Contacts of the strand formed by residues 226 - 230 (chain D) in PDB entry 1RD3
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 GLY 226 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D CYS* 3.1 9.9 - - - +
183D ALA 3.0 37.4 + - - -
189D ASP* 4.8 8.2 + - - -
215D TRP 3.4 11.4 - - - -
216D GLY* 4.6 7.2 - - - -
217D LYS 4.9 1.3 - - - -
225D TYR* 1.3 72.8 - - - +
227D PHE* 1.3 62.2 + - - -
228D TYR* 3.5 12.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ASN 5.6 3.4 - - - -
171D SER* 4.8 5.6 - - - -
172D THR* 3.5 34.1 - - + -
174D ILE* 4.5 12.1 - - + -
176D ILE* 3.7 11.4 - - + -
180D MET* 5.3 14.4 - - + -
181D PHE 3.8 3.4 - - - +
182D CYS* 3.6 25.1 - - - -
213D VAL* 4.3 0.2 - - - -
214D SER* 2.9 12.4 + - - +
215D TRP* 2.8 71.1 + + + +
217D LYS* 3.0 29.4 - - - -
225D TYR* 4.0 6.5 - - + -
226D GLY* 1.3 76.9 - - - -
228D TYR* 1.3 66.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D VAL* 3.6 12.7 - - + +
160D LEU* 3.4 26.2 - - - +
180D MET* 3.0 10.4 - - - +
181D PHE* 2.8 59.9 + + + +
183D ALA* 3.5 24.5 + - + -
189D ASP* 4.8 1.9 + - - -
190D ALA* 3.9 12.3 - - + +
199D PHE* 3.5 33.9 - + + -
212D ILE 3.2 16.6 - - - +
213D VAL* 3.8 20.2 - - + -
214D SER* 4.0 3.1 - - - -
215D TRP 6.1 0.2 - - - -
216D GLY* 6.1 1.1 - - - -
226D GLY* 3.5 25.7 - - - -
227D PHE* 1.3 77.0 - - - +
229D THR* 1.3 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D LEU 5.2 0.2 + - - -
101D ARG 4.7 0.2 - - - -
102D ASP* 2.8 45.8 + - - +
103D ILE* 4.2 5.4 - - + -
179D ASN 3.7 8.5 - - - +
180D MET* 4.4 1.6 - - - +
181D PHE* 4.5 0.4 - - - -
211D GLY* 3.0 20.1 - - - -
212D ILE* 3.0 23.8 + - + +
214D SER* 3.8 7.1 - - - -
228D TYR* 1.3 71.4 - - - +
230D HIS* 1.3 61.6 + - - +
231D VAL* 3.0 9.8 + - - +
234D LEU* 3.5 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D ALA* 4.8 5.4 - - + -
130D LEU* 3.9 28.3 - - + +
165D ARG* 4.7 6.5 - - - -
178D ASP 4.0 11.4 - - - -
179D ASN 3.0 26.8 + - - -
180D MET* 3.7 2.5 - - - +
181D PHE* 4.0 24.0 - + + -
210D MET* 4.0 6.2 + - + -
228D TYR 3.5 3.2 + - - -
229D THR* 1.3 67.8 - - - +
231D VAL* 1.3 66.3 + - - +
232D PHE* 3.7 21.2 + + + -
233D ARG* 3.3 48.7 + - + +
234D LEU* 3.5 12.6 + - - +
248D PO4 5.0 2.5 + - - -
----------------------------------------------------------
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