Contacts of the strand formed by residues 151 - 155 (chain A) in PDB entry 2B2T
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 151 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ILE* 3.5 29.4 - - + -
138A ALA 3.7 1.1 - - - -
139A HIS* 3.9 23.1 - - + -
148A TYR* 5.4 2.8 - + - -
149A PRO* 3.4 27.2 - - + +
150A ASP* 1.3 73.6 - - - +
152A TYR* 1.3 58.5 + - - +
153A CYS* 3.7 4.3 + - - -
164A SER 3.4 1.6 - - - +
165A TRP* 3.2 5.3 - - - -
166A GLU* 2.6 41.6 + - - +
168A GLY* 3.6 29.6 - - - -
171A ILE* 4.0 23.6 - - + -
179A ILE* 3.6 29.5 - - + +
182A TYR* 4.5 2.7 - + - -
183A PHE* 3.6 27.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ILE* 3.7 2.8 - - - -
137A ILE* 2.9 60.2 + - + +
138A ALA* 3.0 17.7 + - + +
151A TYR* 1.3 72.7 - - - +
153A CYS* 1.3 59.6 + - - +
160A TYR* 4.5 3.4 + + - -
163A CYS* 3.3 26.7 - - + +
164A SER* 3.5 17.5 - - - -
165A TRP* 3.1 54.9 - + + -
97B LYS* 2.9 32.9 - - - +
100B GLU* 6.0 1.4 - - - +
101B THR* 5.6 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A VAL* 3.9 31.9 - - + -
135A ARG 3.9 2.7 - - - -
136A ILE* 4.4 3.4 - - - +
137A ILE* 5.7 0.2 - - - -
151A TYR* 3.9 14.8 - - - -
152A TYR* 1.3 77.9 - - - +
154A LYS* 1.3 61.3 + - - +
155A TRP* 3.8 17.3 + - + -
163A CYS* 2.9 30.7 - - - -
164A SER 2.9 13.4 + - - +
166A GLU* 4.1 16.6 - - - -
171A ILE* 4.1 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A VAL* 3.7 3.3 - - - -
134A GLY* 2.8 32.8 + - - -
135A ARG* 2.9 24.5 + - + +
137A ILE* 5.1 3.8 - - + +
152A TYR 4.2 0.2 + - - -
153A CYS* 1.3 73.0 - - - +
155A TRP* 1.3 71.2 + - - +
156A GLN* 4.4 5.3 - - - +
157A GLY 4.5 2.4 - - - +
158A LEU 3.2 23.3 + - - +
159A PRO* 4.7 1.1 - - - +
160A TYR* 3.6 45.8 - - + -
163A CYS* 3.6 17.9 - - - -
115B TYR* 4.2 15.8 + - + +
119B GLN* 3.5 32.1 + - - +
123B THR* 5.8 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A SER* 3.6 15.8 - - - -
70A ILE* 4.0 22.7 - - + -
130A TYR 3.3 26.0 - - - +
131A GLN 3.5 18.8 - - - -
132A ILE 3.6 15.5 - - - -
133A VAL* 3.4 27.1 - - + -
134A GLY* 4.5 0.4 - - - -
153A CYS* 3.8 16.5 + - + -
154A LYS* 1.3 96.4 + - - +
156A GLN* 1.3 67.2 + - - +
158A LEU* 3.2 30.3 + - + +
159A PRO 5.8 0.6 + - - -
162A GLU* 3.3 23.9 + - + +
163A CYS* 5.2 0.8 - - - +
164A SER* 3.1 19.5 + - - -
166A GLU* 3.6 28.9 - - + -
171A ILE* 5.6 2.5 - - + -
175A PHE* 4.9 2.0 - + - -
----------------------------------------------------------
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