Contacts of the helix formed by residues 126 - 135 (chain A) in PDB entry 1BJX
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 GLY 126 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ASP* 1.3 77.2 - - - +
127A ALA* 1.3 62.0 + - - +
128A ALA 3.0 0.9 + - - -
129A ALA* 3.0 15.4 + - - +
130A GLU* 3.3 10.6 + - - +
174A ASP* 4.0 15.0 + - - -
175A VAL* 3.3 13.4 - - - +
178A LYS* 3.7 36.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PRO* 5.7 1.3 - - + -
125A ASP* 2.7 23.6 + - - +
126A GLY* 1.3 78.6 - - - +
128A ALA* 1.3 58.0 + - - +
130A GLU* 3.9 5.0 + - - +
131A SER* 3.4 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 3.4 24.5 - - + -
124A PRO* 3.5 27.8 - - + -
125A ASP 3.0 5.8 + - - +
127A ALA* 1.3 76.7 - - - +
129A ALA* 1.3 60.7 + - - +
130A GLU 3.1 2.2 - - - -
131A SER* 3.2 9.6 + - - +
132A LEU* 2.7 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 4.4 2.8 - - + +
125A ASP 3.6 3.7 + - - +
126A GLY* 3.0 20.8 + - - +
128A ALA* 1.3 79.3 - - - +
130A GLU* 1.3 61.3 + - - +
133A VAL* 3.3 24.3 + - - +
141A ILE* 3.5 25.5 - - + +
175A VAL* 4.5 11.2 - - + -
178A LYS* 4.4 7.9 - - + -
179A TYR* 4.1 23.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLY 3.3 5.6 + - - +
127A ALA* 4.3 5.4 - - - +
128A ALA 3.1 0.4 - - - -
129A ALA* 1.3 79.7 - - - +
131A SER* 1.3 64.1 + - - +
132A LEU 3.3 0.4 + - - -
133A VAL* 3.8 6.4 + - - +
134A GLU* 3.6 29.0 + - - +
178A LYS* 3.5 35.5 - - - +
179A TYR* 4.6 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ALA 3.4 12.6 + - - -
128A ALA* 3.2 16.3 + - - +
130A GLU* 1.3 77.8 - - - +
132A LEU* 1.3 63.7 + - - +
134A GLU* 3.1 12.7 + - - +
135A SER* 2.9 33.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A THR* 4.3 12.6 - - + -
123A LEU* 4.1 19.1 - - + -
128A ALA* 2.7 23.5 + - + +
130A GLU 3.3 0.2 - - - -
131A SER* 1.3 75.0 + - - +
133A VAL* 1.3 64.1 + - - +
135A SER* 2.8 25.7 + - - +
136A SER* 3.5 4.7 + - - -
139A ALA* 4.1 11.9 - - + +
140A VAL 3.8 2.0 - - - +
141A ILE* 3.0 39.7 - - + -
166A PRO* 3.8 32.9 - - + +
168A GLY* 4.3 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA 3.3 18.2 - - - +
130A GLU* 3.8 7.5 + - - +
131A SER 3.4 0.2 - - - -
132A LEU* 1.3 75.8 - - + +
134A GLU* 1.3 57.7 + - + +
136A SER 2.6 23.2 - - - +
137A GLU 5.3 0.4 - - - +
139A ALA* 4.1 10.1 - - + -
141A ILE* 4.5 4.5 - - + -
189A PHE* 3.2 55.6 - - + +
190A LYS 4.6 11.2 - - - +
191A LYS* 4.3 13.9 + - + +
195A GLY 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU* 3.6 19.8 + - - +
131A SER* 3.1 14.4 + - - +
132A LEU 2.9 1.0 - - - -
133A VAL* 1.3 79.8 - - + +
135A SER* 1.3 65.2 + - - +
136A SER* 3.1 3.3 + - - -
191A LYS* 4.0 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER* 2.9 17.1 + - - -
132A LEU* 2.8 18.5 + - - +
134A GLU* 1.3 78.0 - - - +
136A SER* 1.3 61.8 + - - +
166A PRO* 5.7 3.1 - - - -
----------------------------------------------------------
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