Contacts of the helix formed by residues 264 - 273 (chain A) in PDB entry 5UFL
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 ASN 264 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 4.0 23.9 - - + +
218A ASN* 3.2 27.5 + - - +
260A ASP 4.0 1.2 + - - -
261A LEU 3.1 14.5 + - - +
262A LEU 4.2 0.4 - - - -
263A LYS* 1.3 76.3 - - - +
265A PRO* 1.4 72.0 - - - +
266A LYS* 3.0 46.5 + - - +
267A ILE* 3.5 17.1 + - + +
268A ALA* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU 5.3 0.4 - - - +
263A LYS 3.3 10.1 - - - +
264A ASN* 1.4 87.4 - - - +
266A LYS* 1.3 59.0 + - + +
268A ALA* 3.6 6.8 + - + +
269A ASP* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ASN* 5.8 2.2 + - - -
226A PHE 4.7 8.7 + - - -
264A ASN* 3.0 17.7 + - - +
265A PRO* 1.3 78.4 - - + +
267A ILE* 1.3 61.6 + - + +
269A ASP* 3.2 7.8 + - - +
270A TYR* 2.9 64.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 3.3 34.3 - - + -
226A PHE* 4.1 22.4 - - + +
231A ILE* 4.5 8.5 - - + -
235A PHE* 3.6 24.5 - - + -
258A LEU* 6.3 0.2 - - + -
261A LEU* 3.6 41.5 - - + +
262A LEU* 5.8 1.6 - - + -
264A ASN* 3.4 16.5 + - + +
266A LYS* 1.3 75.9 - - + +
268A ALA* 1.3 64.5 + - - +
270A TYR* 3.3 16.4 + - + -
271A LEU* 3.1 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU 4.3 1.4 + - - -
262A LEU* 3.8 32.1 - - + +
264A ASN 3.1 17.2 + - - +
265A PRO* 3.7 7.6 - - + +
267A ILE* 1.3 76.0 - - - +
269A ASP* 1.3 61.3 + - - +
271A LEU* 3.5 10.7 + - - +
272A THR* 3.6 17.7 + - - +
309A VAL* 3.9 27.9 - - + +
312A LEU* 4.6 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A PRO 2.9 19.3 + - - +
266A LYS* 3.2 8.0 + - - +
268A ALA* 1.3 76.6 - - - +
270A TYR* 1.3 64.2 + - - +
272A THR* 2.6 31.4 + - - +
273A ARG* 2.6 31.8 + - - -
309A VAL* 5.9 0.4 - - - -
311A GLN* 6.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A PHE 4.3 13.8 + - - -
227A HIS* 5.5 0.2 - - - -
228A ALA* 3.4 38.4 + - + +
231A ILE* 4.1 26.1 - - + +
235A PHE* 3.9 13.1 - - + -
266A LYS* 2.9 58.2 + - + +
267A ILE* 3.3 13.9 + - + +
269A ASP* 1.3 79.8 - - - +
271A LEU* 1.3 58.1 + - - +
273A ARG* 3.2 29.8 + - - +
274A TYR* 2.9 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A PHE* 3.7 28.4 - - + -
239A PHE* 3.7 20.0 - - + -
258A LEU* 4.5 12.3 - - + -
262A LEU* 3.7 25.1 - - + -
267A ILE 3.1 16.4 + - - +
268A ALA* 3.8 6.7 - - - +
269A ASP 3.3 0.4 - - - -
270A TYR* 1.3 74.7 - - - +
272A THR* 1.3 63.4 + - - +
274A TYR* 3.4 15.1 - - + +
277A PHE* 3.7 32.5 - - + +
306A PHE* 3.8 23.3 - - + -
312A LEU* 4.0 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ALA 3.6 13.0 - - - +
269A ASP* 2.6 28.0 + - - +
271A LEU* 1.3 78.9 - - - +
273A ARG* 1.3 66.8 + - - +
274A TYR 3.4 4.9 + - - +
277A PHE* 5.2 0.9 - - - +
309A VAL* 4.3 6.5 - - + -
311A GLN* 3.7 33.0 - - + +
312A LEU* 3.5 27.6 - - + -
315A MET* 3.5 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ALA* 5.9 2.0 - - - +
269A ASP* 2.6 47.1 + - - -
270A TYR* 3.2 26.2 + - - +
272A THR* 1.3 84.0 + - - +
274A TYR* 1.3 63.4 + - - +
275A GLU* 3.4 14.7 + - - +
----------------------------------------------------------
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