Contacts of the helix formed by residues 279 - 290 (chain B) in PDB entry 1FBZ
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 GLY 279 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B PHE* 4.0 16.2 - - - +
277B PHE* 2.9 6.6 + - - +
278B PRO* 1.3 78.1 - - - +
280B LEU* 1.3 66.5 + - - -
281B HIS 3.2 2.5 - - - -
282B GLU* 3.4 16.4 + - - +
283B LEU* 3.3 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B TRP* 3.9 15.3 - - + -
206B PHE* 4.2 13.7 - - + -
231B ILE* 3.7 24.2 - - + -
241B PHE* 3.6 34.1 - - + -
261B ILE* 3.8 30.1 - - + -
269B PHE* 3.9 30.2 - - + -
279B GLY* 1.3 73.0 - - - -
281B HIS* 1.3 56.5 + - - +
283B LEU* 3.1 10.5 + - + +
284B VAL* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B GLU* 5.7 1.8 - - + +
205B TRP* 3.9 29.7 - - + -
279B GLY* 3.2 0.8 - - - -
280B LEU* 1.3 78.2 - - - +
282B GLU* 1.3 78.7 + - - +
284B VAL* 3.2 3.8 + - + +
285B ARG* 3.0 67.2 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
277B PHE* 4.1 14.5 - - + -
278B PRO* 3.5 23.1 - - + +
279B GLY* 3.4 31.8 - - - +
281B HIS* 1.3 92.7 - - - +
283B LEU* 1.3 63.0 + - - +
285B ARG* 3.5 10.8 + - - +
286B HIS* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ILE* 5.3 2.2 - - + -
243B LEU* 5.0 9.2 - - + -
261B ILE* 3.7 36.1 - - + -
269B PHE* 4.1 6.3 - - + -
270B TYR* 4.0 16.2 - - - +
271B ILE* 4.0 16.6 - - + -
277B PHE* 3.2 33.1 - - + -
279B GLY 3.3 8.3 + - - +
280B LEU* 3.1 15.1 + - + +
282B GLU* 1.3 80.4 - - - +
284B VAL* 1.3 65.4 + - + +
286B HIS* 3.9 0.3 - - - +
287B TYR* 3.0 49.2 + - + -
298B LEU* 5.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B TRP* 3.6 38.1 - - + +
229B PHE* 3.8 21.5 - - + -
231B ILE* 3.5 27.1 - - + -
280B LEU 2.9 16.4 + - - +
281B HIS* 3.5 8.3 - - + +
283B LEU* 1.3 75.7 - - + +
285B ARG* 1.3 60.8 + - + +
287B TYR* 3.4 2.3 + - - +
288B THR* 2.6 47.1 + - - +
298B LEU* 4.5 7.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
281B HIS* 3.0 58.6 + - + +
282B GLU* 3.5 10.7 + - - +
284B VAL* 1.3 76.9 - - + +
286B HIS* 1.3 61.9 + - - +
288B THR* 3.2 8.7 + - - -
289B ASN* 2.8 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ILE* 3.3 28.8 - - + +
277B PHE* 3.3 29.8 - + + -
282B GLU 3.1 16.0 + - - +
283B LEU 3.9 1.1 - - - +
285B ARG* 1.3 77.9 - - - +
287B TYR* 1.3 72.1 + + - +
289B ASN* 2.8 24.8 + - - +
290B ALA* 3.1 15.7 + - + +
292B ASP* 3.0 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ILE* 3.8 25.9 + - + +
272B SER* 4.4 7.8 + - - -
275B ILE* 3.0 26.2 - - + +
277B PHE* 3.2 22.9 - + - -
283B LEU* 3.0 41.1 + - + +
284B VAL 3.7 0.2 - - - -
286B HIS* 1.3 79.8 - + - +
288B THR* 1.3 59.8 + - - +
289B ASN 3.2 0.2 - - - -
290B ALA 3.1 22.9 - - - +
291B SER* 3.1 28.8 - - - -
292B ASP* 3.9 16.7 + - + -
294B LEU* 3.5 24.4 - - + +
297B ARG* 3.5 0.7 - - - +
298B LEU* 3.0 40.4 + - + -
350B CC1 4.9 1.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B PHE* 4.2 3.1 - - - -
284B VAL* 2.6 36.4 + - - +
285B ARG* 3.3 9.4 - - - +
286B HIS 3.0 0.4 - - - -
287B TYR* 1.3 78.9 - - - +
289B ASN* 1.3 61.3 + - - +
297B ARG* 2.8 29.6 + - - +
298B LEU* 3.2 28.9 + - - +
299B SER* 4.3 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ARG* 2.8 34.5 + - - +
286B HIS* 2.8 10.3 + - - +
288B THR* 1.3 84.5 - - - +
290B ALA* 1.3 62.1 + - + +
297B ARG* 4.0 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B HIS* 3.1 8.4 + - + +
287B TYR* 3.1 25.9 + - - -
288B THR 3.4 1.8 - - - -
289B ASN* 1.3 83.7 - - + +
291B SER* 1.3 65.7 + - - +
292B ASP* 3.2 13.0 + - + +
297B ARG* 3.6 6.2 - - - +
----------------------------------------------------------
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