Contacts of the helix formed by residues 266 - 286 (chain A) in PDB entry 5H1Y
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 SER 266 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A CYS* 3.3 2.0 - - - +
265A PRO* 1.3 85.4 - - - +
267A ARG* 1.3 63.9 + - - +
268A GLU* 3.7 5.5 + - - +
269A LEU* 3.2 24.1 + - - +
270A ALA* 3.0 21.8 + - - +
320A THR* 3.6 6.9 - - - +
348A ARG* 4.9 13.0 + - - -
352A MET* 5.6 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A SER* 1.3 71.6 - - - +
268A GLU* 1.3 58.1 + - - +
270A ALA* 3.3 4.6 + - - +
271A ARG* 3.0 41.1 + - - +
298A ILE* 3.7 25.2 - - + +
299A GLY* 3.4 35.1 + - - +
300A GLY* 3.6 8.3 - - - +
320A THR* 3.8 11.6 - - + +
323A ARG* 2.9 31.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A SER* 3.2 6.3 + - - +
267A ARG* 1.3 76.2 - - - +
269A LEU* 1.3 66.7 + - - +
271A ARG* 3.4 23.4 + - - +
272A GLN* 3.0 34.2 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
231A LYS* 6.4 0.2 - - - -
232A THR* 5.9 2.0 - - - +
264A CYS* 3.8 11.7 - - + -
265A PRO* 3.9 17.0 - - + -
266A SER* 3.2 20.4 + - - +
268A GLU* 1.3 77.5 - - - +
270A ALA* 1.3 61.5 + - - +
272A GLN* 3.7 23.7 - - - +
273A THR* 2.9 30.3 + - - +
344A ASP* 3.5 25.1 - - - +
345A GLU* 3.6 36.8 - - + +
348A ARG* 6.2 0.2 - - - +
502A MG 4.7 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A CYS* 3.7 9.8 - - + -
266A SER 3.0 13.7 + - - +
267A ARG 3.5 8.1 - - - +
269A LEU* 1.3 77.9 - - - +
271A ARG* 1.3 57.4 + - - +
274A HIS* 2.8 31.0 + - - +
296A LEU* 3.8 3.4 - - + -
298A ILE* 3.6 26.9 - - + -
318A VAL* 3.4 28.9 - - + +
319A ALA 4.9 0.2 - - - -
320A THR* 4.5 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ARG* 3.0 28.9 + - - +
268A GLU* 3.8 24.9 - - - +
270A ALA* 1.3 74.4 - - - +
272A GLN* 1.3 54.0 - - - +
274A HIS* 3.3 4.3 + - - +
275A GLY* 2.7 33.3 + - - -
296A LEU* 3.7 24.7 - - + +
298A ILE* 3.8 25.8 - - + +
300A GLY 5.8 4.2 + - - -
301A MET* 5.6 7.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A THR* 6.2 0.2 - - - +
232A THR* 5.2 5.2 + - - -
268A GLU* 3.0 26.4 + - - +
269A LEU* 3.7 24.0 - - - +
271A ARG* 1.3 77.8 - - - +
273A THR* 1.3 59.5 + - - +
275A GLY* 3.3 2.7 + - - -
276A ILE* 3.1 38.8 + - + +
501A SO4 5.4 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A THR* 4.0 12.7 + - + +
235A PHE* 3.9 28.7 - - + -
236A THR* 4.0 13.9 - - + -
262A ILE* 4.2 18.4 - - + -
264A CYS* 4.9 2.5 - - - -
269A LEU* 2.9 30.8 + - - +
270A ALA 4.0 2.2 - - - -
272A GLN* 1.3 76.2 + - - +
274A HIS* 1.3 66.2 + - - +
276A ILE* 3.2 9.9 + - - +
277A LEU* 3.0 22.1 + - + +
318A VAL* 4.5 8.1 - - + -
344A ASP* 4.5 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ALA 2.8 18.8 + - - +
271A ARG 3.5 4.8 + - - +
273A THR* 1.3 75.9 - - - +
275A GLY* 1.3 66.0 + - - +
277A LEU* 3.2 5.3 + - - +
278A GLU* 3.0 51.2 + - - +
294A CYS* 2.9 42.6 + - + -
295A ALA* 4.0 13.6 + - - -
296A LEU* 3.6 32.6 - - + +
318A VAL* 3.9 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ARG 2.7 20.3 + - - -
272A GLN* 3.3 3.8 + - - -
273A THR 3.2 0.2 - - - -
274A HIS* 1.3 77.5 - - - +
276A ILE* 1.3 60.8 + - - +
278A GLU* 3.4 7.8 + - - +
279A TYR* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A THR* 3.8 25.1 - - + +
233A LEU* 4.5 7.2 - - + -
236A THR* 4.2 19.5 - - + +
272A GLN* 3.1 29.7 + - + +
273A THR* 3.2 10.3 + - - +
275A GLY* 1.3 73.2 - - - +
277A LEU* 1.3 66.5 + - - +
