Contacts of the strand formed by residues 368 - 376 (chain A) in PDB entry 2BTO
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 LYS 368 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A PRO* 3.8 8.8 - - - +
289A GLU* 3.2 39.3 + - + +
290A LEU 3.1 28.0 + - - +
292A ILE* 3.7 23.3 - - + +
295A MET* 3.8 19.2 - - + +
323A TYR* 3.3 28.7 - - + +
324A ARG 3.1 12.3 - - - +
326A ILE* 4.1 16.1 - - + +
362A PRO* 5.2 0.4 - - - -
366A HIS* 3.1 11.5 + - - +
367A ARG* 1.3 81.2 - - - +
369A SER* 1.3 65.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A PHE* 3.8 22.6 - - - -
277A ALA 3.3 14.8 - - - -
278A PRO* 3.8 4.3 - - - -
295A MET* 4.3 4.6 - - - -
323A TYR* 3.9 1.3 - - - -
324A ARG* 2.7 61.3 + - - +
363A GLY* 4.8 4.9 + - - -
366A HIS* 4.3 12.6 + - - +
368A LYS* 1.3 76.2 - - - +
370A MET* 1.3 66.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A PHE* 3.5 9.3 - - - -
277A ALA* 2.8 36.8 + - + +
292A ILE* 6.1 1.3 - - - -
295A MET* 3.3 52.5 - - + +
296A ILE* 3.5 25.8 - - - +
299A LEU* 3.7 20.0 - - + +
321A VAL* 4.7 14.4 - - + -
322A LEU 3.7 5.6 - - - +
323A TYR* 3.4 39.7 - - + -
324A ARG* 5.5 0.2 - - - -
337A LEU* 5.3 1.6 - - - -
369A SER* 1.3 73.6 - - - +
371A VAL* 1.3 61.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ALA* 3.8 26.7 - - + +
239A GLY* 3.7 30.3 - - - +
240A ILE* 4.1 12.3 - - + +
274A CYS* 5.9 0.7 - - + -
275A ALA 3.3 8.1 - - - +
276A PHE* 3.5 28.9 - - + -
299A LEU* 4.1 3.1 - - - -
320A ALA 3.8 0.7 - - - +
321A VAL* 3.5 5.5 - - - +
322A LEU* 3.0 53.3 + - + +
324A ARG* 6.5 0.2 - - + -
370A MET* 1.3 72.4 - - - +
372A LEU* 1.3 59.8 + - - +
373A LEU 4.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A CYS* 3.0 10.7 - - - +
275A ALA* 2.8 41.3 + - + +
299A LEU* 3.4 43.8 - - + +
300A PHE* 4.1 21.3 - - + -
305A VAL* 5.0 8.5 - - + -
311A PRO* 6.3 1.3 - - + -
316A PHE* 4.9 5.8 - - + -
319A THR* 3.5 25.8 - - + +
320A ALA 3.5 4.5 - - - +
321A VAL* 4.3 2.2 - - + -
371A VAL* 1.3 73.2 - - - +
373A LEU* 1.3 77.9 + - - +
374A ALA* 4.1 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU* 6.4 1.1 - - + -
204A LEU* 3.7 30.1 - - + -
240A ILE* 3.4 41.5 - - + -
259A LEU* 4.3 10.8 - - + -
260A LEU* 6.0 1.1 - - + -
263A LEU* 3.5 33.8 - - + +
272A LEU* 4.5 10.8 - - + -
273A MET 3.6 6.1 - - - +
274A CYS* 3.7 16.2 - - + -
319A THR* 3.5 1.2 - - - -
320A ALA* 2.8 40.8 + - + +
322A LEU* 5.5 4.2 - - + +
371A VAL 4.1 0.4 - - - -
372A LEU* 1.3 73.4 - - - +
374A ALA* 1.3 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 4.8 0.8 - - - +
272A LEU* 3.3 11.6 - - - +
273A MET* 2.9 42.8 + - + +
311A PRO* 6.2 0.4 - - + -
316A PHE* 4.0 30.5 - - + -
318A SER 3.6 4.7 - - - +
319A THR* 4.7 0.2 - - - +
372A LEU* 4.1 14.4 - - + -
373A LEU* 1.3 77.3 - - - +
375A ASN* 1.3 61.0 + - - +
376A ASN* 3.8 6.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 2.9 29.1 + - - +
264A VAL* 4.2 0.8 - - - +
265A PRO* 3.9 5.7 - - - +
269A LEU 3.1 23.4 + - - -
270A HIS* 4.4 1.8 - - - +
271A PHE 3.0 10.9 + - - +
272A LEU* 3.9 10.9 - - + +
316A PHE* 3.5 3.8 - - - +
317A LEU* 2.7 49.2 + - + +
318A SER* 3.0 14.2 + - - +
374A ALA* 1.3 71.0 - - - +
376A ASN* 1.3 55.8 + - - +
427A TYR* 3.0 34.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PHE 4.7 1.6 + - - -
273A MET* 3.5 19.7 - - + +
311A PRO* 3.0 28.9 + - - +
315A ARG 3.1 22.5 + - - +
316A PHE* 3.7 19.3 - - + -
317A LEU* 4.5 0.4 - - - -
374A ALA* 3.8 3.4 + - + -
375A ASN* 1.3 78.4 + - - +
377A THR* 1.3 63.8 + - - +
378A GLU* 2.8 50.9 + - - +
379A ILE* 3.2 23.9 + - - +
427A TYR* 4.0 5.4 - - - -
----------------------------------------------------------
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