Contacts of the helix formed by residues 21 - 32 (chain A) in PDB entry 2JNU
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 21 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TRP* 2.9 23.9 + - - +
17A ARG* 2.8 45.9 + - - +
18A LEU 3.2 2.8 - - - +
20A GLN* 1.3 78.0 - - - +
22A PRO* 1.4 77.4 - - - +
23A LEU* 3.4 15.6 + - - +
24A GLY 2.9 13.6 + - - -
25A LEU* 2.9 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLN 3.7 7.8 - - - +
21A ASP* 1.4 94.8 - - - +
23A LEU* 1.3 58.5 + - + +
25A LEU* 3.5 5.5 + - + +
26A ALA* 2.9 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 5.1 12.8 - - + -
11A TRP* 4.0 8.3 - - + -
21A ASP* 3.3 13.8 + - - +
22A PRO* 1.3 81.1 - - + +
24A GLY* 1.3 64.2 + - - +
26A ALA* 3.1 6.3 + - + +
27A TYR* 2.9 54.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TRP* 3.3 30.1 - - - -
18A LEU* 3.5 19.4 - - - +
21A ASP* 2.9 14.3 + - - -
23A LEU* 1.3 77.2 - - - +
25A LEU* 1.3 59.8 + - - +
27A TYR* 3.5 0.7 + - - -
28A PHE* 3.0 25.5 + - - +
121A PHE* 4.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU 3.2 4.6 + - - +
19A LEU* 3.3 50.7 - - + +
20A GLN 5.8 0.2 - - - -
21A ASP 2.9 16.4 + - - +
22A PRO* 3.9 4.5 - - + +
24A GLY* 1.3 75.3 - - - +
26A ALA* 1.3 50.9 + - - +
28A PHE* 3.5 13.8 - - + +
29A THR* 2.7 56.3 + - - +
41A VAL* 4.6 6.7 - - + -
44A TRP* 4.7 4.3 - - + -
45A LYS* 3.4 39.0 - - + +
48A GLU* 5.9 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PRO 2.9 20.2 + - - +
23A LEU* 3.1 9.8 + - + +
25A LEU* 1.3 77.1 - - - +
27A TYR* 1.3 55.9 + - + +
29A THR* 3.1 7.3 + - - -
30A GLU* 2.7 41.4 + - + +
33A LYS* 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 6.0 0.2 - - + -
11A TRP* 3.8 13.9 - + - -
23A LEU* 2.9 60.1 + - + +
26A ALA* 1.3 77.8 - - + +
28A PHE* 1.3 62.6 + - - +
30A GLU* 3.0 21.8 + - + +
31A PHE* 3.3 19.6 + - - -
121A PHE* 3.6 20.4 - - + -
126A LEU* 4.0 35.9 - - + -
130A CYS* 3.5 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 4.1 19.3 - + - -
18A LEU* 4.3 13.0 - - + -
19A LEU* 5.1 2.7 - - + -
24A GLY 3.0 20.7 + - - +
25A LEU* 3.5 16.4 - - + +
27A TYR* 1.3 78.4 - - - +
29A THR* 1.3 55.6 + - - +
31A PHE* 3.6 4.5 + - + +
32A LEU* 3.1 29.7 + - + +
41A VAL* 3.4 31.4 - - + -
113A MET* 4.4 1.1 - - - -
117A SER* 3.2 52.7 - - - -
118A TYR* 4.0 5.6 - - - -
121A PHE* 3.5 33.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 2.7 44.0 + - - +
26A ALA* 3.6 5.8 - - - -
28A PHE* 1.3 71.9 - - - +
30A GLU* 1.3 57.3 + - - +
32A LEU* 2.8 33.0 - - - +
33A LYS* 2.7 37.7 + - + +
38A ALA* 5.1 3.6 - - + -
41A VAL* 4.2 14.9 - - + +
45A LYS* 4.3 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 2.7 21.7 + - + +
27A TYR* 3.0 18.8 + - + +
29A THR* 1.3 78.0 - - - +
31A PHE* 1.3 60.0 + - - +
33A LYS* 2.8 40.6 + - - +
34A LYS* 2.6 37.1 + - - +
126A LEU* 4.1 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR 3.3 18.0 + - - -
28A PHE* 3.8 4.7 - - + +
30A GLU* 1.3 79.6 - - - +
32A LEU* 1.3 57.8 + - + +
33A LYS 2.8 9.2 + - - -
34A LYS* 3.4 15.9 + - + +
35A GLU* 3.2 14.3 - - - +
121A PHE* 3.7 24.7 - + + -
124A SER* 3.8 10.8 - - - -
125A PRO* 3.1 56.5 - - + -
126A LEU* 3.5 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE* 3.1 28.8 + - + +
29A THR* 2.8 17.7 - - - +
31A PHE* 1.3 74.6 - - + +
33A LYS* 1.3 60.7 + - - +
35A GLU* 3.4 22.9 - - - +
37A SER* 3.5 31.9 - - - +
38A ALA* 3.0 18.4 - - - +
40A ASN* 3.6 9.6 - - - +
41A VAL* 3.6 37.2 - - + -
117A SER* 4.8 11.4 - - - -
120A ARG* 6.3 1.1 - - - +
----------------------------------------------------------
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