Contacts of the helix formed by residues 279 - 292 (chain G) in PDB entry 3Q84
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 ASP 279 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G SER* 3.0 18.9 + - - +
80G LEU* 4.8 2.2 - - - +
277G GLY 4.2 6.7 - - - +
278G ALA* 1.3 74.9 - - - +
280G ALA* 1.3 65.8 + - - +
281G GLN* 2.9 23.3 + - - +
282G GLU* 2.8 42.3 + - + +
283G ASP* 3.3 15.0 + - - +
285G ARG* 4.9 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 280 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80G LEU* 4.5 7.0 - - + +
278G ALA 4.2 0.8 + - - -
279G ASP* 1.3 71.0 + - - +
281G GLN* 1.3 78.0 + - - +
283G ASP* 2.8 26.0 + - - +
284G LEU* 3.0 16.2 + - - +
239H GLU* 4.6 7.2 - - + -
242H LEU* 4.1 29.1 - - + +
243H VAL* 4.3 15.7 - - + +
246H LYS* 5.9 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 281 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279G ASP* 2.9 28.0 + - - +
280G ALA* 1.3 87.3 - - - +
282G GLU* 1.3 57.3 + - - +
284G LEU* 3.1 14.4 + - + +
285G ARG* 2.9 50.7 + - - +
239H GLU* 3.1 27.3 - - - +
243H VAL* 4.4 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 282 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G SER* 6.1 2.0 - - - -
82G ARG* 5.9 0.9 + - - -
279G ASP* 2.8 39.3 + - + +
280G ALA 3.1 0.6 - - - -
281G GLN* 1.3 80.5 - - - +
283G ASP* 1.3 64.8 + - - +
285G ARG* 3.2 24.9 + - + +
286G TRP* 3.0 21.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 283 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G TYR 3.9 4.6 - - - +
78G GLY* 3.8 10.9 - - - -
79G SER* 3.0 46.4 + - - -
80G LEU* 3.6 13.9 + - - +
82G ARG* 5.2 1.4 + - - -
279G ASP 3.3 4.8 + - - +
280G ALA 2.8 13.5 + - - +
282G GLU* 1.3 77.1 - - - +
284G LEU* 1.3 65.7 + - - +
286G TRP* 3.2 17.0 + - + +
287G PHE* 3.0 19.8 + - - +
242H LEU* 4.5 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 284 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280G ALA 3.0 17.2 + - - +
281G GLN* 3.4 13.7 - - + +
283G ASP* 1.3 75.6 - - - +
285G ARG* 1.3 65.1 + - - +
287G PHE* 3.2 3.6 + - - +
288G ARG* 2.9 20.3 + - - +
31H ARG* 3.8 22.0 - - - +
235H GLN* 3.3 38.1 - - + +
238H GLU* 4.1 17.9 - - + -
239H GLU* 3.6 35.9 - - + -
242H LEU* 4.3 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 285 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279G ASP* 4.9 3.4 + - - -
281G GLN* 2.9 29.5 + - - +
282G GLU* 3.2 43.9 + - + +
284G LEU* 1.3 75.8 - - - +
286G TRP* 1.3 64.4 + - - +
288G ARG* 3.2 7.4 + - - +
289G SER* 3.0 24.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 286 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G TYR* 4.3 32.5 - + + -
78G GLY* 5.4 8.3 - - - -
282G GLU* 3.0 12.3 + - + +
283G ASP* 3.3 18.6 - - + +
284G LEU 3.1 0.2 - - - -
285G ARG* 1.3 78.0 - - - +
287G PHE* 1.3 87.1 + + + +
289G SER* 3.2 5.3 + - - -
290G THR* 2.8 61.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 287 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283G ASP 3.0 12.4 + - - +
284G LEU 3.2 5.8 + - - +
286G TRP* 1.3 97.5 - + + +
288G ARG* 1.3 57.8 + - - +
290G THR* 4.3 2.0 - - - +
291G SER* 2.8 55.9 + - - -
292G GLY 3.2 4.3 + - - -
27H ARG* 4.3 10.8 - - + -
28H THR* 3.7 33.0 - - - -
31H ARG* 3.2 52.0 - - + +
231H PHE* 4.0 8.5 - + - -
235H GLN* 4.0 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 288 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284G LEU 2.9 16.4 + - - +
285G ARG* 3.7 7.2 - - - +
287G PHE* 1.3 76.4 - - - +
289G SER* 1.3 60.0 + - - +
292G GLY 3.3 11.1 + - - -
293G PRO* 3.8 18.8 + - + +
294G GLY* 2.9 47.9 + - - +
228H GLU* 3.6 25.7 + - - -
231H PHE* 3.9 28.2 - - + -
232H GLU* 5.9 2.5 - - - -
235H GLN* 4.1 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 289 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285G ARG 3.0 16.2 + - - -
286G TRP* 3.9 4.7 + - - -
288G ARG* 1.3 78.1 - - - +
290G THR* 1.3 60.7 + - - +
294G GLY* 4.1 22.0 - - - +
295G MSE 4.4 6.7 - - - +
296G PRO* 5.5 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 290 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286G TRP* 2.8 57.4 + - + +
287G PHE* 4.6 0.7 - - - +
289G SER* 1.3 83.5 + - - +
291G SER* 1.3 69.3 + - - +
292G GLY 3.8 0.4 - - - -
295G MSE 3.6 20.9 - - - +
27H ARG* 5.5 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 291 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G PHE* 2.8 38.2 + - - -
290G THR* 1.3 88.8 + - - +
292G GLY* 1.3 63.2 + - - +
295G MSE 3.5 11.2 - - - -
19H PHE* 3.4 12.3 - - - +
24H ASN 4.7 0.9 - - - +
27H ARG* 3.3 40.6 + - - +
28H THR* 4.6 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 292 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G PHE 3.2 4.8 + - - -
288G ARG 3.3 6.4 + - - -
290G THR 3.8 0.2 - - - -
291G SER* 1.3 81.7 - - - +
293G PRO* 1.3 69.9 - - - +
294G GLY 2.9 12.6 + - - -
295G MSE 2.9 21.8 + - - +
19H PHE* 3.4 13.1 - - - +
231H PHE* 3.8 12.8 - - - -
----------------------------------------------------------
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