Contacts of the helix formed by residues 47 - 57 (chain A) in PDB entry 1ADR
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 GLY 47 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ASN* 1.3 73.3 - - - +
48A GLU* 1.3 55.8 + - - +
50A LEU* 3.3 10.5 + - - +
51A LEU* 2.8 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ASN* 3.0 11.3 + - - +
47A GLY* 1.3 69.6 - - - +
49A ASN* 1.3 90.5 + - - +
51A LEU* 3.1 13.9 + - - +
52A ALA* 2.8 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 4.1 4.3 + - - +
29A GLY 5.7 1.2 + - - -
30A VAL* 3.7 14.2 - - - +
38A TRP* 3.3 34.6 - - + -
45A PRO* 4.2 4.5 - - + -
46A ASN* 2.8 25.8 + - - +
48A GLU* 1.3 103.0 + - - +
50A LEU* 1.3 52.5 + - - +
52A ALA* 3.6 6.6 - - - +
53A LEU* 2.8 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A MET* 3.6 40.2 - - + -
45A PRO* 3.9 18.5 - - + +
46A ASN 2.7 18.4 + - - +
47A GLY* 3.5 13.7 - - - +
49A ASN* 1.3 69.2 - - - +
51A LEU* 1.3 55.6 + - + +
53A LEU* 3.3 6.3 - - + +
54A SER* 2.8 45.1 + - - +
61A PRO* 4.6 8.5 - - + -
64A LEU* 4.4 11.0 - - + -
65A LEU* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLY* 2.8 28.0 + - - +
48A GLU* 3.4 11.0 - - + +
50A LEU* 1.3 72.9 - - + +
52A ALA* 1.3 56.7 + - - +
54A SER* 3.1 6.8 + - - -
55A LYS* 2.8 39.5 + - + +
61A PRO* 3.8 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET 5.4 0.2 - - - +
28A VAL* 3.7 31.4 - - + +
48A GLU* 2.8 30.9 + - - +
49A ASN* 3.6 9.2 - - - +
51A LEU* 1.3 71.2 - - - +
53A LEU* 1.3 57.3 + - - +
55A LYS* 3.3 8.0 + - - +
56A ALA* 2.8 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.9 16.8 - - + -
24A LEU* 4.3 10.3 - - + -
28A VAL* 3.7 16.9 - - + +
35A ILE* 4.5 0.4 - - + -
38A TRP* 3.4 41.5 - - + -
45A PRO* 3.4 35.0 - - + -
49A ASN 2.8 14.6 + - - +
50A LEU* 3.3 10.8 - - + +
52A ALA* 1.3 71.3 - - - +
54A SER* 1.3 53.6 + - - +
56A ALA* 3.1 1.7 + - - -
57A LEU* 2.7 63.6 + - + +
64A LEU* 5.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 2.8 25.2 + - - +
51A LEU 3.5 5.4 - - - -
53A LEU* 1.3 71.7 - - - +
55A LYS* 1.3 59.2 + - - +
57A LEU 3.1 2.6 - - - -
58A GLN 2.9 9.4 + - - -
59A CYS* 2.8 49.5 + - - -
60A SER 3.8 2.5 - - - -
61A PRO* 3.3 28.1 - - - +
64A LEU* 3.1 21.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 2.8 26.7 + - + +
52A ALA* 3.6 7.6 - - - +
54A SER* 1.3 75.1 - - - +
56A ALA* 1.3 58.6 + - - +
58A GLN* 2.8 31.1 + - - +
59A CYS 4.5 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 3.8 14.9 - - - +
24A LEU* 3.6 12.3 - - + -
27A MET* 3.7 24.7 - - + +
28A VAL* 3.5 26.5 - - + +
52A ALA 2.8 20.5 + - - +
53A LEU 3.6 0.7 - - - +
55A LYS* 1.3 72.0 - - - +
57A LEU* 1.3 55.6 + - - +
58A GLN* 2.8 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.9 26.9 - - + -
13A ARG* 2.6 39.4 + - + -
14A ARG* 4.0 30.3 - - + +
17A LEU* 3.6 11.9 - - + -
19A ILE* 4.6 2.2 - - + -
24A LEU* 3.7 30.3 - - + -
53A LEU* 2.7 45.8 + - + +
54A SER 3.1 5.2 - - - +
56A ALA* 1.3 69.4 - - - +
58A GLN* 1.3 56.3 + - - +
59A CYS* 3.1 7.1 + - - -
64A LEU* 4.8 8.3 - - + -
----------------------------------------------------------
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