Contacts of the helix formed by residues 120 - 129 (chain D) in PDB entry 1BI8
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 120 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D GLY 2.9 14.1 + - - -
119D HIS* 1.3 69.3 - - - +
121D ALA* 1.3 60.8 + - + +
122D VAL 3.1 0.2 + - - -
123D VAL* 3.1 3.3 + - - +
124D SER* 2.7 29.4 + - - -
153D ASP* 2.7 33.6 + - + +
154D LEU* 3.7 10.9 - - - +
157D ILE* 3.7 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D LEU* 3.7 18.0 - - + +
119D HIS 3.4 0.6 - - - -
120D THR* 1.3 82.2 - - + +
122D VAL* 1.3 58.4 + - + +
124D SER* 3.4 9.8 - - - -
125D PHE* 2.8 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D ALA* 4.1 10.5 - - + +
85D GLY* 4.2 20.9 - - - +
87D LEU* 4.3 14.1 - - + -
90D LEU* 3.4 25.4 - - + -
114D ALA* 3.9 15.9 - - + -
119D HIS* 2.8 31.6 + - + +
121D ALA* 1.3 74.0 - - + +
123D VAL* 1.3 58.2 + - - +
124D SER 3.0 1.1 - - - -
125D PHE* 2.8 8.3 + - - +
126D LEU* 2.6 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 123 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D ILE* 4.0 8.0 - - + +
114D ALA* 3.4 28.5 - - + -
115D VAL* 3.6 21.8 - - + +
119D HIS 2.9 10.3 + - - +
120D THR 3.3 7.9 - - - +
122D VAL* 1.3 77.0 - - - +
124D SER* 1.3 63.3 + - - +
127D ALA* 2.8 29.6 + - - +
154D LEU* 3.4 29.2 - - + -
157D ILE* 3.6 11.7 - - + -
158D LEU* 4.1 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D THR* 2.7 18.5 + - - -
121D ALA* 3.4 11.4 - - - -
123D VAL* 1.3 80.0 - - - +
125D PHE* 1.3 64.0 + - - +
126D LEU 3.2 0.3 + - - -
127D ALA* 3.6 9.4 + - - +
128D ALA* 4.2 5.0 + - - +
157D ILE* 3.5 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D LEU* 3.6 14.1 - - + -
90D LEU* 3.4 31.6 - - + -
91D LYS* 3.4 37.5 - - + -
94D VAL* 4.0 25.8 - - + -
95D GLU* 4.6 2.9 - - - -
121D ALA 2.8 17.0 + - - +
122D VAL 2.8 8.2 + - - +
124D SER* 1.3 74.2 + - - +
126D LEU* 1.3 79.0 + - + +
128D ALA* 4.1 10.7 - - - +
129D GLU* 3.8 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D ALA* 4.3 4.5 - - + -
90D LEU* 3.9 9.2 - - + -
100D VAL* 3.4 26.0 - - + -
110D PRO* 3.6 14.8 - - + +
111D ILE* 3.3 39.7 - - + +
114D ALA* 4.7 0.7 - - + -
122D VAL* 2.6 37.2 + - + +
123D VAL 4.0 1.6 - - - +
125D PHE* 1.3 97.1 - - + +
127D ALA* 1.3 67.3 + - - +
128D ALA 3.1 2.9 - - - -
129D GLU* 2.8 20.0 + - - +
130D SER* 2.8 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D ILE* 3.3 19.8 - - + +
123D VAL 2.8 22.3 + - - +
124D SER 3.9 5.6 - - - +
126D LEU* 1.3 70.4 - - - +
128D ALA* 1.3 66.0 + - - +
130D SER 3.1 17.2 + - - +
132D LEU* 3.8 15.1 - - + +
157D ILE* 4.4 14.8 - - + +
158D LEU* 4.2 15.3 - - + -
160D GLY 5.4 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D SER 4.2 4.7 + - - +
125D PHE 4.1 8.7 - - - +
126D LEU 2.8 3.4 + - - -
127D ALA* 1.3 78.3 - - - +
129D GLU* 1.3 68.7 + - + +
130D SER 3.3 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D VAL* 4.5 11.7 - - - +
100D VAL* 3.8 23.9 - - + +
101D ASN* 2.8 22.9 + - - +
125D PHE* 3.8 36.7 - - - +
126D LEU* 2.8 10.5 + - - +
128D ALA* 1.3 81.0 - - + +
130D SER* 1.3 57.8 + - - +
----------------------------------------------------------
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