Contacts of the helix formed by residues 44 - 58 (chain E) in PDB entry 3AG2
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 GLU 44 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ASP* 3.2 29.2 + - - +
42E VAL 3.4 3.7 + - - +
43E PRO* 1.3 74.6 - - - +
45E PRO* 1.3 80.6 - - - +
46E LYS* 3.9 28.0 - - + +
47E ILE* 2.9 23.9 + - + +
48E ILE* 3.2 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 45 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E PRO 3.6 2.8 - - - +
44E GLU* 1.3 96.5 - - + +
46E LYS* 1.3 56.4 + - - +
48E ILE* 3.2 10.0 + - + +
49E ASP* 2.8 31.5 + - - +
84E TYR* 4.1 17.7 - - + +
85E VAL* 4.5 17.3 - - + -
88E GLU* 3.8 38.1 - - + +
89E LEU* 3.8 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E GLU* 5.4 11.1 + - - +
12E ASP* 3.9 26.1 + - + +
13E ALA* 6.3 0.4 - - - -
16E VAL* 3.5 26.8 - - + +
44E GLU* 3.9 25.1 + - + +
45E PRO* 1.3 79.5 - - - +
47E ILE* 1.3 65.1 + - + +
49E ASP* 3.6 10.6 - - - +
50E ALA* 3.3 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 47 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E PHE* 4.4 11.7 - - + -
12E ASP* 3.7 41.1 - - - +
15E TRP* 3.8 25.8 - - + -
16E VAL* 4.0 8.5 - - + +
19E PHE* 4.0 10.6 - - + -
36E LEU* 3.7 27.8 - - + -
41E LEU* 5.7 0.2 - - + -
43E PRO* 4.2 10.1 - - + -
44E GLU* 2.9 26.4 + - + +
46E LYS* 1.3 76.6 - - + +
48E ILE* 1.3 67.6 + - + +
50E ALA* 3.2 6.0 + - - +
51E ALA* 3.0 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 48 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E MET* 5.0 9.2 - - + -
43E PRO* 3.7 31.4 - - + +
44E GLU 3.7 11.4 - - - +
45E PRO* 3.2 8.0 + - + +
47E ILE* 1.3 77.9 - - + +
49E ASP* 1.3 53.0 + - - +
51E ALA* 3.0 4.9 + - - +
52E LEU* 2.7 46.5 + - + +
67E ILE* 3.9 25.6 - - + -
68E LEU* 4.2 4.9 - - + -
71E VAL* 3.6 27.6 - - + -
85E VAL* 4.7 4.5 - - + -
89E LEU* 3.6 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 49 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E PRO 2.8 17.3 + - - +
46E LYS* 3.6 12.1 - - - +
48E ILE* 1.3 76.3 - - - +
50E ALA* 1.3 62.7 + - - +
52E LEU* 3.2 5.5 + - - +
53E ARG* 3.0 45.8 + - - +
89E LEU* 3.8 14.5 - - + +
92E THR* 2.9 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 50 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E VAL* 3.9 17.7 - - + +
19E PHE* 3.5 20.9 - - + +
20E ASN* 3.4 26.7 - - - +
46E LYS 3.3 9.2 + - - +
47E ILE 3.2 8.1 + - - +
49E ASP* 1.3 80.5 + - - +
51E ALA* 1.3 58.3 + - - +
53E ARG* 3.3 6.5 + - - +
54E ALA* 3.0 27.4 + - - +
57E ARG* 4.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E PHE* 3.7 34.2 - - + +
29E LEU* 4.1 1.8 - - + +
33E MET* 4.0 10.1 - - - -
47E ILE 3.0 11.9 + - - +
48E ILE* 3.6 10.1 - - - +
50E ALA* 1.3 76.9 - - - +
52E LEU* 1.3 58.9 + - - +
54E ALA* 3.2 4.4 + - - +
55E CYS* 2.9 30.3 + - - -
67E ILE* 3.9 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D TRP* 4.8 0.2 - - - -
48E ILE* 2.7 37.1 + - + +
49E ASP* 3.6 4.3 - - - +
51E ALA* 1.3 72.1 - - - +
53E ARG* 1.3 58.8 + - - +
55E CYS* 3.1 9.4 + - - +
56E ARG* 3.0 24.8 + - - +
64E ALA* 3.5 40.2 - - + +
67E ILE* 4.2 15.7 - - + -
68E LEU* 4.2 8.7 - - + -
89E LEU* 4.2 13.7 - - + -
92E THR* 4.6 6.7 - - + -
93E LEU* 4.1 24.7 - - + -
96E LEU* 4.2 8.3 - - + +
98E ILE* 4.1 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 53 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ASN* 5.3 5.2 - - - +
49E ASP* 3.0 39.6 + - - +
50E ALA* 3.8 6.7 - - - +
52E LEU* 1.3 74.4 - - - +
54E ALA* 1.3 59.9 + - - +
56E ARG* 3.1 10.3 + - + +
57E ARG* 2.9 42.3 + - - +
92E THR* 3.5 25.3 + - + +
95E GLU* 3.1 41.4 + - - -
96E LEU* 3.9 18.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E PHE* 3.5 22.7 - - + +
24E ILE* 3.9 17.3 - - + -
29E LEU* 4.1 14.6 - - + -
50E ALA 3.0 9.3 + - - +
51E ALA* 3.3 11.0 - - - +
53E ARG* 1.3 73.4 - - - +
55E CYS* 1.3 66.7 + - - +
57E ARG* 3.2 15.5 + - - +
58E LEU* 2.9 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 55 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D TRP* 3.8 2.9 - - + -
29E LEU* 4.0 19.0 - - - +
51E ALA 2.9 19.8 + - - -
52E LEU* 3.1 9.8 + - - +
54E ALA* 1.3 74.4 - - - +
56E ARG* 1.3 62.8 + - - +
58E LEU* 3.1 7.8 + - - +
59E ASN 3.0 4.5 + - - -
60E ASP* 3.0 38.0 + - - +
63E SER* 3.9 4.7 - - - -
64E ALA* 3.6 26.9 - - + -
67E ILE* 3.5 25.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D GLU 3.1 17.8 + - - -
45D LYS 3.4 11.2 + - - -
46D ALA 3.0 23.0 + - - -
47D SER* 3.8 2.8 - - - +
48D TRP* 3.1 51.9 - - + +
52E LEU 3.0 12.9 + - - +
53E ARG* 3.1 12.1 + - - +
55E CYS* 1.3 77.0 - - - +
57E ARG* 1.3 64.5 + - + +
59E ASN* 2.9 42.4 + - - +
96E LEU* 4.1 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E PHE 2.8 27.7 + - - -
20E ASN* 3.4 14.3 + - - +
21E LYS 2.9 19.2 + - - -
22E PRO* 3.0 36.2 + - - +
24E ILE* 3.6 8.7 - - + +
50E ALA 4.8 0.2 + - - -
53E ARG* 2.9 37.0 + - - +
54E ALA* 3.2 12.1 + - - +
56E ARG* 1.3 77.6 - - + +
58E LEU* 1.3 62.2 + - + +
59E ASN* 3.7 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E ILE* 3.3 34.1 - - + +
25E ASP* 3.8 15.5 - - - +
26E ALA* 3.7 23.3 - - + +
29E LEU* 3.9 25.6 - - + -
54E ALA* 2.9 21.7 + - + +
55E CYS* 3.1 6.2 + - - +
57E ARG* 1.3 79.0 - - + +
59E ASN* 1.3 72.3 + - - +
60E ASP* 3.2 11.8 + - + +
----------------------------------------------------------
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