Contacts of the strand formed by residues 214 - 222 (chain E) in PDB entry 3RBQ
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 THR 214 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E HIS* 5.4 4.3 - - - +
166E TYR 3.2 11.2 - - - +
167E PHE* 3.2 20.5 - - - -
172E LEU* 4.0 10.1 - - + -
207E MET* 3.3 25.6 + - + +
210E HIS 4.4 1.4 + - - -
212E TYR* 3.3 1.0 - - - +
213E GLU* 1.3 76.5 - - - +
215E GLN* 1.3 68.0 + - - +
233E ASP* 3.4 1.7 - - - +
234E TYR* 3.0 39.9 + - + -
236E TYR* 3.4 35.8 - - - +
500K DAO 5.7 0.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
71E ILE* 3.6 40.2 - - + +
165E HIS* 3.5 2.1 - - - +
166E TYR* 2.8 36.0 + - + +
212E TYR 3.2 20.4 + - - +
213E GLU* 4.1 8.7 - - - +
214E THR* 1.3 81.6 - - - +
216E SER* 1.3 60.8 + - - +
231E LYS* 5.4 0.5 + - - -
232E ALA 3.3 8.7 - - - +
233E ASP* 3.6 14.9 + - + -
234E TYR* 4.1 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 216 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E ILE* 3.4 10.5 - - - +
163E GLU* 4.5 8.3 - - - +
164E ARG 3.1 13.9 - - - -
165E HIS* 3.6 28.1 + - - -
215E GLN* 1.3 74.7 - - - +
217E ASP* 1.3 58.7 + - - +
218E SER* 4.2 3.6 + - - -
231E LYS* 3.4 8.0 - - - +
232E ALA* 2.9 37.6 + - - +
234E TYR* 2.7 22.8 + - - -
501K GLY 4.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 217 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E LEU* 5.4 0.2 - - - +
70E ARG 4.5 0.5 - - - +
71E ILE* 3.3 15.5 - - + +
72E THR* 3.0 29.2 + - - +
162E ILE 3.6 2.1 - - - +
163E GLU* 3.3 3.5 - - - -
164E ARG* 2.9 34.0 + - + +
166E TYR* 4.4 3.6 + - - -
216E SER* 1.3 72.1 - - - +
218E SER* 1.3 60.1 + - - +
219E PHE* 3.4 25.0 - - + -
229E HIS* 2.8 18.5 + - - +
230E ASN 3.6 2.9 - - - -
231E LYS* 2.6 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 218 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E MET* 4.1 3.6 - - - -
162E ILE 3.7 4.3 - - - -
163E GLU* 2.6 31.5 + - - +
216E SER* 4.6 1.9 + - - -
217E ASP* 1.3 72.1 - - - +
219E PHE* 1.3 60.7 + - - +
220E TYR* 3.6 27.8 - - - -
229E HIS* 3.2 5.9 - - - -
230E ASN* 2.8 41.0 + - - +
501K GLY* 3.0 19.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 219 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E VAL* 3.9 29.4 - - + -
68E LEU* 4.0 9.4 - - + -
72E THR* 3.9 12.1 - - + -
76E LEU* 3.4 16.4 - - + -
161E MET* 3.3 3.2 - - - +
162E ILE 2.8 48.6 + - - +
164E ARG* 4.2 15.0 - - - -
166E TYR* 5.5 0.2 - - - -
217E ASP* 3.4 36.8 - - + -
218E SER* 1.3 71.9 - - - +
220E TYR* 1.3 60.6 + - - +
221E PHE* 3.5 23.8 - - + -
226E LEU* 3.7 11.7 - - + -
228E MET 3.7 2.7 - - - -
229E HIS* 3.4 36.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 220 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E PHE* 3.3 24.7 - + - -
159E PHE* 3.9 29.2 - + + -
160E ARG 3.3 3.6 - - - -
161E MET* 3.5 38.9 - - + -
179E PHE* 4.5 5.2 - + - -
218E SER* 3.6 27.1 - - - -
219E PHE* 1.3 74.3 - - - +
221E PHE* 1.3 55.1 + - - +
226E LEU* 3.3 4.2 - - - +
227E VAL* 2.8 34.5 + - + -
228E MET* 2.8 37.1 + - + +
230E ASN* 3.9 16.8 - - - -
501K GLY 3.9 1.0 - - - -
502K ALA* 3.4 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 221 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E ILE* 3.6 9.2 - - + -
61E GLY 3.4 8.3 - - - -
62E PRO* 3.4 47.3 - - + -
65E VAL* 3.8 15.5 - - + -
158E ASN 3.3 3.3 - - - +
159E PHE* 3.3 5.7 - - - -
160E ARG* 2.7 49.5 + - + +
162E ILE* 3.8 20.6 - - + -
219E PHE* 3.5 30.7 - - + -
220E TYR* 1.3 73.4 - - - +
222E VAL* 1.3 63.9 - - - +
224E ASP* 4.0 7.4 - - - +
225E ARG 3.3 11.7 - - - +
226E LEU* 3.4 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 222 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E TYR* 3.6 45.8 + - + +
86E ILE* 4.1 3.4 - - + -
156E VAL* 3.9 13.7 - - + -
157E ASN 3.6 22.9 - - - +
158E ASN 3.8 2.9 - - - -
159E PHE* 3.7 18.2 - - + -
221E PHE* 1.3 75.2 - - - +
223E ASP* 1.3 77.4 + - + +
225E ARG* 3.0 23.7 + - - +
227E VAL* 3.8 19.0 - - + +
----------------------------------------------------------
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