Contacts of the helix formed by residues 380 - 390 (chain D) in PDB entry 2ONL
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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PHE* 3.9 6.5 - - - -
161B ASP* 3.2 26.3 + - + -
163B GLU* 2.9 41.7 - - + +
379D SER* 1.3 74.4 + - - +
381D PRO* 1.3 70.5 - - + +
382D LEU* 2.9 33.3 + - - +
383D LEU* 3.0 32.3 + - - +
384D LEU* 2.8 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 381 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLU* 3.5 15.9 - - - +
163B GLU* 3.1 20.4 - - - +
380D ASN* 1.3 82.4 - - + +
382D LEU* 1.3 64.9 + - - +
384D LEU* 3.0 15.5 + - + +
385D LYS* 3.0 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 382 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLU* 3.8 12.7 + - - +
82B ASN* 4.6 1.6 - - - +
129B PHE* 3.5 30.1 - - + -
132B TYR* 4.2 8.7 - - + -
133B GLN* 3.6 25.4 - - + +
136B ARG* 3.9 25.1 - - - +
163B GLU* 5.4 0.9 - - + +
316B ASP* 4.1 4.9 - - - +
380D ASN* 2.9 13.7 + - - +
381D PRO* 1.3 74.9 - - - +
383D LEU* 1.3 56.1 + - - +
385D LYS* 2.7 29.4 + - - +
386D ARG* 3.0 50.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 383 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PHE* 3.0 44.9 - - + -
161B ASP 4.5 0.7 - - - +
311B TYR* 3.8 15.9 - - + -
375D ILE* 4.0 23.6 - - + +
378D ALA* 3.3 28.3 - - + +
379D SER* 5.0 0.2 - - - -
380D ASN* 3.0 31.0 + - - +
382D LEU* 1.3 79.1 - - - +
384D LEU* 1.3 56.0 + - - +
386D ARG* 3.9 4.3 - - + +
387D ARG* 2.8 56.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 384 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379D SER* 3.9 21.3 - - - +
380D ASN* 2.8 37.9 + - - +
381D PRO* 3.3 12.1 - - + +
383D LEU* 1.3 74.5 - - - +
385D LYS* 1.3 63.9 + - - +
387D ARG* 3.5 6.3 + - - +
388D LYS* 2.8 44.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 385 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLU* 4.0 12.1 + - - -
136B ARG* 3.8 9.3 - - - +
313B ASP* 5.6 0.3 - - - +
316B ASP* 2.8 46.3 + - - +
381D PRO* 3.0 22.1 + - + +
382D LEU* 2.7 16.8 + - - +
384D LEU* 1.3 72.3 - - - +
386D ARG* 1.3 66.2 + - - +
388D LYS* 2.8 19.8 + - - +
389D LYS* 3.3 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 386 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B TYR* 2.7 28.2 + - - -
136B ARG* 4.2 0.2 - - - +
310B GLN 4.3 12.3 - - - +
311B TYR* 2.3 60.3 + - + +
312B HIS 4.9 0.2 - - - -
313B ASP* 3.8 23.6 + - - +
316B ASP* 2.5 46.5 + - - +
382D LEU* 3.0 31.9 + - + +
383D LEU* 4.1 7.2 - - + +
385D LYS* 1.3 82.2 - - - +
387D ARG* 1.3 60.8 + - - +
388D LYS 3.3 0.2 - - - -
389D LYS* 3.6 13.0 + - - +
390D ALA* 3.1 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 387 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B TYR* 6.5 0.7 - - - -
375D ILE* 3.8 21.8 + - - +
376D GLU* 4.6 11.5 + - - +
378D ALA 3.2 23.8 + - - -
379D SER* 4.0 12.9 + - - -
383D LEU* 2.8 46.5 + - - +
384D LEU* 4.1 8.2 - - - +
385D LYS 3.3 0.2 - - - -
386D ARG* 1.3 80.0 - - - +
388D LYS* 1.3 61.9 + - + +
389D LYS 3.3 0.4 - - - -
390D ALA* 3.8 9.1 - - + +
391D ARG* 3.7 14.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 388 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384D LEU* 2.8 24.7 + - + +
385D LYS* 2.8 49.8 + - - +
387D ARG* 1.3 79.7 - - + +
389D LYS* 1.3 59.4 + - - +
390D ALA 3.4 0.4 - - - -
391D ARG* 4.1 2.1 - - - +
392D ALA* 3.8 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 389 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B ALA 5.3 2.6 + - - -
310B GLN 6.3 0.4 - - - -
312B HIS 2.6 30.9 + - - -
313B ASP* 3.3 35.2 - - + +
314B PRO* 5.0 3.4 - - - +
385D LYS 3.3 15.2 + - - +
386D ARG* 3.6 13.9 + - - +
388D LYS* 1.3 76.0 - - - +
390D ALA* 1.3 59.0 + - - +
391D ARG 3.2 6.5 + - - -
392D ALA* 3.7 19.4 - - - +
393D LEU* 4.2 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 390 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B GLN 5.8 3.1 - - - +
386D ARG 3.1 18.4 + - - +
387D ARG* 3.7 12.3 + - + +
389D LYS* 1.3 79.1 - - + +
391D ARG* 1.3 55.8 + - - +
393D LEU* 4.6 7.7 + - - +
----------------------------------------------------------
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