Contacts of the helix formed by residues 255 - 281 (chain A) in PDB entry 2Y4U
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 HIS 255 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A THR* 2.7 44.8 + - + +
223A GLU* 4.8 2.5 - - - -
226A TYR* 5.6 1.1 - - + -
248A CYS* 4.4 1.1 - - - -
249A LEU* 4.4 2.1 - - + +
252A ASP* 3.3 28.4 + - - +
253A GLN 3.6 1.0 - - - +
254A ASP* 1.3 74.0 - - - +
256A LYS* 1.3 62.8 + - - +
257A ARG* 3.0 48.5 + - + +
258A CYS* 3.3 46.0 - - + -
259A PHE* 3.3 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ASP 2.8 13.8 + - - +
255A HIS* 1.3 73.2 - - - +
257A ARG* 1.3 58.5 + - + +
259A PHE* 4.5 3.8 - - - +
260A ALA* 3.4 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A GLU* 2.2 37.2 + - - -
226A TYR* 3.6 41.8 + - + +
255A HIS* 3.0 29.5 + - + +
256A LYS* 1.3 81.8 - - - +
258A CYS* 1.3 65.1 + - - +
259A PHE 3.3 0.2 - - - -
260A ALA* 3.4 7.9 - - + +
261A HIS* 3.2 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A TYR* 4.1 22.0 - - - -
245A VAL* 3.4 12.9 - - + +
248A CYS* 2.1 51.4 - - + -
249A LEU* 4.1 10.1 - - + -
255A HIS* 3.3 27.1 - - + -
257A ARG* 1.3 76.7 - - - +
259A PHE* 1.3 59.8 - - - +
261A HIS* 3.2 2.1 + - - +
262A TYR* 2.8 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU* 3.8 25.7 - - + +
253A GLN* 4.6 8.7 - - - +
255A HIS 3.3 17.4 + - - +
256A LYS* 4.5 4.5 - - - +
258A CYS* 1.3 77.7 - - - +
260A ALA* 1.3 56.0 + - - +
262A TYR* 2.7 40.2 + + - +
263A LYS* 2.9 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LYS 3.4 19.8 + - - +
257A ARG* 3.4 12.5 + - + +
259A PHE* 1.3 81.8 - - - +
261A HIS* 1.3 62.2 + - - +
263A LYS* 3.6 16.0 + - - +
264A GLN* 3.6 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A TYR* 4.1 21.3 - + + +
229A SER* 3.0 33.2 + - - -
230A THR* 4.8 6.9 + - - -
233A TYR* 3.6 26.0 - + + -
241A SER* 3.3 6.9 + - - -
245A VAL* 3.6 20.0 - - + -
257A ARG 3.2 8.6 + - - +
258A CYS 3.2 7.7 + - - +
260A ALA* 1.3 80.1 - - - +
262A TYR* 1.3 57.7 + - - +
264A GLN* 3.0 10.8 - - - +
265A VAL* 3.0 48.5 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
242A LEU* 3.8 20.6 - - + -
245A VAL* 4.1 12.1 - - + -
246A ARG* 4.5 25.5 + - + -
249A LEU* 3.7 28.3 - - + -
258A CYS 2.8 13.2 + - - +
259A PHE* 2.7 31.3 + + - +
261A HIS* 1.3 73.5 - - - +
263A LYS* 1.3 71.5 + - + -
264A GLN 2.9 2.2 + - - -
265A VAL* 3.5 6.3 - - - +
266A LYS* 3.0 67.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A PHE* 2.9 50.5 + - + +
260A ALA* 3.8 11.0 - - - +
262A TYR* 1.3 81.0 - - + +
264A GLN* 1.3 62.6 + - - +
266A LYS* 3.8 8.4 - - - +
267A LYS* 3.2 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A TYR* 2.8 36.7 + - + +
260A ALA 3.6 6.8 + - - +
261A HIS* 3.0 18.8 + - - +
262A TYR 2.9 1.4 - - - -
263A LYS* 1.3 77.1 - - - +
265A VAL* 1.3 67.6 + - - +
267A LYS* 3.2 17.0 + - - +
268A LEU* 2.9 27.7 + - - +
297A THR* 3.8 19.3 + - - +
298A GLU* 3.4 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A TYR* 3.2 34.3 - - + -
238A HIS* 4.6 7.1 - - + +
241A SER* 3.5 14.8 - - - +
242A LEU* 3.6 27.6 - - + -
245A VAL* 3.9 17.5 - - + -
261A HIS* 3.0 24.2 + - + +
262A TYR 3.5 6.3 - - - +
264A GLN* 1.3 77.6 - - - +
266A LYS* 1.3 57.5 + - - +
268A LEU* 2.9 6.5 + - - -
269A ASN* 2.6 38.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
242A LEU* 4.1 19.3 - - + -
262A TYR* 3.0 61.7 + - + +
263A LYS* 3.8 8.1 - - - +
265A VAL* 1.3 79.6 - - - +
267A LYS* 1.3 55.8 + - - +
269A ASN* 3.6 1.4 + - - +
270A LYS* 2.8 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LYS 3.2 15.1 + - - +
264A GLN* 3.2 13.6 + - - +
266A LYS* 1.3 80.9 - - - +
268A LEU* 1.3 60.8 + - - +
270A LYS* 3.7 9.6 + - - +
271A LEU* 3.4 29.2 + - + +
297A THR* 3.4 37.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
233A TYR* 3.6 16.4 - - + +
238A HIS* 4.5 8.5 - - + -
264A GLN* 2.9 19.8 + - - +
265A VAL* 2.9 6.9 + - - +
