Contacts of the helix formed by residues 328 - 338 (chain A) in PDB entry 4BHT
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 328 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ASN 5.1 3.5 - - - +
326A GLU 4.1 1.0 - - - -
327A LEU* 1.3 74.3 - - - +
329A VAL* 1.3 72.3 + - - +
330A ASP* 3.3 9.6 - - + +
331A ALA* 2.8 13.2 + - + +
332A ALA* 2.8 29.5 + - - +
352A THR* 3.0 31.4 + - + +
354A GLU* 4.7 3.8 - - - +
355A ALA* 3.6 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ASP* 1.3 81.0 + - - +
330A ASP* 1.3 84.5 + - - +
332A ALA* 3.4 10.1 - - - +
333A HIS* 2.5 53.6 + - + +
354A GLU* 3.3 65.5 - - + +
355A ALA* 3.6 1.7 - - - +
358A LEU* 4.1 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ASP* 3.3 7.9 - - + +
329A VAL* 1.3 97.5 + - - +
331A ALA* 1.3 61.6 + - - +
333A HIS* 3.4 12.7 + - - +
334A GLN* 3.2 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A GLN* 4.9 4.3 - - - +
311A TRP* 3.4 36.4 - - + +
327A LEU* 4.1 7.0 - - + -
328A ASP* 2.8 17.2 + - + +
330A ASP* 1.3 75.8 - - - +
332A ALA* 1.3 61.7 + - - +
334A GLN* 3.2 13.9 + - - +
335A LEU* 3.0 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU* 3.9 0.8 - - + +
328A ASP 2.8 12.1 + - - +
329A VAL* 3.4 9.2 - - - +
331A ALA* 1.3 74.7 - - - +
333A HIS* 1.3 59.2 + - - +
335A LEU* 3.1 2.6 + - - +
336A ILE* 2.8 36.3 + - - +
355A ALA* 3.9 18.6 - - + +
358A LEU* 4.1 11.4 - - + -
359A PHE* 3.4 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A VAL* 2.5 34.8 + - + +
330A ASP* 3.6 12.4 + - - +
332A ALA* 1.3 73.0 - - - +
334A GLN* 1.3 63.5 + - + +
336A ILE* 3.3 4.9 + - + +
337A ALA* 2.9 25.9 + - - +
358A LEU* 3.3 33.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A TRP* 3.7 11.1 - - - +
312A SER* 3.4 35.8 + - - -
330A ASP* 3.2 15.5 + - - +
331A ALA* 3.2 13.6 + - - +
333A HIS* 1.3 80.2 - - + +
335A LEU* 1.3 57.6 + - - +
337A ALA* 3.3 5.5 + - - +
338A ASN* 2.9 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A SER* 5.0 0.2 - - - +
311A TRP* 3.4 36.3 - - + +
313A LEU 4.1 6.5 - - - +
314A PRO* 5.9 0.2 - - + -
315A VAL* 3.9 28.4 - - + +
318A ALA* 4.2 13.0 - - + -
327A LEU* 3.9 28.5 - - + -
331A ALA 3.0 18.6 + - - +
332A ALA 3.5 7.2 - - - +
334A GLN* 1.3 77.2 - - - +
336A ILE* 1.3 61.7 + - - +
338A ASN* 3.4 4.5 + - - +
339A GLY 3.2 4.9 + - - -
340A VAL* 3.0 37.5 + - + +
343A VAL* 5.3 0.4 - - + -
359A PHE* 4.1 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ALA 2.8 23.4 + - - +
333A HIS* 3.9 6.1 - - + +
335A LEU* 1.3 70.5 - - - +
337A ALA* 1.3 56.6 + - - +
339A GLY* 2.7 26.9 + - - -
340A VAL* 3.9 6.2 + - + +
358A LEU* 3.6 46.0 - - + +
359A PHE* 3.9 21.8 - - + -
362A ALA* 3.7 24.9 - - + -
364A VAL* 4.1 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A HIS 2.9 18.8 + - - +
334A GLN* 3.6 5.6 - - - +
336A ILE* 1.3 78.2 - - - +
338A ASN* 1.3 66.0 + - - +
339A GLY* 3.4 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A TRP 4.8 0.4 + - - -
312A SER* 3.2 28.7 + - - +
313A LEU 4.2 0.8 + - - +
314A PRO* 3.7 39.4 - - + +
315A VAL 4.4 4.9 + - - +
334A GLN* 2.9 25.7 + - - +
335A LEU* 3.7 6.0 - - + +
337A ALA* 1.3 81.7 - - - +
339A GLY* 1.3 59.1 + - - +
340A VAL 3.8 0.2 - - - -
----------------------------------------------------------
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