Contacts of the helix formed by residues 380 - 390 (chain A) in PDB entry 2OZA
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 ASN 380 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A SER* 1.3 75.7 - - - +
381A PRO* 1.3 66.5 - - + +
382A LEU* 3.3 8.1 + - - +
383A LEU* 2.7 48.2 + - - +
384A LEU* 2.8 39.1 + - - +
129B PHE* 4.0 11.9 - - - -
161B ASP* 2.9 24.2 + - + +
163B GLU* 3.5 31.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ASN* 1.3 89.7 - - + +
382A LEU* 1.3 63.5 + - - +
384A LEU* 3.0 7.9 + - + +
385A LYS* 3.0 37.9 + - - +
81B GLU* 3.7 10.8 - - - +
163B GLU* 3.4 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ASN* 3.3 5.5 + - - +
381A PRO* 1.3 78.1 - - - +
383A LEU* 1.3 63.3 + - - +
385A LYS* 3.0 12.1 + - - +
386A ARG* 3.0 67.6 + - + +
81B GLU* 3.3 22.3 + - - +
82B ASN* 4.1 21.5 - - - +
129B PHE* 4.3 12.8 - - + -
132B TYR* 4.5 8.7 - - + -
133B GLN* 4.1 25.8 - - + +
136B ARG* 4.2 11.0 - - - +
163B GLU* 6.4 0.4 - - + -
316B ASP* 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ILE* 4.6 5.8 - - + +
378A ALA* 3.7 38.4 - - + +
379A SER* 4.0 1.1 - - - +
380A ASN* 2.7 43.7 + - - +
382A LEU* 1.3 74.1 - - - +
384A LEU* 1.3 57.9 + - + +
386A ARG* 5.0 1.6 - - - -
387A ARG* 3.2 59.0 + - + +
129B PHE* 4.0 28.7 - - + -
161B ASP 4.7 0.2 - - - +
162B CYS* 5.2 0.2 - - + -
311B TYR* 4.1 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A SER* 4.1 26.7 - - - +
380A ASN 2.8 20.8 + - - +
381A PRO* 3.0 6.2 + - + +
383A LEU* 1.3 79.6 - - + +
385A LYS* 1.3 65.2 + - + +
387A ARG* 4.6 10.1 - - + +
388A LYS* 3.3 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A PRO* 3.0 26.5 + - - +
382A LEU* 3.0 10.3 + - - +
384A LEU* 1.3 78.9 - - + +
386A ARG* 1.3 72.8 + - - +
388A LYS* 3.2 20.9 - - - +
389A LYS* 3.3 9.9 + - - +
81B GLU* 3.2 33.7 + - - -
316B ASP* 4.0 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A LEU* 3.0 34.1 + - + +
383A LEU 4.5 2.0 - - - +
385A LYS* 1.3 86.4 - - - +
387A ARG* 1.3 66.2 - - - +
389A LYS* 2.9 21.7 + - + +
390A ALA* 3.0 15.4 + - - +
132B TYR* 2.9 18.6 + - - -
136B ARG* 3.2 12.5 - - - +
310B GLN 4.0 7.8 - - - +
311B TYR* 3.0 50.6 + - + +
312B HIS 5.4 0.2 - - - +
313B ASP* 3.6 22.0 - - + +
316B ASP* 2.4 56.0 + - - +
317B GLU* 4.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ILE* 3.3 32.1 + - - +
376A GLU* 3.4 21.2 + - - +
378A ALA 2.9 26.0 + - - -
379A SER* 4.8 2.4 + - - +
383A LEU* 3.2 41.3 + - + +
384A LEU* 4.6 10.9 - - + +
386A ARG* 1.3 77.5 - - - +
388A LYS* 1.3 65.1 + - - +
390A ALA* 3.2 21.5 + - + +
310B GLN 5.6 0.2 - - - -
311B TYR* 5.5 6.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A LEU 3.3 15.5 + - - +
385A LYS* 3.2 14.4 - - - +
387A ARG* 1.3 82.6 - - - +
389A LYS* 1.3 60.9 + - + +
390A ALA 3.2 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A LYS 3.3 7.8 + - - +
386A ARG* 2.9 14.2 + - + +
388A LYS* 1.3 80.2 - - + +
390A ALA* 1.3 60.2 + - + +
312B HIS 5.0 5.2 - - - +
313B ASP* 2.7 35.8 + - + +
314B PRO* 6.2 0.4 - - - +
315B ASP* 5.1 8.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ARG 3.0 13.8 + - - +
387A ARG* 3.7 16.6 - - + +
388A LYS 3.1 5.8 - - - -
389A LYS* 1.3 82.9 - - + +
309B ALA 5.8 0.4 - - - +
310B GLN* 4.1 28.0 - - - +
----------------------------------------------------------
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