Contacts of the helix formed by residues 346 - 357 (chain H) in PDB entry 2BWB
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 ASP 346 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344H PHE 3.7 0.6 - - - -
345H PHE* 1.3 74.8 - - - +
347H PHE* 1.3 61.2 + - - +
348H ASP* 3.1 18.6 + - - +
349H ARG* 3.3 39.9 + - + +
350H ASN* 2.9 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 347 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356G ARG* 3.1 67.8 - - + +
328H PRO* 4.0 15.9 - - + -
329H GLU* 3.6 39.7 - - + -
336H LEU* 4.0 13.0 - - + -
345H PHE 3.1 8.5 + - - +
346H ASP* 1.3 69.7 + - - +
348H ASP* 1.3 75.5 + - - +
350H ASN* 3.2 7.0 + - - +
351H VAL* 2.8 59.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 348 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356G ARG* 5.2 4.0 + - - -
346H ASP* 3.1 9.3 + - - +
347H PHE* 1.3 94.1 - - - +
349H ARG* 1.3 58.9 + - + +
351H VAL* 3.5 4.1 + - - +
352H ALA* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 349 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344H PHE* 5.6 2.4 - - - -
346H ASP* 3.3 34.7 + - + +
347H PHE 3.3 0.6 - - - -
348H ASP* 1.3 75.8 - - + +
350H ASN* 1.3 60.6 + - - +
352H ALA* 3.7 6.1 - - - +
353H ALA* 3.0 30.8 + - - +
367H SER 5.3 2.6 + - - -
368H LEU* 3.3 52.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 350 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356G ARG 5.6 0.2 + - - -
336H LEU* 3.9 17.2 - - + +
339H LEU* 3.8 17.0 - - + +
340H ASN* 3.6 14.6 + - - -
344H PHE* 2.9 34.3 + - - +
345H PHE 4.0 2.4 + - - -
346H ASP* 2.9 28.2 + - - +
347H PHE* 3.5 6.9 - - - +
349H ARG* 1.3 76.5 - - - +
351H VAL* 1.3 57.4 + - - +
353H ALA* 3.4 2.8 + - - +
354H LEU* 3.0 34.5 + - - +
368H LEU* 3.7 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 351 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328H PRO* 4.0 25.6 - - + -
332H TYR* 4.3 7.4 - - + -
336H LEU* 4.5 9.4 - - + -
347H PHE* 2.8 57.8 + - + +
348H ASP* 4.0 5.2 - - - +
350H ASN* 1.3 69.6 - - - +
352H ALA* 1.3 67.1 + - - +
354H LEU* 3.2 7.6 + - - +
355H ARG* 2.9 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 352 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348H ASP 3.0 18.4 + - - +
349H ARG* 3.7 7.9 - - - +
351H VAL* 1.3 76.0 - - - +
353H ALA* 1.3 61.5 + - - +
355H ARG* 3.4 8.1 + - - +
356H ARG* 3.3 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 353 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349H ARG 3.0 19.5 + - - +
350H ASN 3.6 4.3 - - - +
352H ALA* 1.3 76.3 - - - +
354H LEU* 1.3 58.6 + - - +
356H ARG* 3.4 7.5 + - - +
357H SER* 3.1 27.5 + - - -
364H ALA* 3.8 31.2 - - + +
367H SER* 3.8 20.9 - - - +
368H LEU* 4.1 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 354 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332H TYR* 3.9 33.3 - - + -
335H GLN* 3.7 40.4 - - + -
336H LEU* 4.5 8.5 - - + -
339H LEU* 3.8 13.7 - - + -
350H ASN 3.0 23.1 + - - +
351H VAL 3.2 4.9 + - - +
353H ALA* 1.3 76.4 - - - +
355H ARG* 1.3 58.8 + - - +
357H SER* 3.2 2.2 + - - -
358H GLY 3.0 7.6 + - - -
359H GLY* 2.7 37.4 + - - -
360H SER 3.7 21.8 - - - +
361H VAL* 4.4 2.0 - - - +
364H ALA* 3.8 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 355 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332H TYR* 3.5 24.7 - - - +
351H VAL* 2.9 42.4 + - + +
352H ALA* 3.7 7.8 - - - +
353H ALA 3.3 0.2 - - - -
354H LEU* 1.3 76.3 - - - +
356H ARG* 1.3 63.2 + - + +
358H GLY* 3.4 11.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 356 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352H ALA* 3.3 16.9 + - - +
353H ALA* 3.8 10.3 - - - +
355H ARG* 1.3 77.2 - - + +
357H SER* 1.3 59.0 + - - +
358H GLY 3.4 0.4 + - - -
367H SER* 5.2 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 357 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353H ALA 3.1 14.4 + - - -
354H LEU* 3.2 12.0 + - - -
355H ARG 3.3 0.2 - - - -
356H ARG* 1.3 75.6 - - - +
358H GLY* 1.3 59.0 + - - +
360H SER* 2.5 50.3 + - - -
363H GLY* 3.9 10.5 - - - -
364H ALA 3.5 11.7 - - - -
----------------------------------------------------------
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