Contacts of the helix formed by residues 141 - 148 (chain A) in PDB entry 1AII
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 LEU 141 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 3.6 34.3 - - + -
104A MET* 4.0 15.3 - - + -
118A LEU* 4.7 0.9 - - + -
126A MET* 4.5 7.4 - - - -
129A ILE* 4.5 9.0 - - + -
130A SER* 3.9 28.8 + - - +
133A TYR* 3.7 40.3 - - + +
140A SER* 1.3 72.8 - - - +
142A GLY* 1.3 56.7 + - - +
144A ASP* 3.1 2.8 + - - -
145A ILE* 2.8 45.0 + - + +
161A ALA* 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A SER* 3.2 5.0 + - - -
141A LEU* 1.3 78.6 - - - +
143A ASP* 1.3 55.9 + - - +
145A ILE* 3.3 2.4 + - - -
146A SER* 2.8 32.4 + - - -
158A LEU* 3.2 22.9 - - - +
161A ALA* 5.1 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LYS* 5.2 5.3 - - + +
140A SER* 3.3 29.7 + - - +
141A LEU 3.3 0.6 - - - -
142A GLY* 1.3 73.4 - - - +
144A ASP* 1.3 61.1 + - - +
146A SER* 3.4 8.1 - - - -
147A SER* 2.6 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LYS* 4.6 4.7 - - - +
104A MET* 3.7 11.0 - - + -
133A TYR* 2.5 40.5 + - + +
139A LYS* 3.4 39.3 - - - +
140A SER 3.2 4.5 + - - +
141A LEU 3.1 7.5 + - - +
143A ASP* 1.3 77.1 - - - +
145A ILE* 1.3 66.6 + - - +
147A SER* 3.2 15.6 + - - -
148A GLU* 3.3 22.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A MET* 3.7 24.9 - - + -
114A LEU* 4.8 4.7 - - + -
118A LEU* 3.8 22.4 - - + -
141A LEU* 2.8 28.6 + - + +
142A GLY 3.7 3.6 - - - +
144A ASP* 1.3 77.2 - - - +
146A SER* 1.3 58.8 + - - +
148A GLU* 3.2 1.9 + - - -
149A THR* 2.7 43.7 + - + +
154A ARG 4.7 0.7 - - - +
157A LEU* 3.8 28.0 - - + +
158A LEU* 3.8 15.7 - - + -
161A ALA* 3.8 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLY 2.8 19.1 + - - -
143A ASP* 3.4 10.1 - - - -
145A ILE* 1.3 78.3 - - - +
147A SER* 1.3 55.9 + - - -
149A THR* 3.2 22.1 - - - +
154A ARG* 3.2 40.9 + - - +
158A LEU* 4.4 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ASP* 2.6 23.5 + - - +
144A ASP* 3.2 10.6 + - - -
146A SER* 1.3 74.3 - - - +
148A GLU* 1.3 74.1 + - - +
149A THR 3.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A MET* 3.7 33.4 - - + +
107A ALA 5.4 0.5 - - - +
109A THR* 3.8 25.1 + - + +
111A GLU* 5.4 0.7 - - - +
144A ASP* 3.3 18.7 - - + +
145A ILE 3.2 4.2 + - - +
147A SER* 1.3 93.4 - - - +
149A THR* 1.3 68.1 + - + +
357A CA 2.9 24.5 - - - -
----------------------------------------------------------
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