Contacts of the helix formed by residues 279 - 285 (chain B) in PDB entry 4B92
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 279 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B THR 5.7 0.4 - - - +
278B LEU* 1.3 77.9 - - - +
280B GLY* 1.3 58.1 + - - +
281B LEU* 3.1 26.2 + - - +
282B HIS* 3.0 30.9 + - - -
300B LEU* 3.7 10.9 - - - +
301B ARG 3.8 8.7 - - - -
302B LEU 4.5 6.7 - - - -
303B ASP 4.5 2.7 - - - +
304B THR* 4.0 30.7 - - + +
306B THR* 6.3 0.2 - - - -
307B SER* 4.5 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLU* 3.5 21.1 - - - -
279B THR* 1.3 67.8 - - - +
281B LEU* 1.3 61.1 + - - +
282B HIS* 3.0 6.3 - - - -
283B TYR* 2.9 27.8 + - - +
284B TYR* 3.8 6.2 - - - -
300B LEU* 3.5 17.6 - - - +
301B ARG 2.9 15.9 + - - -
302B LEU* 4.2 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B THR* 3.1 18.3 + - - +
280B GLY* 1.3 76.2 - - - +
282B HIS* 1.3 64.7 + - + +
284B TYR* 2.9 32.0 + - + +
285B HIS* 3.7 3.1 + - - -
302B LEU* 4.0 20.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B LEU* 4.3 16.1 - - + +
279B THR* 3.0 34.0 + - - +
280B GLY 3.0 1.8 - - - +
281B LEU* 1.3 83.5 - - + +
283B TYR* 1.3 63.1 + - + +
284B TYR 3.0 1.7 + - - -
285B HIS* 3.2 14.5 + - - +
290B HIS* 3.4 4.2 + + - -
291B ALA* 3.4 15.3 - - - -
294B TYR* 3.4 50.6 - + + -
300B LEU* 5.3 0.7 - - + -
426B LEU 5.0 1.3 - - - -
1484B ZN 2.2 37.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B PRO* 4.3 5.9 - - + +
214B GLU* 3.7 36.7 + - + +
216B ILE* 3.9 19.5 - - + -
217B GLU* 4.0 12.1 - - + -
280B GLY* 2.9 22.8 + - - +
282B HIS* 1.3 76.8 - - - +
284B TYR* 1.3 62.1 + - + +
285B HIS 3.4 1.2 - - - +
291B ALA* 3.4 29.1 - - - +
294B TYR* 2.6 46.5 + - + -
295B VAL* 3.7 13.0 - - + -
296B THR* 4.1 3.8 + - - +
299B PRO* 3.8 7.4 - - + +
300B LEU* 3.2 51.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B GLU* 3.4 37.8 + - + +
217B GLU* 3.4 26.8 + - - -
218B ILE* 4.0 19.4 - - + +
280B GLY 3.8 13.0 - - - -
281B LEU* 2.9 23.8 + - + +
283B TYR* 1.3 81.3 - - + +
285B HIS* 1.3 64.0 + - - +
286B GLN* 3.8 2.4 + - - +
302B LEU* 4.2 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LEU 3.7 2.7 + - - +
282B HIS* 3.2 16.3 + - - +
283B TYR 3.4 0.9 - - - +
284B TYR* 1.3 82.8 - - - +
286B GLN* 1.3 89.1 + - + +
287B ASP* 3.1 34.9 + - + +
288B TRP* 5.2 0.2 - - - -
290B HIS* 3.5 31.3 + + + +
291B ALA* 4.3 5.4 - - - +
1484B ZN 3.6 21.5 - - - -
----------------------------------------------------------
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