Contacts of the strand formed by residues 228 - 232 (chain D) in PDB entry 1Z1G
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 228 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C LYS* 3.8 36.3 - - + -
353C ILE 4.3 8.7 + - - -
354C GLU* 3.5 26.0 + - - -
355C ILE* 5.5 3.1 + - + +
223D ASP 3.6 1.6 - - - +
224D ILE* 3.3 7.4 - - - +
225D VAL 3.1 36.4 + - - +
226D ASP 4.7 6.1 - - - -
227D GLY* 1.3 88.7 - - - +
229D LEU* 1.3 60.9 + - - +
230D TYR* 3.7 8.8 + - + -
241D ALA* 4.3 20.2 - - + -
242D ILE 3.4 2.0 - - - +
243D PRO* 3.4 31.2 - - + -
244D THR* 4.1 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D THR* 4.6 1.6 - - + -
219D MSE 3.9 40.6 - - + -
220D LYS 4.8 0.7 - - - +
223D ASP* 3.6 26.5 - - + +
224D ILE* 3.9 20.2 - - + -
228D TYR* 1.3 70.5 - - - +
230D TYR* 1.3 68.1 + - - +
231D VAL* 3.7 12.7 + - + +
240D ILE 3.5 1.0 - - - +
241D ALA* 3.2 4.1 - - - -
242D ILE* 2.6 45.1 + - + +
244D THR* 4.9 2.4 - - + +
255D MSE 3.5 29.8 - - + -
259D LEU* 5.1 9.2 - - + -
271D ILE* 5.6 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C TRP* 3.9 54.1 - + + -
352C LYS* 4.1 19.8 + - + -
223D ASP* 2.9 57.2 + - - +
225D VAL* 3.6 34.6 - - + +
228D TYR* 4.2 12.2 - - + -
229D LEU* 1.3 72.5 - - - +
231D VAL* 1.3 62.3 + - - +
240D ILE 3.4 2.9 - - - -
241D ALA* 4.4 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C TRP* 4.8 3.9 - - - -
211D GLN* 3.8 18.6 - - - +
215D ASP* 4.5 19.7 - - + +
219D MSE 4.1 26.7 - - + -
223D ASP* 4.9 3.1 - - - +
229D LEU* 3.8 15.5 - - + +
230D TYR* 1.3 80.8 - - - +
232D GLU* 1.3 62.7 + - - +
233D GLN 3.8 1.1 - - - +
238D VAL 3.7 1.7 - - - +
239D LYS* 3.6 4.7 - - - +
240D ILE* 2.8 39.3 + - + +
242D ILE* 3.7 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C TRP* 4.2 24.9 - - + -
215D ASP* 3.0 16.7 - - - +
223D ASP* 5.6 0.2 + - - -
230D TYR 4.3 0.4 + - - -
231D VAL* 1.3 73.7 - - - +
233D GLN* 1.3 62.5 + - - +
234D SER* 3.2 2.1 + - - -
237D GLY* 4.7 12.1 - - - +
238D VAL 4.0 2.0 - - - -
239D LYS* 4.3 17.0 - - + -
----------------------------------------------------------
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