Contacts of the helix formed by residues 265 - 276 (chain A) in PDB entry 2ILU
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 265 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ALA* 1.3 68.3 - - - +
266A LEU* 1.3 63.6 + - - +
267A GLU* 3.0 18.8 + - - +
268A LEU* 2.7 50.1 + - + +
269A ALA* 3.1 19.6 + - - +
416A TYR* 5.7 1.1 - - - +
417A THR 5.5 0.2 + - - -
418A GLN* 3.2 18.6 + - - +
438A ASN* 5.6 2.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
260A VAL* 5.8 0.2 - - + -
264A ALA 2.6 11.6 + - - +
265A ASP* 1.3 69.5 + - - +
267A GLU* 1.3 63.0 + - + +
269A ALA* 3.6 3.6 + - - +
270A VAL* 3.1 33.4 + - + +
297A ILE* 4.1 15.0 - - + -
300A GLN* 3.4 40.8 - - + +
301A PHE* 3.6 42.4 - - + +
304A ARG* 3.5 37.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ASP* 3.0 11.1 + - - +
266A LEU* 1.3 76.5 - - + +
268A LEU* 1.3 57.6 + - - +
270A VAL* 3.9 3.6 - - - +
271A LYS* 3.0 32.9 + - - +
304A ARG* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ASP* 2.7 36.3 + - + +
267A GLU* 1.3 73.1 - - - +
269A ALA* 1.3 55.6 + - - +
271A LYS* 3.1 8.4 + - - +
272A ALA* 2.6 40.1 + - + -
416A TYR* 3.9 15.3 - - + -
438A ASN* 3.6 48.7 - - + +
439A ARG* 4.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A VAL* 4.3 11.2 - - + -
264A ALA* 5.3 0.4 - - + -
265A ASP 3.1 14.5 + - - +
266A LEU* 4.0 4.3 - - - +
268A LEU* 1.3 77.3 - - - +
270A VAL* 1.3 65.8 + - - +
272A ALA* 3.8 0.2 - - - -
273A ILE* 2.9 31.2 + - - +
301A PHE* 4.1 15.7 - - + -
416A TYR* 3.9 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU* 3.1 23.3 + - + +
267A GLU* 3.9 3.4 - - - +
269A ALA* 1.3 75.7 - - - +
271A LYS* 1.3 62.9 + - - +
273A ILE* 4.0 0.5 - - - +
274A VAL* 3.0 30.4 + - - +
301A PHE* 3.8 30.5 - - + +
304A ARG* 3.8 29.6 - - + +
305A LEU* 3.7 31.4 - - + +
308A ALA* 4.1 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLU 3.0 19.7 + - - +
268A LEU* 3.4 7.2 - - - +
270A VAL* 1.3 77.1 - - - +
272A ALA* 1.3 54.1 + - - +
274A VAL* 3.3 3.7 + - - -
275A ASP* 2.7 63.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 2.6 27.1 + - + +
269A ALA 3.8 0.4 - - - +
271A LYS* 1.3 74.8 - - - +
273A ILE* 1.3 56.6 + - - +
275A ASP* 3.8 5.7 - - - +
276A SER* 3.0 30.5 + - - -
416A TYR* 3.6 30.3 - - + +
439A ARG* 4.6 0.2 - - - -
440A GLU* 3.9 25.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ALA* 4.5 5.2 - - + -
260A VAL* 4.1 11.4 - - + -
269A ALA 2.9 21.9 + - - +
270A VAL 4.1 2.5 - - - +
272A ALA* 1.3 71.4 - - - +
274A VAL* 1.3 60.9 + - - +
276A SER* 3.6 4.2 - - - -
277A ARG* 3.3 26.1 + - + +
288A ALA* 4.2 20.6 - - + +
291A VAL* 3.8 16.6 - - + -
301A PHE* 3.5 31.0 - - + -
305A LEU* 4.5 8.7 - - + -
389A LEU* 3.9 26.9 - - + -
416A TYR* 4.1 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A VAL 3.0 20.0 + - - +
271A LYS* 3.8 2.9 - - - +
273A ILE* 1.3 73.7 - - - +
275A ASP* 1.3 68.9 + - - +
276A SER 3.0 13.1 + - - +
277A ARG* 4.2 3.5 - - - +
278A VAL* 4.1 11.4 + - + +
305A LEU* 3.7 19.5 - - + -
308A ALA* 3.7 40.4 - - + +
309A MET* 4.9 7.2 - - + +
312A VAL* 4.6 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LYS* 2.7 57.2 + - - +
272A ALA* 3.9 6.6 - - - +
274A VAL* 1.3 78.1 - - - +
276A SER* 1.3 61.6 + - - +
278A VAL 5.2 0.9 - - - +
279A ILE* 3.3 13.9 - - - +
440A GLU* 5.0 11.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ALA 3.0 18.2 + - - -
273A ILE* 3.6 6.3 - - - -
274A VAL 3.0 1.6 - - - +
275A ASP* 1.3 82.9 - - - +
277A ARG* 1.3 60.4 + - - -
278A VAL 2.5 21.8 + - - -
279A ILE* 3.1 15.6 + - - +
286A ASN 4.3 0.3 + - - -
287A CYS* 3.4 29.3 - - - +
288A ALA 5.0 1.8 - - - -
440A GLU* 4.7 10.1 - - - -
441A ASN* 3.4 22.7 + - - +
----------------------------------------------------------
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