Contacts of the helix formed by residues 279 - 300 (chain G) in PDB entry 2R9R
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 279 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G ASP 2.8 17.1 + - - -
276G LYS* 3.0 21.8 + - - -
277G ILE 3.4 0.4 - - - -
278G LEU* 1.3 81.8 - - - +
280G GLU* 1.3 66.1 + - - +
281G GLU* 3.8 7.3 + - - +
282G GLY 3.1 6.6 + - - -
283G ARG* 3.0 20.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 280 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279G SER* 1.3 73.6 - - - +
281G GLU* 1.3 62.5 + - - +
283G ARG* 3.2 9.9 + - + +
284G ARG* 3.1 54.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 281 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276G LYS 5.3 0.2 - - - +
279G SER* 3.3 8.1 + - - +
280G GLU* 1.3 78.0 - - - +
282G GLY* 1.3 64.0 + - - +
284G ARG* 3.1 42.8 + - - +
285G GLN* 3.0 47.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 282 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250G ILE* 5.9 1.8 - - - +
276G LYS 3.1 25.8 + - - -
277G ILE* 3.4 15.9 - - - +
279G SER* 3.1 4.2 + - - -
281G GLU* 1.3 80.0 - - - +
283G ARG* 1.3 57.9 + - - +
285G GLN* 3.5 15.5 + - - +
286G GLN* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 283 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255G TYR 3.0 21.8 + - - -
256G ASP 3.3 22.2 + - - -
257G SER* 5.3 1.0 - - - +
258G GLY* 5.2 1.8 - - - +
277G ILE* 2.7 39.8 + - - +
278G LEU* 3.3 32.4 - - - +
279G SER 3.0 6.8 + - - +
280G GLU* 3.4 11.4 - - - +
282G GLY* 1.3 76.4 + - - +
284G ARG* 1.3 65.3 + - + +
286G GLN* 3.1 22.1 + - - +
287G ALA* 3.1 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 284 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280G GLU* 3.1 52.7 + - + +
281G GLU* 3.1 37.0 + - - +
283G ARG* 1.3 76.2 - - + +
285G GLN* 1.3 62.2 + - - +
287G ALA* 3.1 20.1 + - - +
288G LYS* 3.4 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 285 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220G PHE* 3.7 53.7 + - + +
247G ALA* 6.0 0.3 - - - +
250G ILE* 4.0 29.6 - - + +
281G GLU* 3.0 41.3 + - - +
282G GLY* 3.6 12.7 - - - +
284G ARG* 1.3 75.3 - - - +
286G GLN* 1.3 64.6 + - - +
288G LYS* 3.1 17.2 + - - +
289G LEU* 3.3 16.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 286 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250G ILE* 4.6 7.5 - - - +
253G GLY* 3.4 23.0 + - - -
255G TYR* 3.5 22.8 + - - +
256G ASP* 3.6 40.0 + - - +
277G ILE* 5.3 0.3 - - - +
282G GLY 3.0 14.0 + - - +
283G ARG* 3.2 25.1 + - - +
285G GLN* 1.3 78.2 - - - +
287G ALA* 1.3 59.3 + - - +
289G LEU* 3.4 45.5 + - - +
290G LYS* 3.8 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 287 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283G ARG 3.1 10.6 + - - +
284G ARG* 3.4 12.8 - - - +
285G GLN 3.1 0.4 - - - -
286G GLN* 1.3 74.1 - - - +
288G LYS* 1.3 63.9 + - + +
289G LEU 3.2 2.0 - - - -
290G LYS* 3.4 21.1 + - - +
291G GLU* 3.8 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 288 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220G PHE* 4.5 21.3 - - + -
284G ARG* 3.4 20.4 + - - +
285G GLN* 3.1 8.1 + - - +
287G ALA* 1.3 76.5 - - + +
289G LEU* 1.3 65.6 + - - +
290G LYS 3.2 0.2 - - - -
291G GLU* 3.2 18.1 + - - +
292G LEU* 3.1 28.6 + - + +
354G ILE* 3.5 26.0 + - + +
355G LEU* 2.8 30.9 + - + +
356G GLY* 5.1 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 289 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220G PHE* 4.2 19.7 - - + -
250G ILE* 3.2 28.9 - - + +
251G VAL* 4.1 25.1 - - + +
253G GLY* 3.8 9.9 - - - +
285G GLN 3.3 13.8 + - - +
286G GLN* 3.4 39.7 - - - +
287G ALA 3.2 0.4 - - - -
288G LYS* 1.3 78.4 - - - +
290G LYS* 1.3 51.8 + - + +
292G LEU* 3.0 15.5 + - + +
293G GLN* 2.6 38.4 + - - +
