Contacts of the helix formed by residues 259 - 268 (chain A) in PDB entry 1ACL
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 ASP 259 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 3.4 19.8 - - - +
161A SER* 4.0 16.6 - - - -
242A ARG* 2.8 35.6 + - - -
256A LEU 5.8 0.7 - - - -
257A ASN 2.9 8.9 + - - +
258A SER* 1.3 69.1 - - - +
260A GLU* 1.3 61.6 + - - +
262A LEU* 3.1 23.2 + - - +
263A ILE* 3.1 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLU* 6.3 2.7 - - + -
258A SER* 2.9 9.4 + - - +
259A ASP* 1.3 77.6 + - - +
261A GLU* 1.4 52.9 + - + +
263A ILE* 3.5 10.4 - - - +
264A HIS* 2.8 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ASN* 3.0 37.7 + - + +
257A ASN* 3.9 1.6 - - - +
258A SER* 2.6 52.4 + - - +
260A GLU* 1.4 72.0 - - + +
262A LEU* 1.3 58.6 + - - +
263A ILE 3.2 1.1 - - - -
264A HIS* 4.0 8.7 + - + +
265A CYS* 2.8 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 3.7 25.4 - - + -
245A ALA* 3.7 18.2 - - + +
246A VAL* 3.6 31.4 - - + -
249A GLY* 4.5 6.7 - - - -
254A CYS* 4.9 1.3 - - + -
255A ASN 3.5 14.7 + - - +
256A LEU* 4.8 11.0 - - + +
258A SER 3.2 2.4 + - - -
259A ASP* 3.1 19.8 + - - +
261A GLU* 1.3 79.8 - - - +
263A ILE* 1.3 66.6 + - - +
265A CYS* 3.5 3.4 - - - +
266A LEU* 3.0 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 4.5 3.5 - - + -
156A LEU* 4.3 9.9 - - + -
158A LEU* 3.3 26.7 - - + -
161A SER* 4.9 3.8 - - - -
163A GLU* 3.8 18.4 - - + +
164A ALA* 3.3 30.5 - - + -
259A ASP* 3.1 17.0 + - - +
260A GLU* 3.5 10.8 - - - +
262A LEU* 1.3 83.0 - - + +
264A HIS* 1.3 63.3 + - - +
266A LEU* 4.0 3.5 - - - +
267A ARG* 3.0 64.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A GLU 2.8 17.8 + - - +
261A GLU* 3.2 10.5 + - + +
262A LEU 3.1 0.4 - - - -
263A ILE* 1.3 78.2 - - - +
265A CYS* 1.3 71.9 + - - +
267A ARG* 2.8 19.1 + - + +
268A GLU* 3.0 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ASN 4.7 0.7 - - - -
254A CYS* 2.0 56.8 - - + -
255A ASN* 4.2 4.3 - - + +
261A GLU 2.8 18.3 + - - +
262A LEU 3.5 1.8 - - - +
264A HIS* 1.3 81.9 + - - +
266A LEU* 1.3 61.9 + - - +
268A GLU* 2.9 16.3 + - - +
269A LYS* 3.2 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG* 2.7 24.1 + - - -
45A PHE* 3.9 17.9 - - + -
156A LEU* 3.8 22.2 - - + -
245A ALA 4.7 0.4 - - - +
248A LEU* 3.4 38.8 - - + +
249A GLY* 4.6 1.6 - - - -
252A LEU* 3.9 18.6 - - + -
254A CYS* 3.7 19.5 - - - -
262A LEU* 3.0 37.0 + - + +
263A ILE* 4.0 2.0 - - - +
265A CYS* 1.3 75.1 - - - +
267A ARG* 1.3 61.2 + - - +
268A GLU 3.0 1.2 + - - -
269A LYS* 3.1 11.1 + - + +
274A LEU* 4.2 3.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLY* 3.4 32.2 - - - +
42A ASN* 3.0 23.6 + - - +
44A ARG* 2.6 53.1 + - - +
45A PHE* 3.7 13.2 - - + -
46A ARG* 3.9 3.6 - - - +
163A GLU* 2.9 55.3 + - - +
263A ILE* 3.0 36.0 + - + +
264A HIS* 2.8 15.3 + - + +
266A LEU* 1.3 77.3 - - - +
268A GLU* 1.4 58.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A HIS* 3.0 43.0 + - + +
265A CYS* 2.9 10.7 + - - +
267A ARG* 1.4 79.8 - - - +
269A LYS* 1.3 66.4 + - + +
270A LYS* 3.8 4.7 + - - +
----------------------------------------------------------
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