267A LYS* 1.3 74.5 - - - +
269A ASN* 1.3 65.1 - - - +
271A LEU* 3.5 5.9 + - - +
272A ILE* 3.2 50.7 + - + +
294A VAL* 4.5 7.9 - - + +
297A THR* 3.5 18.4 - - - +
298A GLU* 3.1 36.8 - - + -
304A TYR* 3.8 22.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
238A HIS* 3.0 43.8 + - + +
239A GLU* 4.1 9.0 - - - +
242A LEU* 3.7 26.0 - - + +
265A VAL 2.6 19.8 + - - +
266A LYS 3.6 2.2 + - - +
268A LEU* 1.3 71.1 - - - +
270A LYS* 1.3 61.0 + - - +
271A LEU 2.9 2.3 + - - -
272A ILE 3.1 0.7 + - - -
273A GLU* 2.7 68.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
266A LYS* 2.8 27.3 + - + +
267A LYS* 3.7 10.5 - - - +
269A ASN* 1.3 77.1 - - - +
271A LEU* 1.3 57.1 + - + +
273A GLU* 4.1 3.3 - - - +
274A SER* 3.0 27.8 + - - -
290A LYS* 5.1 0.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
267A LYS* 3.4 23.9 + - + +
268A LEU* 3.7 3.6 - - - +
269A ASN 2.9 0.8 - - - -
270A LYS* 1.3 80.5 - - + +
272A ILE* 1.3 55.8 + - - +
274A SER* 3.2 4.2 + - - -
275A ALA* 2.7 34.1 + - - +
290A LYS* 3.7 43.5 - - + +
293A SER* 4.3 20.9 - - - +
294A VAL* 3.7 16.4 - - + -
297A THR* 3.9 29.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
238A HIS* 3.7 35.9 - - + +
268A LEU* 3.2 39.3 - - + +
269A ASN 3.1 1.9 + - - +
271A LEU* 1.3 72.8 - - - +
273A GLU* 1.3 66.5 + - - +
275A ALA* 3.7 5.3 - - - +
276A GLU* 3.0 28.5 + - + +
291A TYR* 3.3 25.8 - - + +
294A VAL* 3.8 25.1 - - + -
304A TYR* 4.6 6.7 - - + -
308A SER* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A HIS* 5.4 2.8 - - + -
239A GLU* 4.4 17.2 - - - +
269A ASN* 2.7 49.6 + - - +
270A LYS* 4.4 3.6 - - - +
272A ILE* 1.3 73.8 - - - +
274A SER* 1.3 62.8 + - - +
276A GLU* 3.8 6.4 + - + +
277A GLU* 3.4 18.9 + - - +
280A ARG* 5.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LYS 3.0 24.0 + - - -
271A LEU 3.3 4.9 - - - -
273A GLU* 1.3 75.7 - - - +
275A ALA* 1.3 67.7 + - - +
277A GLU* 2.9 21.2 + - - +
278A LEU* 3.1 19.1 + - - +
290A LYS* 3.3 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU 2.7 19.7 + - - +
272A ILE* 3.7 4.3 - - - +
274A SER* 1.3 72.0 - - - +
276A GLU* 1.3 64.4 + - - +
278A LEU* 2.8 25.1 + - - +
279A ILE* 3.0 16.6 + - - +
287A ALA* 3.9 3.8 - - - +
290A LYS* 3.8 17.0 - - + +
291A TYR* 3.4 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ILE* 3.0 24.5 + - + +
273A GLU* 4.0 6.1 - - - +
275A ALA* 1.3 75.1 - - - +
277A GLU* 1.3 61.1 + - - +
279A ILE* 2.8 31.8 - - - +
280A ARG* 3.0 21.8 + - - +
291A TYR* 2.3 30.9 + - - +
311A ARG* 2.9 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A GLU 3.4 10.6 + - - +
274A SER* 2.9 14.7 + - - +
276A GLU* 1.3 80.2 - - - +
278A LEU* 1.3 62.5 + - + +
280A ARG* 3.2 28.2 + - - +
281A ASP* 3.2 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A SER* 3.1 26.9 + - - +
275A ALA* 2.8 8.3 + - - +
277A GLU* 1.3 77.0 - - + +
279A ILE* 1.3 58.3 + - - +
280A ARG 3.2 0.4 - - - -
281A ASP* 3.3 6.0 + - - +
282A GLY 3.2 5.4 + - - -
283A ARG* 2.9 82.9 + - + +
286A ASP* 4.4 6.7 - - + +
287A ALA* 4.1 8.5 - - + +
290A LYS* 3.7 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ALA 3.0 9.3 + - - +
276A GLU* 2.8 34.0 + - + +
278A LEU* 1.3 75.7 - - - +
280A ARG* 1.3 64.8 + - + +
282A GLY* 3.5 10.1 + - - +
284A TYR* 4.1 20.4 + - + -
287A ALA* 3.3 27.4 - - + -
291A TYR* 5.0 7.9 - - + -
311A ARG* 3.1 29.6 - - + +
314A HIS* 5.0 12.0 + - + +
315A CYS* 3.9 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A GLU* 3.0 27.3 + - - +
277A GLU* 3.4 35.9 - - + +
278A LEU 3.2 0.2 - - - -
279A ILE* 1.3 85.6 - - + +
281A ASP* 1.3 62.2 + - - +
282A GLY 3.3 1.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A GLU* 3.2 25.4 + - - +
278A LEU* 3.3 4.6 + - - +
279A ILE 3.3 0.4 - - - -
280A ARG* 1.3 85.4 - - - +
282A GLY* 1.3 61.5 + - - +
283A ARG* 3.1 28.5 + - + +
----------------------------------------------------------
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