303G LEU* 3.9 12.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 290 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256G ASP* 2.6 43.4 + - - -
286G GLN* 3.8 7.9 + - - +
287G ALA* 3.4 14.5 + - - +
288G LYS 3.2 0.4 - - - -
289G LEU* 1.3 79.8 - - + +
291G GLU* 1.3 63.3 + - + +
293G GLN* 3.3 20.3 + - + +
294G ALA* 3.4 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 291 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G ALA* 4.0 10.5 - - - +
288G LYS* 3.2 14.6 + - - +
290G LYS* 1.3 77.9 - - + +
292G LEU* 1.3 58.3 + - - +
294G ALA* 3.0 25.9 - - - +
295G ILE* 3.1 10.7 - - - +
354G ILE* 3.6 43.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 292 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G MET* 3.8 20.2 - - + -
220G PHE* 5.2 1.1 - - + -
251G VAL* 6.1 0.2 - - + -
288G LYS* 3.1 21.3 + - + +
289G LEU* 3.0 20.5 + - + +
291G GLU* 1.3 71.5 - - - +
293G GLN* 1.3 63.4 + - - +
294G ALA 2.9 6.3 + - - -
295G ILE* 3.1 9.2 + - + +
296G ALA 3.1 16.6 + - - -
303G LEU* 3.8 19.5 - - + +
306G LEU* 3.9 4.6 - - + +
351G ILE* 3.8 33.0 - - + +
354G ILE* 3.8 26.0 - - + -
355G LEU* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 293 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252G SER 5.4 1.6 - - - +
289G LEU 2.6 20.1 + - - +
290G LYS* 3.5 17.7 - - + +
291G GLU 3.3 0.2 - - - -
292G LEU* 1.3 73.2 - - - +
294G ALA* 1.3 56.5 + - - +
296G ALA* 3.5 8.8 - - - +
297G GLU* 3.0 53.3 + - - +
301G CYS 5.0 3.0 + - - -
302G THR* 5.4 1.8 - - - +
303G LEU* 3.6 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 294 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290G LYS 3.4 6.0 + - - +
291G GLU* 3.0 18.1 + - - +
292G LEU 2.9 0.2 - - - -
293G GLN* 1.3 77.1 - - - +
295G ILE* 1.3 68.3 + - + +
297G GLU* 3.2 11.5 + - - +
298G ARG* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 295 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G GLU 3.1 21.3 - - - +
292G LEU* 3.1 12.3 + - + +
294G ALA* 1.3 77.4 - - + +
296G ALA* 1.3 65.0 + - - +
298G ARG* 3.1 14.5 + - - +
299G LEU* 3.0 41.4 + - + +
306G LEU* 4.4 10.3 - - + -
347G ILE* 3.8 26.7 - - + -
350G GLU* 3.7 25.1 - - - +
351G ILE* 4.8 8.7 - - + -
354G ILE* 3.4 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 296 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292G LEU 3.1 11.7 + - - +
293G GLN* 3.5 14.8 - - - +
294G ALA 3.1 0.8 - - - -
295G ILE* 1.3 76.9 - - - +
297G GLU* 1.3 64.4 + - - +
299G LEU* 2.9 13.2 + - - +
300G GLY 3.0 10.4 + - - -
301G CYS* 3.2 33.7 + - - +
302G THR 3.9 18.8 - - - +
303G LEU* 4.0 9.6 - - - +
306G LEU* 4.3 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 297 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293G GLN* 3.0 40.0 + - - +
294G ALA* 3.6 11.9 - - - +
296G ALA* 1.3 79.2 - - - +
298G ARG* 1.3 61.2 + - - +
300G GLY* 3.4 11.5 + - - +
301G CYS 3.9 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 298 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294G ALA* 3.0 16.1 + - - +
295G ILE* 3.3 25.5 - - - +
296G ALA 3.1 0.2 - - - -
297G GLU* 1.3 79.3 - - - +
299G LEU* 1.3 63.2 + - + +
300G GLY 3.6 0.3 + - - -
347G ILE* 4.0 18.5 - - - +
350G GLU* 2.8 41.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 299 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295G ILE* 3.0 26.5 + - + +
296G ALA 2.9 6.0 + - - +
298G ARG* 1.3 81.3 - - + +
300G GLY* 1.3 61.9 + - - +
301G CYS* 3.4 8.8 - - - +
306G LEU* 3.7 31.0 - - + -
339G VAL* 4.7 9.6 - - + -
342G LYS* 3.8 57.9 - - + +
343G LEU* 4.8 1.8 - - + -
347G ILE* 4.4 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 300 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296G ALA 3.0 3.8 + - - -
297G GLU* 3.4 9.4 + - - -
298G ARG 3.3 4.2 + - - -
299G LEU* 1.3 79.3 - - - +
301G CYS* 1.3 59.7 + - - +
305G GLN* 5.0 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