Contacts of the strand formed by residues 225 - 232 (chain B) in PDB entry 5E5R
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 TYR 225 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A VAL* 5.4 1.1 - - + -
226A HIS* 3.5 20.0 - + + -
288A PHE* 3.4 35.2 - + + -
299A VAL* 4.1 15.1 - - + +
137B GLY 3.8 7.8 + - - -
139B GLY* 3.0 33.1 + - - -
184B ALA 3.9 1.9 + - - -
222B MET* 4.2 10.3 - - - -
223B GLY 3.2 20.9 - - - -
224B GLU* 1.3 74.9 - - - +
226B GLU* 1.3 90.6 + - - +
228B LYS* 5.6 0.4 - - + -
252B LEU* 4.2 3.7 - - + +
253B GLY* 3.7 17.9 + - - -
254B ASN* 2.8 26.6 + - + +
301B ASN* 3.0 17.8 + - - -
303B ARG* 3.7 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LYS 3.9 9.7 - - - +
225A VAL* 3.7 33.9 - - + +
226A HIS* 2.8 28.6 + - + +
229A LYS* 3.5 14.4 + - - -
225B TYR* 1.3 85.4 - - - +
227B PRO* 1.3 72.7 - - + +
228B LYS 3.6 0.2 + - - -
252B LEU 3.9 0.2 - - - +
301B ASN* 4.1 3.6 - - - -
303B ARG* 3.3 25.4 - - - +
304B GLY* 4.2 7.8 - - - -
305B LYS 5.2 2.7 - - - -
306B ASN* 3.3 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A HIS* 3.6 1.7 - - - -
225B TYR 3.7 0.2 - - - -
226B GLU* 1.3 86.1 - - + +
228B LYS* 1.3 57.0 + - - +
229B ILE 4.1 0.4 - - - -
251B ALA* 4.1 0.9 - - + -
252B LEU 3.2 7.6 - - - +
253B GLY* 4.3 2.2 - - - -
257B PRO* 3.8 20.2 - - + -
299B ALA* 3.4 33.2 - - + +
300B GLU* 3.5 16.4 - - - +
301B ASN* 3.5 15.0 - - - +
304B GLY 3.2 21.3 - - - +
305B LYS* 4.3 1.6 - - - +
306B ASN* 2.7 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A HIS* 3.5 38.8 - - + +
227A HIS* 3.5 30.6 + - - +
228A GLU* 5.6 3.5 + - - -
290A THR* 3.2 29.5 - - + +
297A LYS* 4.5 5.4 - - - +
299A VAL* 4.5 14.6 - - + -
226B GLU 3.6 0.2 + - - -
227B PRO* 1.3 73.9 - - - +
229B ILE* 1.3 72.8 + - - +
230B GLU* 3.1 27.3 + - - +
251B ALA* 3.6 2.7 - - - -
252B LEU* 2.7 41.6 + - + +
306B ASN* 4.9 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B PRO 4.1 0.4 + - - -
228B LYS* 1.3 77.2 - - - +
230B GLU* 1.3 61.2 + - - +
231B VAL 3.7 12.3 - - - +
232B GLN* 3.4 29.9 - - + +
249B CYS* 3.7 24.2 - - - -
250B PHE 3.5 13.0 - - - +
251B ALA* 3.7 11.7 - - + -
297B CYS* 4.1 3.6 - - - +
299B ALA* 4.2 9.4 - - + -
306B ASN* 4.1 16.6 - - + +
307B VAL* 3.7 12.3 - - - +
308B ALA* 3.5 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A THR* 5.2 0.7 - - - +
297A LYS* 2.6 38.2 + - - +
141B VAL* 3.6 16.7 - - + +
182B TYR* 3.5 29.2 + - + -
228B LYS* 3.1 35.9 + - - +
229B ILE* 1.3 74.0 - - - +
231B VAL* 1.3 61.8 + - - +
232B GLN* 5.2 1.3 - - - -
250B PHE 2.8 8.8 + - - +
251B ALA* 5.1 0.2 - - - -
252B LEU* 4.3 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B PHE* 4.3 9.4 - - + -
175B SER* 4.0 6.5 - - - +
177B GLU* 5.3 2.7 - - + -
178B THR* 4.1 11.9 - - + -
182B TYR* 3.3 44.0 - - + +
229B ILE* 3.7 1.6 - - - +
230B GLU* 1.3 75.4 - - - +
232B GLN* 1.3 71.5 + - - +
248B GLU* 3.7 22.4 - - + +
249B CYS* 3.5 1.7 - - - -
250B PHE* 3.1 49.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ILE* 3.4 31.2 - - + +
230B GLU 5.2 0.7 - - - -
231B VAL* 1.3 83.4 + - - +
233B PHE* 1.3 76.5 + - + +
234B PRO* 3.8 1.4 - - - +
248B GLU* 3.1 14.1 - - - +
249B CYS* 4.6 1.8 - - - -
307B VAL 5.1 1.2 + - - -
308B ALA* 3.4 32.9 - - + +
309B ARG 4.8 4.9 + - - +
----------------------------------------------------------
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