279A TYR* 3.1 16.9 + - - +
280A TYR* 3.2 35.4 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
236A THR* 3.7 32.3 - - + +
239A VAL* 4.7 2.9 - - + -
240A ILE* 3.8 26.5 - - + -
262A ILE* 4.1 13.2 - - + -
273A THR* 3.0 13.6 + - + +
274A HIS* 3.2 7.8 + - - +
276A ILE* 1.3 76.0 - - - +
278A GLU* 1.3 58.6 + - - +
280A TYR* 3.2 4.3 + - - +
281A CYS* 2.9 34.2 + - - -
294A CYS* 3.8 15.7 - - + -
316A MET* 3.8 27.4 - - + -
317A MET 5.6 0.2 - - - +
318A VAL* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A HIS* 3.0 51.5 + - - +
275A GLY* 3.8 7.2 - - - +
277A LEU* 1.3 76.4 - - - +
279A TYR* 1.3 61.7 + - - +
281A CYS* 4.1 6.2 - - - +
282A ARG* 3.1 26.6 + - - +
292A LEU 6.1 0.2 - - - +
294A CYS* 3.7 20.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLY* 3.0 24.6 + - - -
198A LYS* 3.9 13.1 - - + +
199A LYS* 3.5 39.5 - - + +
275A GLY 3.1 11.6 + - - +
276A ILE* 3.1 13.0 + - - +
278A GLU* 1.3 77.2 - - - +
280A TYR* 1.3 102.6 + + - +
282A ARG* 3.2 35.7 + - - +
283A LEU* 3.2 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ILE* 3.8 29.5 - - + +
195A GLY 4.3 9.7 + - - -
196A LEU* 3.1 35.3 - - + +
199A LYS* 4.5 3.3 - - - +
201A ILE* 4.1 9.0 - - - +
233A LEU* 3.7 24.1 - - + +
236A THR* 5.4 0.4 - - - -
237A LEU* 3.9 15.9 - - + -
240A ILE* 3.6 22.0 - - + -
276A ILE* 3.2 31.8 + - + -
277A LEU 3.2 2.2 + - - -
279A TYR* 1.3 107.3 - + - +
281A CYS* 1.3 63.7 + - - +
283A LEU* 3.2 10.0 + - + +
284A LEU* 3.1 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ILE* 4.2 10.5 - - - -
277A LEU 2.9 19.8 + - - +
278A GLU* 4.1 7.0 - - + +
280A TYR* 1.3 77.3 - - - +
282A ARG* 1.3 60.8 + - - +
284A LEU* 3.4 11.4 + - - +
285A GLN* 3.2 20.4 + - - +
290A PRO 5.1 2.4 - - - +
291A LEU* 4.8 6.6 - - + +
292A LEU* 3.7 43.5 + - + +
294A CYS* 3.7 9.2 - - - -
316A MET* 3.7 20.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A GLU 3.1 19.9 + - - +
279A TYR* 3.5 38.1 + - - +
281A CYS* 1.3 77.0 - - - +
283A LEU* 1.3 74.4 + - - +
285A GLN* 3.2 17.0 + - - +
286A GLU* 3.1 55.1 + - + +
291A LEU* 5.4 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ALA* 3.4 30.2 - - + +
192A ILE* 5.2 1.1 - - + -
195A GLY* 3.3 33.4 - - - +
198A LYS* 6.0 0.2 - - + -
279A TYR* 3.4 32.3 - - + +
280A TYR* 3.2 12.4 + - + +
282A ARG* 1.3 94.0 - - - +
284A LEU* 1.3 65.8 + - - +
286A GLU* 3.5 23.7 + - - +
287A ASP 3.3 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A PRO* 4.2 22.0 - - + -
191A ALA* 4.4 7.2 - - + -
192A ILE* 4.0 23.6 - - + -
240A ILE* 3.5 32.3 - - + -
241A MET* 5.3 1.3 - - - -
244A LEU* 4.3 23.1 - - + -
280A TYR 3.1 16.4 + - - +
281A CYS* 3.6 11.7 - - - +
282A ARG 3.3 0.2 - - - -
283A LEU* 1.3 77.3 - - - +
285A GLN* 1.3 57.7 + - - +
287A ASP* 2.9 21.5 + - + +
289A SER* 3.2 37.0 + - - +
290A PRO 5.1 2.5 - - - +
292A LEU* 4.6 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A CYS 3.2 10.5 + - - +
282A ARG* 3.2 20.8 + - - +
284A LEU* 1.3 75.6 - - - +
286A GLU* 1.3 66.6 + - + +
287A ASP 2.9 4.9 - - - -
288A SER* 2.6 26.9 + - - -
289A SER 3.3 17.8 - - - +
290A PRO 4.7 4.5 - - - +
291A LEU* 3.8 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ARG* 3.1 53.6 + - - +
283A LEU* 3.6 18.0 - - - +
284A LEU 3.3 0.4 - - - -
285A GLN* 1.3 87.1 + - + +
287A ASP* 1.3 56.9 + - - +
288A SER* 3.4 1.8 + - - -
----------------------------------------------------------
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