Contacts of the strand formed by residues 156 - 160 (chain J) in PDB entry 2OHI
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 MET 156 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80J ILE* 3.8 10.1 - - + -
81J GLN 3.6 16.4 - - - +
82J ASN* 2.8 52.8 + - - +
105J TYR 4.0 0.4 - - - +
106J CYS* 4.0 5.4 - - - -
107J THR* 3.7 26.0 - - + -
129J VAL* 3.7 22.7 - - + -
144J PHE* 3.6 29.6 - - + -
145J LEU 3.3 17.3 - - - +
146J GLU* 4.1 1.8 - - - +
147J THR* 3.4 4.3 - - - -
155J SER* 1.3 76.4 - - - +
157J PHE* 1.3 62.0 + - - +
169J ASN* 2.8 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 157 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144J PHE* 3.7 3.1 - - - -
145J LEU* 2.7 52.8 + - + +
147J THR* 3.5 28.2 + - + -
150J LEU* 5.0 8.3 - - + -
156J MET* 1.3 78.1 - - - +
158J THR* 1.3 63.6 + - - +
166J LEU* 3.9 29.6 - - + -
167J PHE 3.4 6.7 - - - +
168J SER* 3.1 37.7 - - - -
169J ASN* 3.7 10.5 - - - -
171J ALA* 3.9 19.3 - - + -
172J PHE* 4.9 6.3 - + - -
213J LYS* 4.1 18.6 - - + -
217J VAL* 5.2 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 158 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J ILE* 4.3 10.0 - - + +
80J ILE* 4.0 3.9 - - + +
82J ASN* 2.7 34.2 + - - -
142J LEU* 3.7 38.1 - - + -
143J THR 3.5 6.3 - - - +
144J PHE* 3.9 17.0 - - + -
157J PHE* 1.3 74.3 + - - +
159J LEU* 1.3 61.9 + - - +
160J LEU 4.2 0.2 - - - -
166J LEU* 3.7 3.8 - - - +
167J PHE* 2.8 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141J THR 3.5 1.9 - - - +
142J LEU* 3.3 6.0 - - - -
143J THR* 2.8 54.1 + - - +
145J LEU* 6.2 3.1 - - + +
157J PHE* 6.2 0.2 - - + -
158J THR* 1.3 75.8 - - - +
160J LEU* 1.3 67.2 + - - +
161J ASP* 3.9 7.1 + - + +
164J GLY* 4.9 1.8 - - - -
165J ILE 3.6 22.0 - - - +
166J LEU* 4.1 21.3 - - + +
222J LEU* 3.9 42.8 - - + +
225J ARG* 4.9 12.3 - - + +
226J ILE* 4.5 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 160 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J VAL* 3.8 20.0 - - + -
40J VAL* 3.9 12.3 - - + -
140J LYS* 3.7 21.1 - - + -
141J THR 3.7 9.0 - - - +
142J LEU* 3.8 17.5 - - + +
158J THR 4.2 0.4 - - - -
159J LEU* 1.3 74.0 - - - +
161J ASP* 1.3 61.6 + - - +
162J GLU* 3.6 20.0 - - - +
163J ASP* 3.2 32.5 - - + +
164J GLY* 3.1 4.7 + - - -
165J ILE* 2.9 39.0 + - + +
167J PHE* 3.9 21.2 - - + -
----------------------------------------------------------
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