Contacts of the helix formed by residues 289 - 301 (chain A) in PDB entry 5Y7G
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 GLY 289 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A PHE* 3.7 9.1 - - - -
288A PRO* 1.3 72.5 - - - +
290A ALA* 1.3 63.6 + - - +
291A ARG 3.4 1.6 - - - -
292A LEU* 3.6 15.0 + - - +
293A ARG* 3.3 21.0 + - - +
319A GLU* 3.2 15.3 + - - -
323A GLU* 4.5 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A PHE* 3.4 26.2 - - + -
282A TYR* 3.6 22.4 - - + +
285A SER* 3.5 24.0 - - - +
287A HIS 2.8 22.1 + - - +
288A PRO 3.1 1.6 + - - -
289A GLY* 1.3 76.0 - - - +
291A ARG* 1.3 66.7 + - - +
293A ARG* 3.2 2.3 + - - -
294A ALA 2.9 19.1 + - - -
319A GLU* 5.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A TYR 5.0 1.3 + - - -
283A ARG* 6.2 1.3 - - - +
285A SER 5.1 0.8 + - - -
287A HIS 4.5 0.6 + - - -
289A GLY 3.4 0.2 - - - -
290A ALA* 1.3 79.1 - - - +
292A LEU* 1.3 61.6 + - - +
294A ALA* 3.1 8.9 + - - +
295A ILE* 3.1 24.4 + - + +
310A LEU* 4.7 22.3 + - + +
313A GLU* 4.2 16.2 + - - +
314A ALA* 3.3 44.8 + - - +
317A ALA* 3.6 23.6 + - - +
319A GLU* 3.7 24.9 + - - +
323A GLU* 2.6 43.1 + - - +
305B ALA* 5.4 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A GLY* 3.6 16.0 + - - +
290A ALA 3.2 0.8 - - - -
291A ARG* 1.3 75.5 - - - +
293A ARG* 1.3 68.2 + - - +
294A ALA 3.1 0.3 + - - -
295A ILE* 3.1 8.5 + - + +
296A ARG* 2.9 25.5 + - + +
322A ALA 4.7 2.2 - - - +
323A GLU* 4.0 26.7 + - + +
326A GLY* 4.1 22.4 - - - -
327A LEU* 3.9 29.8 - - + +
330A LEU* 3.8 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A PHE* 4.2 10.5 - - + -
267A GLN* 5.2 4.3 - - - +
270A GLU* 2.2 43.7 + - - +
282A TYR* 3.2 38.5 + - + +
289A GLY 3.3 13.9 + - - +
290A ALA 3.2 3.6 + - - +
292A LEU* 1.3 79.0 - - - +
294A ALA* 1.3 57.3 + - - +
296A ARG* 3.1 37.5 - - - +
297A SER* 2.8 31.4 + - - -
300A ARG* 4.1 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLN* 4.6 9.8 - - + +
282A TYR* 3.6 20.6 - - + -
283A ARG* 4.3 15.0 - - - +
290A ALA 2.9 12.9 + - - +
291A ARG* 3.3 13.2 - - - +
292A LEU 3.0 0.4 - - - -
293A ARG* 1.3 75.3 - - - +
295A ILE* 1.3 65.6 + - - +
297A SER* 3.0 3.7 + - - -
298A LEU* 2.8 27.6 + - - +
310A LEU* 4.2 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ARG* 3.5 12.3 - - + +
292A LEU* 3.1 11.5 + - + +
294A ALA* 1.3 76.0 - - - +
296A ARG* 1.3 57.6 + - - +
298A LEU* 2.9 10.4 + - - +
299A GLU* 2.8 27.5 + - + +
307A ALA* 4.0 17.6 - - + +
310A LEU* 3.5 31.9 - - + +
311A ALA* 3.6 30.3 - - + +
314A ALA* 4.6 5.2 - - + -
327A LEU* 4.0 16.6 - - + -
330A LEU* 4.3 16.8 - - + -
334A LEU* 4.1 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU* 2.9 16.7 + - + +
293A ARG* 3.1 38.0 - - - +
295A ILE* 1.3 78.3 - - - +
297A SER* 1.3 57.5 + - - +
299A GLU* 3.1 35.5 + - - +
300A ARG* 2.9 66.0 + - - +
330A LEU* 4.4 13.7 - - + +
333A ARG* 3.9 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A GLU* 3.4 15.2 + - - +
275A PHE* 3.5 15.3 - - - +
278A ALA* 3.2 31.5 - - - +
279A GLN 4.4 5.2 - - - -
282A TYR* 4.2 6.5 - - - -
293A ARG 2.8 21.3 + - - -
294A ALA* 3.4 4.7 - - - -
296A ARG* 1.3 77.0 - - - +
298A LEU* 1.3 66.0 + - - +
300A ARG* 2.9 16.0 + - - +
301A GLY 2.9 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A PHE* 5.4 1.3 - - - -
279A GLN* 3.5 34.7 - - + +
283A ARG* 4.1 13.7 - - - +
294A ALA 2.8 16.9 + - - +
295A ILE* 3.5 5.6 - - - +
297A SER* 1.3 70.2 - - - +
299A GLU* 1.3 64.0 + - - +
301A GLY* 3.1 12.1 + - - -
303A ARG* 3.1 47.3 + - + +
306A GLU* 3.5 33.9 - - + +
307A ALA* 3.7 25.6 - - + +
310A LEU* 4.5 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ILE* 2.8 15.7 + - + +
296A ARG* 3.1 31.0 + - - +
298A LEU* 1.3 76.5 - - - +
300A ARG* 1.3 63.5 + - - +
302A GLU* 2.8 16.6 + - - +
303A ARG 4.2 6.4 + - - +
304A PHE* 3.9 23.2 - - + -
307A ALA* 4.2 2.4 - - + +
330A LEU* 3.7 10.4 - - + +
333A ARG* 3.3 20.5 + - - -
334A LEU* 4.1 17.7 - - + -
337A LYS* 2.4 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A GLU* 3.2 48.7 + - - -
271A LYS* 5.1 1.8 - - - +
273A ARG* 5.0 16.6 + - - +
275A PHE* 3.2 41.7 - - + -
293A ARG* 4.1 3.1 - - - +
296A ARG* 2.9 56.0 + - - +
297A SER 2.9 6.9 + - - +
299A GLU* 1.3 76.4 - - - +
301A GLY* 1.3 56.2 + - - +
302A GLU* 3.4 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A PHE* 3.1 22.3 - - - -
276A ASP* 5.0 3.0 - - - +
297A SER 2.9 10.3 + - - -
298A LEU* 3.1 5.1 + - - -
300A ARG* 1.3 74.1 - - - +
302A GLU* 1.3 69.7 - - - +
303A ARG* 3.2 18.3 + - - +
----------------------------------------------------------
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