Contacts of the helix formed by residues 279 - 292 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A SER* 2.9 15.3 + - - -
80A LEU* 4.3 2.7 - - - -
277A GLY 3.5 4.5 + - - +
278A ALA* 1.3 75.0 - - - +
280A ALA* 1.3 64.5 + - - +
281A GLN* 2.6 47.5 + - - +
282A GLU* 2.7 30.9 + - + +
283A ASP* 3.2 18.2 + - - -
285A ARG* 5.7 1.4 + - - -
246B LYS* 4.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 4.5 4.2 - - - +
278A ALA 4.2 0.4 - - - -
279A ASP* 1.3 73.9 + - - +
281A GLN* 1.3 77.3 + - + +
283A ASP* 3.2 4.0 + - - +
284A LEU* 3.1 31.3 + - - +
239B GLU* 4.7 7.6 - - + -
242B LEU* 3.8 34.8 - - + +
243B VAL* 4.1 17.5 - - + +
246B LYS* 5.5 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ASP* 2.6 40.0 + - - +
280A ALA* 1.3 85.3 - - - +
282A GLU* 1.3 62.4 + - - +
284A LEU* 3.9 9.7 - - + +
285A ARG* 3.2 42.4 + - - +
239B GLU* 3.3 26.7 - - - +
243B VAL* 4.5 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLY* 6.1 0.2 - - - -
79A SER* 3.8 18.3 + - - -
82A ARG* 4.6 11.5 + - - -
277A GLY 5.1 2.3 - - - +
279A ASP* 2.7 35.2 + - + +
281A GLN* 1.3 75.2 - - - +
283A ASP* 1.3 72.3 + - - +
285A ARG* 3.4 21.2 + - - +
286A TRP* 3.2 21.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TYR* 3.8 23.2 - - + +
78A GLY* 3.7 8.8 - - - -
79A SER* 2.9 39.5 + - - -
80A LEU* 3.0 32.9 + - - +
279A ASP 3.2 5.1 + - - -
280A ALA 3.2 5.6 + - - +
282A GLU* 1.3 80.3 - - - +
284A LEU* 1.3 65.9 + - - +
285A ARG 3.1 1.8 - - - -
286A TRP* 3.1 9.6 + - - +
287A PHE* 3.0 23.6 + - - +
242B LEU* 4.2 9.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
77A TYR* 4.9 0.4 - - - +
280A ALA 3.1 19.8 + - - +
281A GLN* 3.9 11.4 - - + +
283A ASP* 1.3 76.4 - - - +
285A ARG* 1.3 64.4 + - + +
287A PHE* 3.3 1.9 + - - +
288A ARG* 3.1 14.0 + - - +
31B ARG* 4.1 5.4 - - - +
235B GLN* 3.1 53.6 - - + +
238B GLU* 3.5 31.9 - - + -
239B GLU* 3.9 37.5 - - + +
242B LEU* 4.3 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ASP* 5.3 1.0 + - - -
281A GLN* 3.2 38.8 + - - +
282A GLU* 3.9 21.8 - - - +
283A ASP 3.1 0.8 - - - -
284A LEU* 1.3 82.1 - - - +
286A TRP* 1.3 60.8 + - - +
288A ARG* 3.3 12.9 + - + +
289A SER* 3.2 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TYR* 3.6 41.1 - + + -
78A GLY* 5.4 3.6 - - - -
282A GLU* 3.2 15.0 + - - +
283A ASP* 3.1 11.1 + - - +
285A ARG* 1.3 76.7 - - - +
287A PHE* 1.3 78.4 + + - +
289A SER* 3.1 10.8 + - - -
290A THR* 2.8 65.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TYR* 4.2 17.5 - + + +
283A ASP 3.0 11.5 + - - +
284A LEU 3.6 5.2 - - - +
286A TRP* 1.3 87.4 - + - +
288A ARG* 1.3 62.2 + - - +
290A THR* 2.9 1.2 + - - -
291A SER* 2.6 60.2 + - - -
292A GLY 3.2 3.3 + - - -
27B ARG 3.8 20.9 - - - -
28B THR* 3.5 23.1 - - - -
30B LYS* 4.3 12.1 - - - -
31B ARG* 3.2 53.2 - - + +
231B PHE* 4.1 13.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LEU 3.1 10.6 + - - +
285A ARG* 3.5 15.0 - - - +
286A TRP 3.2 0.2 - - - -
287A PHE* 1.3 79.0 - - - +
289A SER* 1.3 58.9 + - - +
292A GLY 2.9 20.2 + - - +
293A PRO* 3.8 7.5 + - + +
294A GLY* 3.1 40.7 + - - +
228B GLU* 2.8 39.9 + - - -
231B PHE* 4.0 30.3 - - + -
235B GLN* 4.2 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ARG 3.2 7.1 + - - -
286A TRP* 3.1 15.0 + - - -
288A ARG* 1.3 80.5 - - - +
290A THR* 1.3 63.8 + - - +
294A GLY* 3.8 17.1 - - - -
295A MSE 3.3 22.2 + - - +
296A PRO* 5.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A TRP* 2.8 61.7 + - + -
287A PHE* 3.9 1.3 - - - +
289A SER* 1.3 84.4 + - - +
291A SER* 1.3 70.9 + - - +
295A MSE 3.7 17.2 - - - +
27B ARG* 5.0 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A PHE* 2.6 42.5 + - - -
290A THR* 1.3 87.7 + - - +
292A GLY* 1.3 58.9 + - - +
295A MSE 3.7 3.6 - - - -
19B PHE* 3.4 12.3 - - - +
24B ASN 4.8 0.2 - - - +
27B ARG* 3.1 47.1 + - - +
28B THR* 4.3 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A PHE 3.2 3.2 + - - -
288A ARG 2.9 10.3 + - - -
291A SER* 1.3 82.5 - - - +
293A PRO* 1.3 65.6 - - - +
294A GLY 2.8 16.5 + - - -
295A MSE 3.0 13.3 + - - +
19B PHE* 3.5 20.4 - - - +
20B TRP* 4.7 0.2 + - - -
231B PHE* 4.2 10.5 - - - -
----------------------------------------------------------
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