Contacts of the helix formed by residues 279 - 292 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LYS* 5.0 0.7 - - - +
79B SER* 2.8 12.9 + - - +
80B LEU* 4.5 1.3 - - - +
277B GLY 3.9 8.7 - - - +
278B ALA* 1.3 76.4 - - - +
280B ALA* 1.3 65.4 + - - +
281B GLN* 3.7 14.6 + - - +
282B GLU* 3.1 32.2 + - + +
283B ASP* 3.3 23.1 + - - +
285B ARG* 4.6 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLU* 4.5 11.0 - - + +
242A LEU* 4.2 31.6 - - + +
243A VAL* 4.3 20.9 - - + +
246A LYS* 6.1 1.8 - - - +
80B LEU* 4.8 4.5 - - + +
278B ALA 4.3 0.2 - - - -
279B ASP* 1.3 71.2 + - - +
281B GLN* 1.3 69.5 + - + +
283B ASP* 3.1 5.0 + - - +
284B LEU* 2.9 27.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLU* 3.9 27.6 + - - +
279B ASP* 3.5 10.5 - - - +
280B ALA* 1.3 77.2 - - + +
282B GLU* 1.3 58.2 + - - +
284B LEU* 3.2 13.2 + - - +
285B ARG* 2.8 54.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B SER* 4.2 12.6 - - - -
82B ARG* 5.1 5.2 + - - -
279B ASP* 3.1 30.4 + - - +
280B ALA 3.1 0.4 - - - -
281B GLN* 1.3 80.6 - - - +
283B ASP* 1.3 75.3 + - - +
285B ARG* 3.2 22.8 + - + +
286B TRP* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LEU* 4.4 11.8 - - + +
77B TYR 4.6 2.4 - - - +
78B GLY* 3.4 11.4 - - - -
79B SER* 2.8 45.7 + - - -
80B LEU* 3.4 21.5 + - - +
82B ARG* 5.3 0.2 + - - -
279B ASP 3.3 7.2 + - - +
280B ALA 3.1 8.3 + - - +
282B GLU* 1.3 82.3 - - - +
284B LEU* 1.3 59.5 - - - +
286B TRP* 3.2 16.1 + - + +
287B PHE* 2.9 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG* 4.2 3.1 - - - +
235A GLN* 3.5 47.1 - - + +
238A GLU* 4.0 26.2 - - + -
239A GLU* 3.9 33.0 - - + +
242A LEU* 4.4 8.7 - - + -
280B ALA 2.9 17.7 + - - +
281B GLN* 3.5 18.6 - - - +
283B ASP* 1.3 75.8 - - - +
285B ARG* 1.3 64.9 + - - +
287B PHE* 3.6 4.7 - - + +
288B ARG* 2.9 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ASP* 4.6 5.1 + - - -
281B GLN* 2.8 43.1 + - - +
282B GLU* 3.5 31.4 - - + +
284B LEU* 1.3 75.1 - - - +
286B TRP* 1.3 66.0 + - - +
288B ARG* 3.1 17.7 + - - +
289B SER* 3.2 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TYR* 4.2 34.1 - + + -
78B GLY* 4.9 10.3 - - - -
282B GLU* 3.0 12.9 + - + +
283B ASP* 3.2 21.1 - - + +
285B ARG* 1.3 79.7 - - - +
287B PHE* 1.3 91.8 + + + +
289B SER* 3.3 4.4 + - - -
290B THR* 3.0 52.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ARG* 4.3 9.9 - - + -
28A THR* 4.0 27.4 - - - -
31A ARG* 3.8 40.4 - - + +
231A PHE* 4.0 9.9 - + - -
235A GLN* 3.8 16.6 - - - +
283B ASP 2.9 14.4 + - - +
284B LEU* 3.6 11.0 - - + +
286B TRP* 1.3 96.1 - + + +
288B ARG* 1.3 59.0 + - - +
290B THR* 4.3 3.1 - - + -
291B SER* 2.8 53.5 + - - -
292B GLY 3.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A GLU* 2.8 32.5 + - - +
231A PHE* 3.9 32.6 - - + -
232A GLU* 5.1 6.3 + - - -
235A GLN* 4.2 3.1 - - - +
284B LEU 2.9 12.7 + - - +
285B ARG* 3.1 12.1 + - - +
287B PHE* 1.3 75.0 - - - +
289B SER* 1.3 69.8 + - - +
292B GLY* 2.7 23.6 + - - -
293B PRO* 3.4 21.2 + - + +
294B GLY* 3.5 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ARG 3.2 13.1 + - - -
286B TRP* 3.6 4.6 + - - -
288B ARG* 1.3 83.2 - - - +
290B THR* 1.3 64.9 + - - +
294B GLY* 3.7 21.3 - - - -
295B MSE 3.1 26.5 - - - +
296B PRO* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ARG* 4.8 0.7 + - - -
286B TRP* 3.0 51.9 + - + -
287B PHE* 3.9 4.9 - - + +
289B SER* 1.3 82.1 - - - +
291B SER* 1.3 70.9 + - - +
295B MSE 3.5 15.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 3.6 11.7 - - - +
24A ASN 5.0 0.3 - - - +
27A ARG* 3.2 48.6 + - - +
28A THR* 4.3 6.4 + - - -
287B PHE* 2.8 36.5 + - - -
290B THR* 1.3 89.8 + - - +
292B GLY* 1.3 61.1 + - - +
295B MSE 3.8 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 2.9 26.4 - - - +
20A TRP* 4.6 0.5 + - - -
231A PHE* 4.0 7.6 - - - -
287B PHE 3.4 1.0 + - - -
288B ARG 2.7 12.4 + - - -
289B SER 3.6 0.6 + - - -
291B SER* 1.3 79.8 - - - +
293B PRO* 1.3 71.0 - - - +
294B GLY 3.1 6.1 - - - -
295B MSE 3.1 17.3 - - - +
----------------------------------------------------------
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