Contacts of the helix formed by residues 261 - 279 (chain A) in PDB entry 1Y8Q
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 THR 261 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ARG* 3.4 17.9 + - - +
258A SER* 3.2 10.1 + - - -
260A ASP* 1.3 83.4 - - + +
262A TYR* 1.3 53.4 + - - +
263A GLU 3.5 1.8 - - - -
264A GLU* 3.1 34.8 + - - +
265A ASP* 2.6 61.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A SER 3.1 8.4 + - - +
259A SER* 3.5 19.5 - - - +
260A ASP 3.4 2.6 + - - -
261A THR* 1.3 75.1 - - - +
263A GLU* 1.3 70.0 + - + +
264A GLU 3.1 0.2 + - - -
265A ASP 3.1 0.2 + - - -
266A SER* 2.7 60.2 + - - -
292A VAL* 3.8 10.2 - - - +
293A ARG* 3.2 44.1 + - - +
296A PHE* 3.6 32.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A THR 3.5 0.6 - - - -
262A TYR* 1.3 90.4 - - + +
264A GLU* 1.3 67.7 + - + +
266A SER* 3.8 4.5 + - - -
267A GLU* 3.4 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ARG* 5.9 0.2 - - - +
260A ASP 4.6 2.9 - - - +
261A THR* 3.1 35.4 + - - +
263A GLU* 1.3 84.5 - - + +
265A ASP* 1.3 68.0 + - - +
267A GLU* 3.2 8.8 + - - +
268A LEU* 3.2 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A PHE* 3.6 19.6 - - + -
253A LYS* 5.3 1.4 + - - -
255A ARG* 2.6 30.0 + - - -
257A PRO* 4.2 1.3 - - + -
258A SER 2.8 25.2 + - - +
261A THR* 2.6 38.5 + - - +
264A GLU* 1.3 71.3 - - - +
266A SER* 1.3 60.2 + - - +
268A LEU* 3.2 5.0 + - - +
269A LEU* 2.8 35.3 + - - +
296A PHE* 3.6 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A TYR* 2.7 57.7 + - - -
263A GLU* 3.9 6.1 - - - -
265A ASP* 1.3 72.9 - - - +
267A GLU* 1.3 63.8 + - - +
269A LEU* 3.3 3.2 + - - +
270A LEU* 3.0 32.8 + - - +
292A VAL* 3.8 24.9 - - - +
296A PHE* 3.9 3.7 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
263A GLU 3.4 11.6 + - - +
264A GLU* 3.2 13.6 + - - +
265A ASP 3.2 0.2 - - - -
266A SER* 1.3 79.3 - - - +
268A LEU* 1.3 62.3 + - - +
270A LEU* 3.4 14.4 + - - +
271A GLN* 3.3 19.3 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
249A PHE* 3.4 27.1 - - + -
252A ASP* 5.4 8.3 - - + +
253A LYS* 3.9 30.3 - - + -
264A GLU 3.2 8.3 + - - +
265A ASP* 3.2 8.6 + - - +
267A GLU* 1.3 79.8 - - - +
269A LEU* 1.3 55.8 + - - +
271A GLN* 2.9 13.6 + - + +
272A ILE* 2.7 59.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A VAL* 3.9 18.1 - - + +
246A LEU* 4.2 8.3 - - + -
249A PHE* 3.5 33.0 - - + -
257A PRO* 3.8 22.9 - - + -
265A ASP 2.8 23.0 + - - +
266A SER 3.3 4.7 + - - +
268A LEU* 1.3 72.5 - - - +
270A LEU* 1.3 58.2 + - - +
272A ILE* 3.3 5.0 + - - +
273A ARG* 2.9 29.1 + - - +
291A PHE* 3.8 9.7 - - + -
292A VAL* 3.8 18.8 - - + -
295A CYS* 4.3 11.9 - - - -
296A PHE* 3.9 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A SER* 3.0 23.5 + - - +
267A GLU* 3.7 15.3 - - - +
