5 + - - +
257E HIS* 3.7 9.9 + - - +
259E TYR* 3.3 21.9 + - - -
262E HIS* 3.6 14.1 + - - -
550E UMP 3.1 18.3 + - - +
2551E CB3 2.7 43.6 + - - +
----------------------------------------------------------
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