Contacts of the helix formed by residues 45 - 57 (chain A) in PDB entry 3PGE
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 LEU 45 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.6 7.0 - - + -
39A ILE* 4.3 2.2 - - + -
44A PRO* 1.3 70.9 - - - +
46A ARG* 1.3 64.9 + - - +
47A ARG 3.2 1.1 - - - -
48A LEU* 3.2 29.0 + - + +
49A MET* 2.9 34.3 + - + +
72A ILE* 3.9 28.9 - - + -
73A GLN 5.1 0.7 - - - +
74A ALA* 3.3 5.7 + - - +
76A GLN* 3.0 24.3 + - + +
78A PRO* 3.9 28.3 - - + -
81A LEU* 4.0 21.3 - - + -
83A MET* 5.0 3.8 - - + -
89A ILE* 5.1 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PRO* 3.0 19.3 - - + +
45A LEU* 1.3 77.0 - - - +
47A ARG* 1.3 65.5 + - - +
49A MET* 3.0 2.6 + - - -
50A GLU* 2.8 58.1 + - - +
60A MET* 3.8 5.2 - - + -
74A ALA* 3.1 30.3 + - + +
75A ASP* 2.4 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 6.3 0.2 - - + -
38A LYS 5.1 0.2 + - - -
39A ILE* 3.5 14.1 - - - +
40A LYS* 2.9 43.8 - - - +
43A THR* 3.0 29.2 + - + +
44A PRO 3.9 9.9 - - - +
46A ARG* 1.3 77.5 - - - +
48A LEU* 1.3 67.3 + - + +
50A GLU* 3.2 9.1 + - - +
51A ALA* 2.6 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 3.8 21.3 - - + -
28A VAL* 4.9 11.9 - - + +
37A PHE* 3.7 43.0 - - + -
39A ILE* 3.7 46.2 - - + -
45A LEU* 3.2 19.4 + - + +
47A ARG* 1.3 96.6 - - + +
49A MET* 1.3 61.1 + - + +
51A ALA* 3.7 7.4 - - - +
52A PHE* 2.8 30.0 + - - +
89A ILE* 5.6 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 2.9 28.5 - - + +
46A ARG 3.0 2.9 + - - +
48A LEU* 1.3 78.8 - - + +
50A GLU* 1.3 60.6 + - - +
52A PHE 4.1 0.2 - - - -
53A ALA* 3.0 28.6 + - - +
60A MET* 3.8 17.4 - - + +
65A PHE* 3.1 67.8 - - + -
72A ILE* 4.3 16.8 - - + +
73A GLN* 4.4 0.4 - - - -
74A ALA* 3.6 36.1 - - + +
89A ILE* 6.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ARG* 2.8 49.5 + - - +
47A ARG* 3.6 6.1 + - - +
49A MET* 1.3 75.2 - - - +
51A ALA* 1.3 56.5 + - - +
53A ALA* 3.0 3.2 + - - +
54A LYS* 2.7 37.0 + - - +
60A MET* 3.2 32.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 5.0 2.6 - - + +
37A PHE* 3.9 23.3 - - + -
47A ARG 2.6 21.9 + - - +
48A LEU* 3.7 5.2 - - - +
50A GLU* 1.3 74.3 - - - +
52A PHE* 1.3 63.3 + - - +
54A LYS* 3.5 5.8 + - - +
55A ARG* 3.3 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 3.4 43.3 - - + -
29A SER 4.2 1.3 - - - -
30A ASP* 3.6 30.1 - - + -
33A SER* 3.6 17.9 - - - -
35A ILE* 3.8 25.4 - - + -
37A PHE* 4.6 2.2 - - + -
48A LEU 2.8 22.0 + - - +
49A MET* 4.1 4.9 - - - +
51A ALA* 1.3 74.0 - - - +
53A ALA* 1.3 64.1 + - - +
55A ARG* 3.5 3.6 + - - +
56A GLN* 3.1 49.2 + - + +
63A LEU* 4.9 4.7 - - + -
65A PHE* 4.5 8.7 - + + -
91A ALA* 3.7 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A MET 3.0 19.6 + - - +
50A GLU* 3.0 5.8 + - - +
52A PHE* 1.3 78.2 - - - +
54A LYS* 1.3 68.5 + - - +
56A GLN* 3.0 17.2 + - - +
57A GLY 3.3 2.1 + - - -
58A LYS 2.8 19.7 - - - +
59A GLU 4.1 3.1 - - - +
60A MET* 3.8 31.4 - - + +
63A LEU* 4.6 9.9 - - + -
65A PHE* 5.1 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLU 2.7 19.6 + - - +
51A ALA* 3.9 5.8 - - - +
53A ALA* 1.3 70.6 - - - +
55A ARG* 1.3 64.8 + - - +
57A GLY* 2.9 16.6 + - - -
58A LYS 4.5 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A SER* 5.1 2.9 - - - +
35A ILE* 4.4 19.7 - - + -
51A ALA 3.3 10.5 + - - +
52A PHE 3.7 7.9 - - - +
54A LYS* 1.3 79.3 - - - +
56A GLN* 1.3 75.7 + - - +
57A GLY* 3.1 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP* 3.7 18.7 + - - +
33A SER* 3.0 26.6 + - - -
52A PHE* 3.1 40.4 + - + +
53A ALA* 3.0 13.4 + - - +
55A ARG* 1.3 92.1 + - - +
57A GLY* 1.3 55.9 + - - +
58A LYS* 2.9 30.3 + - + +
63A LEU* 5.0 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ALA 3.3 0.4 + - - -
54A LYS* 2.9 15.3 + - - -
55A ARG 3.1 2.4 + - - -
56A GLN* 1.3 75.3 - - - +
58A LYS* 1.3 66.0 + - - +
59A GLU* 4.8 0.2 - - - -
----------------------------------------------------------
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