Contacts of the helix formed by residues 273 - 282 (chain D) in PDB entry 3BUW
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 THR 273 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D LYS* 4.9 4.9 + - - -
81D PRO 4.6 1.3 - - - -
82D PRO* 3.4 22.2 - - + -
152D THR* 3.6 9.2 - - + +
156D LEU* 3.0 37.5 - - + -
272D LEU* 1.3 74.9 - - - +
274D TYR* 1.3 66.8 + - - +
275D ASP* 3.5 6.7 + - - +
276D GLU* 2.9 38.1 + - - +
277D VAL* 3.0 24.9 + - - +
294D ARG* 3.8 6.3 - - - +
297D CYS* 6.4 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 274 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C ASN* 3.3 51.1 - - + +
322C PRO* 2.7 50.8 + - + +
323C PTR 3.7 11.3 + + - +
80D SER* 5.0 0.2 - - - +
81D PRO 4.5 2.5 + - - +
273D THR* 1.3 73.9 - - - +
275D ASP* 1.3 73.4 + - - +
277D VAL* 3.3 2.1 + - - +
278D LYS* 3.2 30.9 + - + +
294D ARG* 3.4 24.9 - - - +
314D ILE 5.2 2.3 + - - -
315D LEU* 5.8 0.3 - - - -
316D GLN* 3.0 59.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 275 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C ASN* 4.4 0.7 - - - +
78D LYS* 2.9 45.8 + - - +
80D SER* 3.2 22.0 + - - -
81D PRO 5.5 0.2 + - - -
273D THR* 3.3 4.2 + - - +
274D TYR* 1.3 90.4 - - - +
276D GLU* 1.3 60.0 + - + +
278D LYS* 3.3 8.0 + - - +
279D ALA* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 276 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D ARG* 3.3 30.4 + - - -
152D THR* 3.5 24.0 + - + +
271D PHE 3.9 2.8 - - - +
272D LEU* 3.0 31.4 - - + +
273D THR* 2.9 38.4 + - - +
275D ASP* 1.3 76.9 - - + +
277D VAL* 1.3 57.7 + - - +
279D ALA* 3.6 6.3 - - - +
280D ARG* 2.8 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 277 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D MET* 5.3 0.9 - - + -
272D LEU* 4.2 10.1 - - + -
273D THR 3.0 8.0 + - - +
274D TYR 3.6 8.3 - - - +
276D GLU* 1.3 74.1 - - - +
278D LYS* 1.3 67.6 + - - +
280D ARG* 3.2 1.1 + - - +
281D LEU* 3.0 35.6 + - + +
292D ILE* 3.7 36.8 - - + +
293D PHE* 5.9 0.2 - - - -
294D ARG* 3.5 36.3 - - + +
304D ALA 5.9 0.4 - - - +
306D GLY* 4.2 7.4 - - - +
314D ILE* 5.2 0.2 - - + -
316D GLN* 3.7 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 278 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D TYR* 3.2 30.1 + - + +
275D ASP* 3.3 12.3 + - - +
277D VAL* 1.3 79.5 - - - +
279D ALA* 1.3 62.5 + - - +
282D GLN* 3.3 19.3 + - - +
314D ILE* 3.3 64.5 - - + +
316D GLN* 4.1 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 279 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D ASP 2.9 16.0 + - - +
276D GLU* 3.6 8.3 - - - +
277D VAL 3.2 0.2 - - - -
278D LYS* 1.3 78.7 - - - +
280D ARG* 1.3 60.7 + - - +
282D GLN* 3.3 20.4 + - - +
283D LYS* 4.5 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 280 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D MET* 3.6 32.1 - - - +
272D LEU* 4.4 10.8 - - + +
276D GLU 2.8 21.7 + - - +
277D VAL 3.2 4.4 + - - +
279D ALA* 1.3 74.1 - - - +
281D LEU* 1.3 61.2 + - + +
282D GLN 3.5 0.2 + - - -
283D LYS* 2.9 44.8 + - - +
284D PHE* 4.0 2.4 - - - -
292D ILE* 4.0 14.1 - - + -
341D ASP* 2.9 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D VAL* 3.0 24.2 + - + +
279D ALA 3.3 0.2 - - - -
280D ARG* 1.3 74.5 - - - +
282D GLN* 1.3 60.4 + - - +
283D LYS 3.2 2.9 - - - -
284D PHE* 2.9 38.7 + - + +
285D ILE 3.4 7.1 + - - -
290D SER* 4.2 17.3 - - - +
291D TYR* 4.2 9.9 - - - +
292D ILE* 3.9 23.1 - - + -
306D GLY 3.6 32.3 - - - +
307D TYR* 3.7 7.9 - - - +
308D VAL* 4.0 6.8 - - + +
314D ILE* 3.7 31.7 - - + +
341D ASP* 5.3 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 282 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D LYS* 3.3 11.6 + - - +
279D ALA* 3.3 16.8 - - - +
280D ARG 3.2 1.0 - - - -
281D LEU* 1.3 77.2 - - - +
283D LYS* 1.3 61.8 + - - +
284D PHE 3.1 0.5 + - - -
285D ILE* 3.1 39.6 + - - +
314D ILE* 4.0 13.5 - - - +
----------------------------------------------------------
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