Contacts of the strand formed by residues 224 - 231 (chain D) in PDB entry 3MY0
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 GLU 224 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D LEU* 3.3 7.3 - - - +
221D TRP* 2.9 51.3 + - - +
222D HIS 3.1 11.0 + - - +
223D GLY* 1.3 77.4 - - - +
225D SER* 1.3 65.2 + - - +
226D VAL* 5.0 7.5 - - + +
260D ILE* 5.6 3.5 - - - +
278D HIS* 6.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D ARG* 4.2 16.6 + - - -
219D GLY 3.4 7.2 + - - -
220D LEU* 4.9 5.8 - - - +
223D GLY 4.1 0.5 + - - -
224D GLU* 1.3 78.8 - - - +
226D VAL* 1.3 65.8 + - - +
278D HIS* 5.0 1.4 - - - -
279D TYR* 3.7 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D VAL* 5.8 1.1 - - + -
202D VAL* 3.7 28.5 - - + -
218D ARG* 3.6 4.5 - - - +
219D GLY* 2.7 47.1 + - - +
221D TRP* 4.4 22.4 - - + -
224D GLU* 4.7 9.2 - - - +
225D SER* 1.3 79.9 - - - +
227D ALA* 1.3 57.0 + - - +
228D VAL* 4.2 2.7 - - + -
260D ILE* 3.6 26.0 - - + -
276D ILE* 4.0 15.7 - - + -
277D THR 3.5 10.8 - - - +
278D HIS* 5.5 0.2 - - - -
279D TYR* 3.5 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D VAL* 4.4 14.4 - - + -
217D TRP 3.5 6.1 - - - +
226D VAL* 1.3 72.4 - - - +
228D VAL* 1.3 61.4 + - - +
229D LYS 4.0 0.9 - - - +
275D LEU 3.7 0.5 - - - +
276D ILE* 3.2 7.1 - - - +
277D THR* 2.8 51.4 + - - +
278D HIS 3.5 8.7 - - - +
279D TYR* 3.6 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D VAL* 3.8 24.2 - - + -
204D LEU* 3.7 31.2 - - + -
215D GLU 3.9 0.2 - - - +
216D VAL* 3.6 1.5 - - - -
217D TRP* 2.9 38.7 + - - +
219D GLY* 4.7 1.3 - - - -
226D VAL* 4.2 6.3 - - + +
227D ALA* 1.3 76.4 - - - +
229D LYS* 1.3 59.8 + - - +
230D ILE* 3.5 10.3 + - + -
274D TRP* 3.7 38.1 - - + -
275D LEU 3.5 3.1 - - - +
276D ILE* 4.0 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D TYR* 3.7 37.9 - - + +
215D GLU 3.4 11.4 - - - +
216D VAL* 3.9 16.8 - - + +
227D ALA* 4.0 1.8 - - + +
228D VAL* 1.3 69.2 - - - +
230D ILE* 1.3 63.4 + - - +
231D PHE* 3.6 45.1 - - + -
235D ASP* 5.0 1.2 + - - -
242D GLU* 4.6 3.8 + - - +
274D TRP* 3.5 3.7 - - - -
275D LEU* 2.8 45.6 + - + +
277D THR* 6.4 0.9 - - + -
348D ASP* 4.4 23.6 + - - +
369D ARG* 5.5 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D LEU* 4.5 14.1 - - + -
214D GLY* 3.4 0.9 - - - -
215D GLU* 2.9 44.0 + - + +
217D TRP* 3.8 28.0 - - + +
228D VAL* 4.3 10.5 - - + +
229D LYS* 1.3 74.5 - - - +
231D PHE* 1.3 66.9 + - - +
268D ASN* 6.2 2.7 - - + -
272D GLN* 3.9 27.8 - - + -
273D LEU 3.6 3.4 - - - -
274D TRP* 3.6 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D TYR 3.6 8.3 - - - -
214D GLY* 4.2 0.2 - - - -
229D LYS* 3.6 43.7 - - + -
230D ILE* 1.3 80.8 - - - +
232D SER* 1.3 65.7 + - - +
235D ASP* 3.7 27.4 - - - +
236D GLU* 5.2 1.3 - - - +
238D SER* 3.9 11.2 - - - -
239D TRP* 3.5 39.3 - + + -
242D GLU* 3.7 19.3 - - - -
272D GLN* 5.4 1.9 - - - +
273D LEU* 3.1 35.5 + - + +
275D LEU* 3.8 24.9 - - + -
348D ASP* 6.1 0.2 - - - -
----------------------------------------------------------
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