Contacts of the strand formed by residues 223 - 231 (chain A) in PDB entry 5O67
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 ASP 223 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 4.0 18.4 - - + -
100A SER* 5.6 4.6 + - - -
213A LYS* 3.3 32.2 + - - +
215A LEU 3.6 2.0 - - - +
216A ASP* 3.6 9.4 - - - +
217A GLU* 3.2 29.0 + - - +
222A PRO* 1.3 69.0 - - - +
224A ALA* 1.3 59.2 + - - +
225A VAL* 5.1 2.4 - - + +
272A SER* 3.5 2.6 + - - +
273A MET* 3.5 4.3 - - - -
274A VAL* 3.0 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LYS* 3.5 3.6 - - - +
214A PHE* 3.1 52.3 + - + -
215A LEU* 3.2 24.9 + - + -
222A PRO* 3.6 7.1 + - + +
223A ASP* 1.3 72.3 - - - +
225A VAL* 1.3 69.2 - - - +
271A LEU* 5.1 1.6 - - + -
272A SER 3.4 5.6 - - - +
273A MET* 4.7 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A SER* 4.8 13.2 - - - +
101A GLY 6.2 0.2 - - - -
102A PHE* 4.0 27.4 - - + -
211A ALA* 4.3 7.9 - - + -
212A TYR 3.4 9.4 - - - +
213A LYS* 3.8 33.4 - - + -
214A PHE* 3.9 2.3 - - - -
223A ASP* 5.1 2.2 - - + -
224A ALA* 1.3 82.9 - - - +
226A VAL* 1.3 68.9 + - - +
227A SER* 4.7 4.0 + - - +
270A GLY 4.0 0.3 - - - +
271A LEU* 3.4 7.3 - - - +
272A SER* 3.0 45.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ALA* 3.4 1.7 - - - +
212A TYR* 2.8 55.3 + - + +
214A PHE* 3.8 21.2 - - + -
225A VAL* 1.3 74.8 - - - +
227A SER* 1.3 70.7 + - - +
228A VAL* 6.0 1.8 - - + -
269A PRO* 6.1 1.8 - - + -
270A GLY 3.4 12.6 - - - +
271A LEU* 4.5 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ILE 3.3 12.6 - - - -
211A ALA* 4.2 9.9 - - - +
225A VAL* 4.7 5.5 + - - +
226A VAL* 1.3 80.9 - - - +
228A VAL* 1.3 72.5 + - - +
268A THR 4.6 0.4 - - - -
269A PRO* 3.3 3.1 - - - +
270A GLY* 2.9 44.0 + - - +
271A LEU* 4.2 0.5 + - - -
501A LDA 4.6 14.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A GLY* 3.1 3.9 - - - -
210A ILE* 3.0 40.0 + - + +
226A VAL* 6.0 1.6 - - + -
227A SER* 1.3 82.3 - - - +
229A ARG* 1.3 66.5 + - - +
230A VAL* 4.9 4.3 - - + -
267A ILE* 3.9 31.9 - - + -
268A THR 3.4 10.8 - - - +
269A PRO* 4.4 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ARG* 6.0 0.6 - - - +
167A ASP* 2.8 42.7 + - - -
169A ASN* 4.6 2.2 - - - +
207A ASN* 2.8 42.4 + - + +
208A PHE* 3.3 18.5 - - - +
209A GLY* 4.2 4.0 - - - -
228A VAL* 1.3 78.5 + - - +
230A VAL* 1.3 66.3 + - - +
231A LYS* 4.2 2.5 + - + +
266A SER* 4.0 0.9 + - - +
267A ILE* 3.5 2.3 - - - +
268A THR* 2.8 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ASN* 3.2 18.2 - - - +
208A PHE* 3.0 48.4 + - + -
228A VAL* 4.9 4.0 - - + -
229A ARG* 1.3 78.1 - - - +
231A LYS* 1.3 61.2 + - - +
232A ALA 4.2 0.2 + - - -
265A TRP* 3.7 31.9 - - + -
266A SER 3.5 8.3 - - - +
267A ILE* 4.3 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ASP* 2.5 50.5 + - + +
206A VAL 3.5 6.3 - - - +
207A ASN* 3.8 11.9 - - + +
229A ARG* 4.2 3.1 - - + +
230A VAL* 1.3 73.8 - - - +
232A ALA* 1.3 61.7 + - - +
233A PRO* 4.9 0.4 - - - +
262A ASN* 2.7 34.3 + - - +
264A VAL 3.2 18.3 + - - +
265A TRP* 3.5 10.7 - - - -
266A SER* 2.9 52.5 + - - +
----------------------------------------------------------
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