Contacts of the helix formed by residues 261 - 273 (chain A) in PDB entry 1XFV
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 ALA 261 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU 4.0 15.6 + - - +
210A PHE* 5.8 0.2 - - + -
212A GLN* 3.9 4.4 + - - +
213A LYS* 3.8 26.7 - - - +
257A LEU* 2.8 28.4 + - + +
260A TYR* 1.3 75.9 - - - +
262A PRO* 1.3 68.1 - - + +
263A ASP 3.6 0.6 + - - +
264A MET* 4.5 13.9 - - + +
265A PHE* 4.0 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A SER* 5.9 1.8 - - - +
205A SER* 3.5 32.5 - - - +
207A ASP* 3.7 24.7 - - + +
258A GLU* 4.5 11.0 - - - +
259A LEU 5.8 0.2 - - - +
260A TYR 3.1 10.0 - - - +
261A ALA* 1.3 82.5 - - + +
263A ASP* 1.3 70.1 + - + +
265A PHE* 4.0 7.5 - - + +
266A GLU* 3.9 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LYS* 2.9 42.3 - - + +
200A SER* 4.6 18.5 - - - +
204A ASP* 6.1 0.5 - - - +
205A SER* 6.3 0.7 - - - -
261A ALA* 3.4 0.6 - - - +
262A PRO* 1.3 81.9 - - + +
264A MET* 1.3 56.6 + - - +
265A PHE 2.5 17.3 + - - -
266A GLU* 2.7 19.8 + - - +
267A TYR* 2.9 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ASN* 5.6 2.7 - - - +
197A LYS* 2.9 38.3 - - + +
213A LYS* 3.8 27.6 - - + +
237A PHE 5.9 0.2 - - - +
240A ALA* 3.7 7.2 - - + +
241A PHE* 3.7 24.2 - - + +
244A ALA* 3.4 29.8 - - + -
257A LEU* 4.3 18.2 - - + -
261A ALA* 4.5 7.1 + - + +
263A ASP* 1.3 77.3 + - - +
265A PHE* 1.3 66.1 + - - +
267A TYR* 3.2 17.1 - - + +
268A MET* 2.9 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A TYR* 3.8 27.1 - + - -
254A ARG 5.7 2.0 - - - -
257A LEU* 3.8 16.2 - - + +
258A GLU* 4.0 59.9 - - + -
261A ALA 4.0 7.6 + - - +
262A PRO 4.0 11.2 - - - +
263A ASP 2.5 4.8 + - - -
264A MET* 1.3 76.7 - - - +
266A GLU* 1.3 81.1 + - + +
267A TYR 2.6 12.5 + - - -
268A MET* 2.9 1.7 + - - +
269A ASN* 2.7 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A PRO 3.9 7.2 + - - +
263A ASP* 2.7 14.1 + - - +
265A PHE* 1.3 97.5 - - + +
267A TYR* 1.3 55.1 + - - +
269A ASN* 3.6 12.7 + - - -
270A LYS* 3.1 37.4 + - - +
273A LYS* 3.6 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A LYS* 3.3 32.3 - - + +
193A LEU* 5.0 10.5 - - + -
194A ASN* 3.6 26.0 + - + +
197A LYS* 2.9 33.9 - - + +
241A PHE* 4.0 28.0 - + - -
263A ASP* 2.9 15.7 + - - +
264A MET* 3.2 26.5 - - - +
265A PHE 2.6 5.3 + - - -
266A GLU* 1.3 71.0 - - - +
268A MET* 1.3 74.0 + - + +
269A ASN 3.0 0.7 - - - -
270A LYS* 2.8 23.8 + - - +
271A LEU* 3.0 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A PHE* 3.2 37.7 - - + +
244A ALA* 3.3 52.3 - - + +
245A PHE* 3.7 16.6 - - - -
248A TYR* 3.3 25.9 - - + -
249A PHE* 5.5 2.8 - - + -
257A LEU* 4.5 1.1 - - + -
264A MET* 2.9 13.6 + - - +
265A PHE 2.9 1.9 + - - +
267A TYR* 1.3 96.2 - - + +
269A ASN* 1.3 52.2 + - - +
271A LEU* 2.6 39.2 + - + +
272A GLU* 2.7 17.0 + - - +
276A PHE* 5.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A TYR* 3.4 28.3 + - + -
265A PHE* 2.7 42.4 + - + +
266A GLU* 3.6 16.2 + - - +
268A MET* 1.3 77.4 - - - +
270A LYS* 1.3 57.7 + - - +
272A GLU* 3.3 4.3 + - - +
273A LYS* 2.6 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 5.2 12.3 - - - +
266A GLU* 3.1 27.2 + - - +
267A TYR* 2.8 16.9 + - + +
269A ASN* 1.3 73.6 + - - +
271A LEU* 1.3 62.3 + - - +
273A LYS* 3.5 22.9 - - + +
274A GLY* 3.3 6.8 + - - -
275A GLY* 2.9 20.1 + - - -
278A LYS* 5.2 12.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
183A SER* 5.4 1.8 - - - +
184A LYS* 5.6 8.1 - - + -
241A PHE* 3.9 26.5 - - + -
267A TYR* 3.0 28.5 + - + +
268A MET* 2.6 34.4 + - + +
270A LYS* 1.3 70.0 - - - +
272A GLU* 1.3 64.1 + - - +
274A GLY 3.1 0.9 + - - -
275A GLY* 2.9 36.5 + - - +
276A PHE* 3.0 53.8 + - + +
278A LYS* 5.0 5.2 - - - +
279A ILE* 5.9 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PRO* 5.2 9.0 - - + +
92A ASP* 5.4 3.5 - - - +
248A TYR* 2.9 37.3 + - + +
249A PHE* 4.7 17.1 - - + -
268A MET 2.7 9.9 + - - +
269A ASN 3.7 6.4 - - - +
271A LEU* 1.3 77.3 - - - +
273A LYS* 1.3 58.2 + - - +
274A GLY* 3.0 6.2 + - - -
276A PHE* 4.3 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLU* 3.6 17.6 + - - -
269A ASN* 2.6 45.7 + - - +
270A LYS* 3.5 26.5 - - + +
271A LEU 3.1 0.2 - - - -
272A GLU* 1.3 76.2 - - - +
274A GLY* 1.3 55.6 + - - +
----------------------------------------------------------
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