Contacts of the strand formed by residues 184 - 192 (chain A) in PDB entry 1Y57
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 184 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ILE* 5.9 2.8 - - + +
149A TYR* 3.5 35.3 + + - -
174A VAL* 4.3 9.6 - - + -
175A ARG 3.3 19.3 - - - +
176A GLU* 4.1 8.3 - - + -
177A SER* 3.8 4.0 - - - +
182A GLY 3.7 17.3 - - - -
183A ALA* 1.3 79.0 - - - +
185A CYS* 1.3 63.6 + - - +
203A LYS* 3.7 8.5 - - - +
204A ILE* 2.8 40.6 + - + +
206A LYS* 6.0 0.4 - - + -
212A PHE* 3.9 31.8 - + - -
223A LEU* 4.3 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ARG* 5.2 0.2 - - - -
173A LEU 3.8 0.3 - - - +
174A VAL* 3.3 5.5 - - - -
175A ARG* 2.8 77.0 + - + +
176A GLU 4.6 1.3 - - - +
184A TYR* 1.3 77.4 - - - +
186A LEU* 1.3 65.7 + - - +
187A SER* 3.9 2.0 - - - -
201A HIS* 3.8 21.5 - - - -
202A TYR 3.6 15.9 - - - -
203A LYS* 4.4 2.0 - - - -
204A ILE* 4.2 4.7 - - - +
535A SO4 3.8 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A PHE* 3.8 25.4 - - + -
173A LEU 3.6 14.8 - - - +
174A VAL* 4.1 9.6 - - + +
185A CYS* 1.3 71.4 - - - +
187A SER* 1.3 60.4 + - - +
188A VAL* 3.9 8.5 - - + -
201A HIS* 3.4 2.3 - - - -
202A TYR* 2.8 47.1 + - + +
204A ILE* 4.0 14.8 - - + +
214A ILE* 3.8 22.7 - - + -
226A LEU* 4.4 9.2 - - + -
227A VAL* 5.3 1.8 - - + -
230A TYR* 4.8 0.7 - - + -
237A LEU* 3.8 23.6 - - + -
241A LEU* 3.9 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A SER* 3.9 4.0 - - - -
162A LEU* 3.6 22.0 - - - +
172A PHE* 3.2 7.3 - - - +
173A LEU* 3.0 39.7 + - - +
175A ARG* 3.1 21.3 + - - -
185A CYS* 3.9 1.1 + - - -
186A LEU* 1.3 72.7 - - - +
188A VAL* 1.3 61.3 + - - +
200A LYS 3.4 4.5 - - - -
201A HIS* 2.8 30.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LEU* 4.8 0.7 - - - -
170A GLY* 3.8 18.2 - - - -
171A THR 3.3 5.2 - - - +
186A LEU* 3.9 15.7 - - + -
187A SER* 1.3 79.3 - - - +
189A SER* 1.3 73.8 + - - +
190A ASP* 3.6 0.7 + - - +
199A VAL* 3.4 7.3 - - - +
200A LYS* 2.9 33.4 + - - +
202A TYR* 4.0 17.0 - - + -
237A LEU* 5.2 1.6 - - + -
238A CYS* 3.9 20.6 - - - -
239A HIS 4.6 5.2 - - - +
241A LEU* 3.8 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LEU* 3.8 27.8 - - - +
163A LEU* 5.6 1.6 - - - -
167A ASN* 4.8 2.3 + - - +
168A PRO 3.0 25.1 + - - -
169A ARG* 3.8 3.6 - - - +
170A GLY* 3.0 20.3 + - - -
171A THR* 2.9 22.5 + - - -
188A VAL* 1.3 76.6 - - - +
190A ASP* 1.3 60.8 + - - +
197A LEU* 5.6 7.0 - - - -
198A ASN 3.7 6.7 - - - -
199A VAL* 4.6 4.7 - - - -
238A CYS* 4.6 1.0 - - - -
239A HIS* 4.9 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ARG* 2.8 49.0 + - - +
188A VAL 3.6 0.2 + - - -
189A SER* 1.3 74.2 - - - +
191A PHE* 1.3 71.3 + - - +
197A LEU* 3.7 12.3 - - - +
198A ASN* 2.8 40.6 + - - +
200A LYS* 2.6 29.7 + - + +
238A CYS* 3.4 29.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ARG* 3.9 28.8 + - + +
190A ASP* 1.3 88.0 + - - +
192A ASP* 1.3 74.6 + - - +
193A ASN* 4.0 22.6 + - - +
196A GLY* 3.6 23.6 - - - -
197A LEU* 3.7 31.4 - - + -
198A ASN* 3.9 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A PHE* 1.3 77.3 - - - +
193A ASN* 1.3 64.4 + - - +
194A ALA* 2.9 20.6 + - - +
195A LYS* 2.9 38.3 + - + +
196A GLY* 2.8 42.0 + - - +
198A ASN* 3.6 9.8 - - - +
----------------------------------------------------------
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