Contacts of the strand formed by residues 283 - 289 (chain A) in PDB entry 6BFN
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 PHE 283 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LEU* 3.8 30.7 - - + -
212A PHE* 3.6 30.7 - + - -
240A ARG* 3.3 46.7 - - + +
241A LEU 5.9 0.2 - - - -
278A CYS* 3.4 1.8 - - - +
279A ALA* 3.3 6.9 - - - -
280A GLN 2.7 39.3 + - - +
281A ASN* 3.4 23.3 - - - -
282A GLY* 1.3 73.4 - - - +
284A TYR* 1.3 64.2 + - - +
285A CYS* 4.6 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LYS 3.7 0.2 - - - +
240A ARG* 3.4 5.9 - - - +
241A LEU* 2.9 54.8 + - + +
249A TRP* 3.3 40.8 - + - -
252A VAL* 4.6 6.7 - - + -
253A LYS* 2.4 45.6 + - + +
256A PHE* 3.8 34.5 - + + -
278A CYS 3.6 1.1 - - - -
279A ALA* 3.9 23.6 - - + -
282A GLY* 3.9 10.3 + - - -
283A PHE* 1.3 75.7 - - - +
285A CYS* 1.3 62.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LEU* 5.4 1.1 - - - -
205A ILE* 4.1 27.6 - - + -
212A PHE* 4.2 30.5 - - - -
238A VAL* 4.3 6.3 - - + -
239A LYS 3.2 4.9 - - - +
240A ARG* 4.3 11.2 - - - -
256A PHE* 3.4 9.5 - - - -
277A TYR* 3.3 4.5 - - - -
278A CYS* 2.8 41.2 + - + +
283A PHE* 4.6 8.1 - - - -
284A TYR* 1.3 84.2 - - - +
286A LEU* 1.3 64.3 + - - +
287A VAL* 5.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A VAL* 3.4 4.6 - - - +
239A LYS* 2.9 46.1 + - + +
241A LEU* 4.7 10.1 - - + -
256A PHE* 3.8 17.0 - - + +
259A GLU* 3.2 37.2 - - + +
260A VAL* 3.6 30.3 - - + -
274A PHE* 3.7 17.0 - - + -
276A GLY 3.8 1.3 - - - -
277A TYR* 4.3 0.7 - - + -
285A CYS* 1.3 81.3 - - - +
287A VAL* 1.3 62.0 + - - +
288A TYR* 3.4 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A TRP* 3.7 26.5 - - + +
205A ILE* 3.8 22.7 - - + -
231A MET* 3.9 11.4 - - + -
236A TYR* 3.7 27.6 - - + -
237A ALA 3.6 3.1 - - - +
238A VAL* 4.4 7.4 - - + -
274A PHE* 3.5 8.7 - - - -
275A ALA* 2.8 36.7 + - + -
276A GLY 2.8 23.7 + - - +
277A TYR* 4.8 1.3 - - - +
286A LEU* 1.3 78.8 - - - +
288A TYR* 1.3 64.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A TYR* 3.3 13.2 - - - +
237A ALA 2.9 43.4 + - - +
239A LYS* 3.4 21.9 - - + -
259A GLU* 2.6 31.3 + - - -
263A LEU* 3.5 25.8 - - + -
272A VAL* 3.8 23.8 - - + -
273A ASP 3.2 13.9 - - - +
274A PHE* 4.4 5.2 - + - -
275A ALA* 4.1 1.1 - - - +
286A LEU* 3.4 33.3 - - + +
287A VAL* 1.3 77.8 - - - +
289A GLY* 1.3 61.9 + - - +
601A DL1 3.6 38.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A VAL 4.7 1.1 - - - -
236A TYR* 4.4 9.5 - - - -
272A VAL* 6.1 0.2 - - - +
273A ASP* 3.1 24.2 + - - +
275A ALA* 4.4 3.4 - - - +
288A TYR* 1.3 74.6 - - - +
290A PHE* 1.3 67.4 + - - -
291A LEU* 3.6 12.7 + - - +
601A DL1 3.8 10.0 - - - -
269B PRO* 4.8 13.0 - - - -
----------------------------------------------------------
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