Contacts of the helix formed by residues 44 - 55 (chain R) in PDB entry 1G4Y
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 THR 44 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B LYS* 4.8 5.8 - - - +
42R ASN 4.7 4.9 - - - +
43R PRO* 1.3 77.2 - - - +
45R GLU* 1.3 65.7 + - - +
46R ALA* 3.5 7.6 + - - +
47R GLU* 3.0 42.3 + - - +
48R LEU* 2.9 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 45 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29R THR* 4.2 15.3 + - - -
44R THR* 1.3 74.6 - - - +
46R ALA* 1.3 62.8 + - - +
48R LEU* 3.3 16.9 + - - +
49R GLN* 2.7 60.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44R THR* 3.2 7.2 + - - +
45R GLU* 1.3 80.6 - - - +
47R GLU* 1.3 60.5 + - + +
49R GLN* 3.3 9.4 + - - +
50R ASP* 2.9 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B GLU* 2.5 33.1 - - - +
472B LYS* 2.9 35.8 + - - -
473B LEU* 3.8 16.8 - - + +
476B GLN* 3.1 31.2 + - - +
43R PRO* 3.4 4.8 - - + +
44R THR* 3.0 39.0 + - - +
46R ALA* 1.3 78.4 - - + +
48R LEU* 1.3 59.1 + - - +
50R ASP* 3.4 3.6 + - - +
51R MET* 3.0 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29R THR* 3.7 31.8 - - - +
30R LYS* 5.7 0.2 - - - -
32R LEU* 4.0 20.3 - - + +
33R GLY* 3.8 26.5 - - - +
36R MET* 4.6 2.2 - - + -
37R ARG* 5.1 4.0 - - - +
43R PRO* 3.4 35.7 - - + +
44R THR 2.9 19.0 + - - +
45R GLU* 3.6 19.5 - - - +
46R ALA 3.2 0.2 - - - -
47R GLU* 1.3 77.2 - - - +
49R GLN* 1.3 62.3 + - - +
51R MET* 3.2 13.5 + - + +
52R ILE* 3.2 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 49 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29R THR* 3.9 16.8 - - + -
45R GLU* 2.7 50.5 + - - +
46R ALA* 3.7 7.4 - - - +
48R LEU* 1.3 74.2 - - - +
50R ASP* 1.3 52.2 + - - +
52R ILE* 3.3 3.2 + - - +
53R ASN* 2.8 52.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 50 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ASP* 2.6 42.9 - - + +
416B LEU* 5.5 2.6 - - - +
469B GLU* 5.2 1.0 - - - +
473B LEU* 3.8 33.0 - - + +
46R ALA* 2.9 30.1 + - - +
47R GLU* 3.6 7.2 - - - +
48R LEU 3.2 0.2 - - - -
49R GLN* 1.3 75.9 - - - +
51R MET* 1.3 65.4 + - - +
53R ASN* 3.9 7.5 - - - +
54R GLU* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 51 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B LEU* 5.2 2.6 - - + +
476B GLN* 3.8 41.5 - - + +
477B ALA* 4.2 6.5 - - + +
480B LEU* 3.7 26.9 - - + -
32R LEU* 3.5 28.5 - - + -
36R MET* 4.2 13.5 - - + -
43R PRO* 5.9 0.9 - - + -
47R GLU 3.0 14.0 + - - +
48R LEU* 3.2 11.4 + - + +
50R ASP* 1.3 77.1 - - - +
52R ILE* 1.3 63.3 + - - +
54R GLU* 3.5 15.4 - - + +
55R VAL* 4.0 8.8 - - - +
63R ILE* 4.5 3.9 - - + +
71R MET* 4.3 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27R ILE* 4.1 7.9 - - + +
28R THR 4.0 6.3 - - - +
29R THR* 3.5 44.9 - - + +
32R LEU* 4.3 8.1 - - + -
48R LEU 3.2 6.3 + - - +
49R GLN* 3.6 6.5 - - - +
50R ASP 3.2 0.4 - - - -
51R MET* 1.3 76.4 - - - +
53R ASN* 1.3 74.5 + - - +
54R GLU 3.0 1.0 + - - -
55R VAL* 3.1 7.6 + - - +
56R ASP* 3.0 22.7 + - - -
61R GLY 3.6 31.6 - - - +
62R THR* 4.0 3.8 - - - +
63R ILE* 3.6 32.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 53 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ASP* 5.0 13.9 - - - +
49R GLN* 2.8 38.3 + - - +
50R ASP* 3.4 11.7 + - - +
52R ILE* 1.3 77.5 - - - +
54R GLU* 1.3 62.7 + - - +
55R VAL 3.2 1.0 + - - -
56R ASP* 3.3 29.9 + - - +
61R GLY* 5.3 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 54 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ASP 5.6 4.3 + - - -
470B GLN* 4.9 10.6 + - - -
474B ASN* 5.6 0.5 - - - +
50R ASP 3.0 16.9 + - - +
51R MET* 3.5 11.2 - - + +
52R ILE 3.0 0.6 + - - -
53R ASN* 1.3 76.4 - - - +
55R VAL* 1.3 67.9 + - + +
74R ARG* 5.5 4.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 55 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51R MET 4.0 9.0 - - - +
52R ILE 3.1 8.0 + - - +
54R GLU* 1.3 89.2 - - + +
56R ASP* 1.3 58.6 + - - +
57R ALA* 3.2 7.4 + - - +
63R ILE* 4.1 21.6 - - + +
67R GLU* 3.3 30.7 - - + +
68R PHE* 5.7 0.4 - - - -
70R THR* 3.4 25.9 - - - +
71R MET* 3.7 30.3 - - + -
74R ARG* 5.6 5.4 - - - +
----------------------------------------------------------
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