269A LEU* 1.3 77.2 - - - +
271A GLN* 1.3 61.1 + - - +
273A ARG* 3.4 12.7 + - - +
274A ASN* 2.8 33.1 + - - +
289A GLU* 3.7 54.1 - - + +
291A PHE* 4.0 13.9 - - + -
292A VAL* 4.1 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLU* 3.3 9.6 + - + +
268A LEU* 2.9 18.0 + - + +
270A LEU* 1.3 76.7 - - - +
272A ILE* 1.3 64.8 + - + +
274A ASN* 3.3 15.7 + - - +
275A ASP* 3.1 47.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A VAL* 3.7 19.5 - - + +
248A LYS* 3.6 34.3 - - + +
249A PHE* 3.6 34.8 - - + +
252A ASP* 4.5 7.6 - - - +
268A LEU* 2.7 50.4 + - + +
269A LEU* 3.7 5.2 - - - +
271A GLN* 1.3 69.8 - - - +
273A ARG* 1.3 60.6 + - - +
275A ASP* 3.3 7.9 + - + +
276A VAL* 2.9 36.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
245A VAL* 3.6 15.9 - - + -
269A LEU 2.9 14.3 + - - +
270A LEU* 3.4 13.6 + - - +
271A GLN 3.2 0.4 - - - -
272A ILE* 1.3 77.4 - - - +
274A ASN* 1.3 96.1 + - - +
277A LEU* 3.0 40.7 + - + +
284A PRO* 3.1 26.8 + - - +
285A ASP* 4.4 10.1 + - - +
287A LEU* 2.7 50.4 + - + -
288A PRO* 4.6 0.2 - - - +
289A GLU* 3.8 34.5 + - - +
291A PHE* 3.9 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU* 2.8 26.0 + - - +
271A GLN* 3.6 20.5 + - - +
272A ILE 3.3 0.2 - - - -
273A ARG* 1.3 109.1 + - - +
275A ASP* 1.3 59.1 + - - +
278A ASP* 2.8 35.7 + - - +
284A PRO* 3.1 21.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
248A LYS* 5.4 9.3 + - - +
271A GLN* 3.1 39.1 + - - +
272A ILE* 3.7 9.5 - - - +
274A ASN* 1.3 78.7 - - - +
276A VAL* 1.3 61.7 + - + +
278A ASP* 3.7 2.7 - - - +
279A SER* 2.8 32.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A PHE* 5.4 0.4 - - + +
244A GLN* 3.8 29.6 - - + +
245A VAL* 4.5 10.3 - - + +
248A LYS* 4.3 19.3 - - + -
272A ILE* 2.9 42.5 + - + +
273A ARG 4.2 1.3 - - - +
275A ASP* 1.3 73.8 - - + +
277A LEU* 1.3 66.2 + - + +
279A SER* 2.9 23.3 + - - +
280A LEU* 3.3 21.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A PHE* 3.6 42.6 - - + -
245A VAL* 5.5 2.9 - - + -
273A ARG* 3.0 30.2 + - + +
276A VAL* 1.3 81.6 - - + +
278A ASP* 1.3 60.3 + - - +
280A LEU* 3.1 10.0 + - + +
282A ILE* 2.9 52.5 + - + +
283A SER 3.6 16.2 - - - +
284A PRO* 3.6 24.2 - - + +
286A LEU* 4.3 6.7 - - + -
287A LEU* 4.1 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ASN* 2.8 24.7 + - - +
275A ASP* 3.7 4.0 - - - +
277A LEU* 1.3 74.1 - - - +
279A SER* 1.3 57.8 + - - +
280A LEU 2.9 9.9 + - - -
281A GLY* 3.0 13.7 + - - -
282A ILE 3.8 5.1 + - - +
284A PRO* 4.6 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ASP 2.8 16.3 + - - -
276A VAL* 2.9 18.7 + - - +
278A ASP* 1.3 75.3 - - - +
280A LEU* 1.3 63.6 + - - +
281A GLY 3.5 0.2 - - - -
----------------------------------------------------------
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