Contacts of the helix formed by residues 283 - 298 (chain C) in PDB entry 2Y4T
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 ARG 283 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C LEU* 3.1 39.6 + - + +
281C ASP* 4.8 19.5 + - + -
282C GLY* 1.3 72.0 - - - +
284C TYR* 1.3 57.8 + - - +
285C THR* 3.6 2.2 - - - -
286C ASP* 3.1 37.7 + - + +
287C ALA* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 284 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ILE* 3.3 38.9 + - + -
282C GLY* 2.8 32.2 + - - -
283C ARG* 1.3 68.5 - - - +
285C THR* 1.3 62.2 + - + +
286C ASP 3.2 1.3 - - - -
287C ALA* 3.1 6.6 + - - +
288C THR* 2.8 33.1 + - - -
314C HIS* 5.5 3.8 - + - -
315C CYS* 3.5 33.6 - - + +
318C LYS* 3.6 43.3 + - + +
319C ASP* 3.7 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 285 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C ARG 5.3 0.3 - - - -
284C TYR* 1.3 74.4 + - + +
286C ASP* 1.3 67.7 + - - +
288C THR* 3.6 8.7 - - - +
289C SER* 3.1 23.0 + - - -
316C PHE* 4.9 11.7 - - + -
319C ASP* 3.8 12.0 + - - +
321C LYS* 3.4 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 286 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C LEU* 3.6 18.4 - - + +
283C ARG* 3.1 53.7 + - + +
285C THR* 1.3 78.2 + - - +
287C ALA* 1.3 65.8 + - - +
289C SER* 3.3 8.2 + - - -
290C LYS* 3.2 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 287 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C ALA* 3.5 11.4 - - + +
278C LEU* 3.6 12.5 - - + +
279C ILE* 3.4 33.7 - - + -
283C ARG 3.0 13.7 + - - +
284C TYR* 3.1 8.9 + - - +
286C ASP* 1.3 74.2 - - - +
288C THR* 1.3 55.9 + - - +
290C LYS* 2.8 23.9 + - - +
291C TYR* 2.9 19.4 + - + +
315C CYS* 3.6 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 288 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C TYR 2.8 27.4 + - - -
285C THR* 3.6 12.1 - - + +
287C ALA* 1.3 71.2 - - - +
289C SER* 1.3 57.1 + - - +
291C TYR 3.6 0.2 + - - -
292C GLU* 3.1 31.6 + - - +
312C ILE* 3.8 40.3 + - + +
315C CYS* 3.3 20.5 - - - +
316C PHE* 4.1 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 289 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C THR 3.1 13.6 + - - -
286C ASP* 3.5 11.2 - - - -
287C ALA 3.2 0.2 - - - -
288C THR* 1.3 74.1 - - - +
290C LYS* 1.3 65.3 + - - +
292C GLU* 3.3 9.1 + - - +
293C SER* 3.2 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 290 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C LEU* 3.7 37.0 - - + +
274C SER* 3.4 26.7 - - - +
275C ALA* 3.6 16.8 - - + -
278C LEU* 3.8 20.8 - - + +
286C ASP 3.2 5.2 + - - +
287C ALA 2.8 8.6 + - - +
289C SER* 1.3 79.0 - - - +
291C TYR* 1.3 58.4 + - - +
293C SER* 3.1 9.9 + - - -
294C VAL* 2.9 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 291 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ILE* 3.6 32.6 - - + +
275C ALA* 3.5 27.1 - - + -
276C GLU* 2.5 40.8 + - - +
279C ILE* 5.0 3.8 - - + -
287C ALA* 2.9 19.2 + - + +
290C LYS* 1.3 72.2 - - - +
292C GLU* 1.3 66.0 + - - +
293C SER 3.1 1.3 - - - -
294C VAL* 3.1 13.3 + - + +
295C MET* 3.1 29.3 + - - +
307C ARG 5.6 0.4 - - - -
308C SER* 3.5 25.6 + - - -
311C ARG* 3.5 35.3 - - + +
312C ILE* 3.9 20.6 - - + -
315C CYS* 5.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 292 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C THR* 3.1 17.8 + - - +
289C SER* 3.3 13.0 + - - +
291C TYR* 1.3 76.2 - - - +
293C SER* 1.3 56.7 + - - +
295C MET* 3.6 19.4 + - - +
296C LYS* 3.3 30.3 + - + +
312C ILE* 3.8 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 293 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C LEU* 3.8 20.2 - - - -
289C SER* 3.2 11.5 + - - -
290C LYS* 3.1 12.4 + - - -
291C TYR 3.1 0.4 - - - -
292C GLU* 1.3 76.3 - - - +
294C VAL* 1.3 54.5 + - - +
295C MET 3.2 0.4 - - - -
296C LYS* 3.1 8.2 + - - +
297C THR* 2.8 38.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 294 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C LEU* 3.7 20.0 - - + -
271C LEU* 3.7 25.9 - - + +
272C ILE* 3.7 25.6 - - + -
290C LYS 2.9 18.2 + - - +
291C TYR* 3.1 21.7 + - + +
293C SER* 1.3 75.5 - - - +
295C MET* 1.3 55.9 + - - +
297C THR* 3.0 13.7 - - - +
298C GLU* 3.0 26.2 + - - +
304C TYR* 4.3 10.8 - - + +
308C SER* 3.3 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 295 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C TYR 3.1 8.5 + - - +
292C GLU* 3.6 47.8 - - - +
293C SER 3.2 0.2 - - - -
294C VAL* 1.3 73.9 - - - +
296C LYS* 1.3 64.4 + - + +
298C GLU 3.3 22.4 - - - +
299C PRO* 3.3 10.2 - - - +
304C TYR 3.6 10.1 - - - +
305C THR* 3.8 32.8 - - + +
308C SER* 3.4 27.4 - - - -
309C LYS* 3.9 16.4 - - - -
312C ILE* 3.8 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 296 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C GLU* 3.3 17.9 + - + +
293C SER* 3.1 11.5 + - - +
295C MET* 1.3 79.0 - - + +
297C THR* 1.3 60.9 + - - +
299C PRO* 3.7 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 297 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C GLN* 2.7 36.6 + - - +
267C LYS* 3.8 20.8 - - - +
268C LEU* 3.7 24.2 - - + -
271C LEU* 3.8 16.4 - - + -
293C SER 2.8 14.8 + - - +
294C VAL* 3.0 23.3 - - - +
296C LYS* 1.3 78.9 - - - +
298C GLU* 1.3 52.9 + - - +
299C PRO* 3.8 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 298 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C TYR* 2.7 27.3 + - + +
264C GLN* 3.5 8.0 + - - +
268C LEU* 3.5 19.1 - - + -
294C VAL 3.0 9.3 + - - +
295C MET* 3.3 8.6 - - - +
297C THR* 1.3 79.2 - - - +
299C PRO* 1.3 67.3 - - - +
300C SER* 3.4 14.7 + - - -
301C ILE* 3.3 40.8 + - + +
304C TYR* 3.7 39.9 - - + +
305C THR* 4.6 3.8 + - - -
----------------------------------------------------------
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