Contacts of the strand formed by residues 156 - 163 (chain A) in PDB entry 2O8U
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 LYS 156 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 3.0 29.5 + - + +
18A GLY* 2.8 32.4 + - - +
19A GLY 4.6 1.1 - - - -
20A GLU* 3.3 18.2 - - - +
21A PHE* 3.6 18.2 - - + -
22A THR* 3.9 3.4 - - - -
139A THR* 3.3 8.0 - - - +
140A GLY 3.0 35.7 + - - +
144A GLU* 2.7 44.8 + - + +
152A PRO* 4.3 8.1 - - + -
154A GLN 3.6 10.8 - - - +
155A LEU* 1.3 77.5 - - - +
157A MET* 1.3 63.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 4.2 5.2 - - - +
19A GLY* 3.5 0.5 - - - -
20A GLU* 2.9 61.6 + - + +
21A PHE 5.2 0.2 - - - +
22A THR* 4.0 30.5 - - + +
26A ASN* 4.3 26.5 - - + +
27A GLN* 5.0 4.3 - - - -
137A GLU* 5.1 14.4 - - + +
138A ILE 3.1 15.5 - - - +
139A THR* 3.7 12.8 - - - +
156A LYS* 1.3 77.9 - - - +
158A THR* 1.3 65.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 3.8 11.9 - - + -
19A GLY* 3.3 16.6 - - - -
20A GLU* 5.4 3.1 - - - -
137A GLU* 3.2 8.4 - - - +
138A ILE* 3.0 59.1 + - + -
157A MET* 1.3 78.0 - - - +
159A VAL* 1.3 74.5 + - - +
160A VAL* 4.5 0.7 - - + -
188A THR* 2.6 36.7 + - + +
189A ASP 4.4 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 6.1 0.9 - - - +
135A SER* 3.8 27.8 - - - +
136A CYS 3.2 14.8 - - - +
137A GLU* 4.7 8.5 - - + +
158A THR* 1.3 82.9 + - - +
160A VAL* 1.3 73.1 + - - +
161A LYS* 5.5 1.3 - - + -
185A ASP* 4.5 4.2 - - - +
188A THR* 3.4 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A THR 3.9 0.2 - - - +
135A SER* 3.6 0.9 - - - -
136A CYS* 2.9 29.4 + - - +
138A ILE* 4.1 30.1 - - + -
158A THR* 4.5 0.4 - - + -
159A VAL* 1.3 82.3 - - - +
161A LYS* 1.3 64.4 + - - +
162A LEU* 5.1 0.2 - - - +
183A ALA* 3.7 20.1 - - + +
184A ALA* 3.8 24.5 - - - +
185A ASP* 4.3 1.1 - - - +
188A THR* 4.0 22.2 - - + +
189A ASP* 4.4 5.4 - - - +
199A LEU* 4.1 18.6 - - + -
228A TYR* 4.4 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLY* 3.6 22.4 + - - +
134A THR 3.3 5.4 - - - +
135A SER* 3.5 26.0 - - - +
159A VAL* 5.5 1.3 - - + -
160A VAL* 1.3 75.6 - - - +
162A LEU* 1.3 66.0 + - - +
163A ILE* 3.5 4.1 + - + +
183A ALA* 3.1 4.1 - - - -
184A ALA 2.8 38.2 + - - +
185A PRO* 4.4 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PRO* 3.6 50.9 - - + +
131A GLN 4.1 2.7 - - - +
132A PHE* 3.6 13.9 - - - +
133A GLY* 2.7 26.4 + - - +
134A THR* 3.0 12.9 + - - +
136A CYS* 3.4 30.3 - - + -
161A LYS* 1.3 75.1 - - - +
163A ILE* 1.3 62.4 + - - +
181A LEU* 5.0 16.2 - - + -
182A CYS 3.6 5.6 - - - +
183A ALA* 4.3 13.5 - - + -
199A LEU* 4.3 11.4 - - + -
201A CYS* 4.2 3.8 - - - -
210A THR* 4.8 3.4 - - + -
1194A BEN 5.2 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A PHE* 4.1 0.9 - - - -
161A LYS* 3.7 9.0 - - + +
162A LEU* 1.3 77.9 - - - +
164A SER* 1.3 76.8 + - - +
165A HIS* 3.7 0.5 + - - -
167A GLU* 3.2 42.6 - - + +
168A CYS* 3.9 10.8 - - + +
171A TYR* 4.5 2.0 - - + -
181A LEU* 5.0 1.4 - - - +
182A CYS* 2.8 30.3 + - + +
183A ALA 4.2 0.2 - - - -
184A ALA* 3.7 18.2 - - + +
186A TRP* 4.7 3.1 - - + -
225A PRO* 3.4 38.1 - - + -
1194A BEN 3.6 10.7 + - - -
----------------------------------------------------------
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