Contacts of the strand formed by residues 234 - 241 (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 THR 234 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A VAL* 3.3 6.4 - - - +
231A MET 2.9 33.9 + - - +
232A ARG 3.0 12.0 + - - -
233A ASN* 1.3 80.1 + - - +
235A VAL* 1.3 65.0 + - - +
236A TYR* 3.3 30.9 + - + -
268B HIS* 2.7 35.0 + - + +
269B PRO* 3.9 21.3 - - + -
324B ARG* 3.6 10.0 - - - +
328B PHE* 4.4 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ARG* 3.8 35.2 - - + +
229A ALA 3.4 10.1 - - - +
230A VAL* 4.2 13.0 - - + -
233A ASN 6.0 0.2 - - - -
234A THR* 1.3 80.6 - - - +
236A TYR* 1.3 67.6 + - - +
290A PHE* 3.4 46.0 + - + +
269B PRO* 4.7 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A TRP* 3.9 16.2 - + - -
228A ARG* 3.6 4.3 - - - -
229A ALA* 2.9 32.7 + - + +
231A MET* 3.4 42.2 - - + -
234A THR* 3.3 39.6 - - + +
235A VAL* 1.3 77.3 - - - +
237A ALA* 1.3 61.2 + - - +
238A VAL* 4.7 2.0 - - + -
275A ALA* 3.7 20.2 - - + -
287A VAL* 3.7 21.5 - - + -
288A TYR 3.3 18.4 - - - +
289A GLY* 4.4 2.5 - - - -
290A PHE* 3.8 10.2 - - - -
267B ARG 5.0 1.9 + - - -
268B HIS* 3.6 5.5 - - - -
269B PRO* 4.6 9.6 - - + -
328B PHE* 3.3 30.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ILE* 4.8 0.7 - - + -
226A VAL* 4.4 6.3 - - + -
227A TYR 3.3 8.3 - - - +
236A TYR* 1.3 74.0 - - - +
238A VAL* 1.3 62.2 + - - +
287A VAL* 3.6 2.8 - - - +
288A TYR* 2.9 38.2 + - + +
290A PHE* 4.0 7.8 - - + +
601A DL1 3.5 49.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ILE* 4.1 24.0 - - + -
209A THR* 4.4 13.9 - - + -
212A PHE* 4.7 5.2 - - + -
225A CYS 3.7 1.6 - - - +
226A VAL* 3.3 5.1 - - - -
227A TYR* 2.9 42.2 + - + +
229A ALA* 3.8 25.6 - - + -
231A MET* 4.5 6.5 - - + -
236A TYR* 4.7 0.7 - - + -
237A ALA* 1.3 77.5 - - - +
239A LYS* 1.3 67.8 + - - +
285A CYS* 4.3 13.9 - - + -
286A LEU 3.4 6.7 - - - +
287A VAL* 4.4 19.5 - - + -
288A TYR* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A PHE* 3.4 43.2 - - + +
225A CYS 3.5 3.6 - - - +
226A VAL* 4.2 6.3 - - + +
237A ALA 4.2 0.6 + - - -
238A VAL* 1.3 73.4 - - - +
240A ARG* 1.3 59.9 + - - +
241A LEU* 4.0 17.3 + - + +
259A GLU* 2.9 28.9 + - - -
284A TYR 3.7 0.9 - - - +
285A CYS* 3.2 5.5 - - - -
286A LEU* 2.9 46.5 + - + +
288A TYR* 3.4 28.1 + - + +
358A ASP* 2.9 26.9 + - - +
601A DL1 3.9 14.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A PHE* 4.0 32.4 - - + +
224A GLY* 3.1 5.2 - - - -
225A CYS* 2.8 40.6 + - - +
227A TYR* 4.1 25.0 + - + -
238A VAL* 3.8 1.4 + - + -
239A LYS* 1.3 73.1 - - - +
241A LEU* 1.3 72.2 + - - +
283A PHE* 3.3 39.1 - - + +
284A TYR 3.4 9.6 - - - +
285A CYS* 4.3 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A PHE* 3.5 22.7 - - + +
239A LYS* 4.1 29.4 - - + +
240A ARG* 1.3 90.2 + - - +
242A LYS* 1.3 67.3 + - - +
252A VAL* 3.6 35.0 - - + +
255A SER* 4.3 6.3 - - - +
256A PHE* 3.6 33.0 - - + +
259A GLU* 5.7 0.4 - - - +
283A PHE* 5.9 0.3 - - - -
284A TYR* 2.9 32.8 + - + +
286A LEU* 4.7 6.5 - - + -
----------------------------------------------------------
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