Contacts of the strand formed by residues 369 - 376 (chain A) in PDB entry 1BU8
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 TYR 369 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LEU* 3.1 5.1 - - - -
357A VAL 2.9 35.6 + - - +
366A SER* 4.1 2.9 - - - -
367A LYS* 3.1 48.0 - - + +
368A GLN* 1.3 75.2 - - - +
370A GLU* 1.3 63.6 + - - +
371A ILE* 3.3 5.1 + - + +
384A ARG* 5.3 3.1 - - - +
386A ILE* 3.8 43.3 - - + -
387A ASP 3.6 20.2 + - - -
388A VAL* 3.5 18.6 - - + +
389A ASP* 3.4 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A TYR* 3.4 33.8 - - + +
355A ILE 3.6 7.4 - - - +
356A LEU* 4.0 14.6 - - + +
369A TYR* 1.3 70.9 - - - +
371A ILE* 1.3 63.4 + - - +
372A PHE* 3.9 17.2 + - - +
373A LYS* 3.6 24.7 + - - +
384A ARG* 2.8 43.1 + - - +
386A ILE* 4.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A VAL* 3.8 33.7 - - + +
344A VAL* 4.4 7.9 - - + -
355A ILE* 2.8 20.2 + - + +
357A VAL* 3.6 28.7 - - + -
369A TYR* 3.7 13.2 - - + +
370A GLU* 1.3 78.0 - - - +
372A PHE* 1.3 62.2 + - - +
382A HIS* 4.2 18.9 - - + +
383A VAL 4.2 4.6 - - - +
384A ARG* 3.7 38.8 - - + +
386A ILE* 4.2 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A TYR* 3.5 1.0 - - - -
355A ILE* 3.0 42.9 + - + +
370A GLU* 3.7 8.2 - - - +
371A ILE* 1.3 82.5 - - - +
373A LYS* 1.3 93.8 + - - +
374A GLY* 3.8 6.3 - - - -
375A SER* 3.3 28.7 - - - -
376A LEU* 3.9 11.9 - - + -
382A HIS* 3.6 42.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A GLY 3.2 6.5 - - - +
354A TYR* 3.4 43.3 + - + +
370A GLU* 3.6 19.3 + - - +
372A PHE* 1.3 92.7 - - - +
374A GLY* 1.3 58.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A SER* 3.5 4.8 - - - -
353A GLY 2.9 33.0 + - - +
372A PHE* 3.8 5.5 - - - -
373A LYS* 1.3 74.5 - - - +
375A SER* 1.3 64.9 + - - -
376A LEU* 3.5 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LYS* 5.1 7.6 - - - -
351A LEU 3.4 8.7 - - - -
352A SER* 4.6 4.7 - - - +
372A PHE* 3.3 21.7 - - - -
374A GLY* 1.3 70.1 - - - -
376A LEU* 1.3 62.0 + - - +
377A LYS* 3.1 32.9 + - - +
382A HIS* 4.6 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 4.0 11.4 - - + -
349A LYS 4.1 1.4 - - - +
350A LYS* 3.5 2.9 - - - -
351A LEU* 2.7 38.1 + - + +
352A SER 4.3 1.8 - - - -
353A GLY* 3.9 33.4 - - - +
354A TYR 4.2 1.1 - - - +
355A ILE* 3.9 23.3 - - + +
372A PHE* 3.9 22.9 - - + -
374A GLY 3.7 15.3 - - - +
375A SER* 1.3 70.4 - - - +
377A LYS* 1.3 62.0 + - - +
378A PRO* 3.8 2.8 - - - +
402A TRP* 4.1 14.1 - - + -
415A LEU* 3.6 33.7 - - + +
----------------------------------------------------------
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