Contacts of the helix formed by residues 143 - 150 (chain J) in PDB entry 2BM8
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 THR 143 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141J ASP* 3.0 21.8 + - - -
142J LEU* 1.3 75.1 - - - +
144J THR* 1.3 66.4 + - - +
145J PHE 3.1 1.4 + - - -
146J GLU* 3.2 36.2 + - + +
147J HIS 4.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 144 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115J ILE* 4.5 12.1 - - + -
136J GLN 4.1 6.4 - - - +
137J GLY* 3.3 28.6 - - - -
138J ASP* 3.1 28.8 + - - +
141J ASP* 3.2 20.8 + - - +
143J THR* 1.3 80.0 - - - +
145J PHE* 1.3 65.1 + - + +
147J HIS* 3.3 25.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 145 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88J LEU* 4.0 21.1 - - + -
115J ILE* 4.2 23.3 - - + -
138J ASP 4.0 18.4 - - - -
139J CYS* 4.3 5.2 - - - -
141J ASP 3.9 11.0 - - - -
142J LEU* 3.2 20.0 + - + +
143J THR 3.1 1.6 + - - -
144J THR* 1.3 78.7 - - + +
146J GLU* 1.3 65.9 + - - +
147J HIS* 3.1 7.9 + - - -
148J LEU* 3.4 15.7 + - + +
157J PHE* 3.9 29.8 - + - -
168J ILE* 3.8 36.1 - - + -
171J TRP* 3.1 38.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 146 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142J LEU* 2.9 27.1 + - - +
143J THR* 3.2 30.8 + - + +
145J PHE* 1.3 76.9 - - - +
147J HIS* 1.3 63.6 + - - +
149J ARG* 3.0 53.4 + - - +
171J TRP* 3.8 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 147 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113J ILE* 4.4 4.6 - - - +
115J ILE* 4.4 11.7 - - + -
135J HIS* 2.8 52.4 + + + -
136J GLN 5.4 2.7 - - - -
143J THR 4.8 0.4 + - - -
144J THR* 3.3 25.3 + - + -
145J PHE* 3.1 1.7 + - - -
146J GLU* 1.3 77.7 - - - +
148J LEU* 1.3 93.5 + - + +
149J ARG 3.1 4.6 + - - -
150J GLU* 3.8 12.6 + - - +
151J MET* 4.4 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86J VAL* 3.8 35.2 - - + -
113J ILE* 4.5 3.4 - - + -
115J ILE* 3.8 18.6 - - + -
145J PHE* 3.4 14.1 - - + +
146J GLU 3.1 0.6 + - - -
147J HIS* 1.3 92.7 - - + +
149J ARG* 1.3 59.3 + - - +
150J GLU 3.4 0.9 - - - -
151J MET* 3.1 38.1 - - + +
155J LEU* 5.0 1.3 - - + +
157J PHE* 4.7 5.8 - - + -
171J TRP* 3.7 10.3 - - + -
176J LEU* 3.2 44.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 149 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145J PHE 4.6 0.2 + - - -
146J GLU* 3.0 48.1 + - - +
147J HIS 3.1 0.2 - - - -
148J LEU* 1.3 80.0 - - - +
150J GLU* 1.3 61.1 + - + +
151J MET 3.2 9.4 + - - +
153J HIS* 5.0 3.8 + - - -
171J TRP* 4.3 7.9 - - + +
175J HIS* 3.0 58.3 + - - +
176J LEU* 4.0 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 150 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147J HIS 3.8 8.8 + - - +
148J LEU 3.4 0.4 - - - -
149J ARG* 1.3 78.4 - - + +
151J MET* 1.3 68.1 + - - +
----------------------------------------------------------
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