Contacts of the helix formed by residues 64 - 76 (chain E) in PDB entry 1QO0
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 ARG 64 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E ASN* 1.3 96.9 - - + +
65E HIS* 1.3 90.8 + - + +
66E HIS 3.1 0.6 + - - -
67E ASP* 3.6 7.8 + - - +
68E GLU* 3.4 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 65 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E TRP* 3.6 39.4 + + + -
44E PRO* 4.9 6.3 - - + -
45E PRO* 4.0 5.2 - - + +
61E PHE* 3.8 27.8 - + + -
63E ASN* 3.1 26.3 + - - +
64E ARG* 1.3 110.9 + - - +
66E HIS* 1.3 60.4 + - - +
68E GLU* 3.0 28.6 + - - +
69E ILE* 2.9 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 66 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E PHE* 3.4 18.9 + - - +
62E GLN* 4.5 7.3 + - - +
63E ASN 3.0 16.6 + - - +
65E HIS* 1.3 78.4 - - - +
67E ASP* 1.3 72.6 + - - +
69E ILE* 3.8 2.7 - - - +
70E ALA* 2.9 36.3 + - + +
96E GLN* 3.2 47.1 + - + +
99E GLU* 4.4 13.3 + - - -
100E LEU* 5.6 0.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 67 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E ASN 5.8 0.7 - - - -
64E ARG* 3.6 8.3 + - - +
65E HIS 3.5 0.2 - - - -
66E HIS* 1.3 96.5 + - - +
68E GLU* 1.3 62.5 + - - +
70E ALA* 4.1 5.2 - - - +
71E ALA* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E PRO* 5.2 1.2 - - - +
45E PRO* 3.4 30.7 - - + +
46E PRO 5.0 2.1 - - - +
64E ARG* 3.4 31.7 + - - +
65E HIS* 3.0 31.8 + - - +
66E HIS 3.2 1.0 - - - -
67E ASP* 1.3 78.9 - - - +
69E ILE* 1.3 57.1 + - - +
71E ALA* 3.8 3.4 - - - +
72E LEU* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E LEU* 4.1 12.8 - - + +
43E TRP* 4.3 11.4 - - + -
45E PRO* 4.0 15.5 - - + -
58E THR* 3.8 21.1 - - + +
59E SER 4.1 4.3 - - - +
61E PHE* 3.9 28.7 - - + +
65E HIS* 2.9 26.9 + - + +
66E HIS* 3.8 3.6 - - - +
68E GLU* 1.3 72.5 - - - +
70E ALA* 1.3 68.5 + - - +
72E LEU* 4.5 4.7 - - - -
73E LEU* 3.0 48.6 + - + +
96E GLN* 5.1 3.4 - - - +
100E LEU* 4.6 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E HIS* 2.9 26.8 + - + +
67E ASP* 4.1 5.8 - - - +
69E ILE* 1.3 76.6 - - - +
71E ALA* 1.3 63.1 + - - +
73E LEU* 4.2 0.9 - - - +
74E ALA* 3.2 25.3 + - - +
100E LEU* 4.0 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E GLU 5.6 0.2 - - - -
67E ASP 2.9 18.4 + - - +
68E GLU* 3.9 3.8 - - - +
70E ALA* 1.3 75.2 - - - +
72E LEU* 1.3 66.7 + - - +
74E ALA* 3.3 7.5 + - - +
75E ALA* 3.2 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E LEU* 4.0 17.5 - - + -
45E PRO* 4.6 4.3 - - + -
46E PRO* 3.5 37.2 - - + +
47E GLU 3.6 8.3 - - - +
48E ALA* 3.5 37.0 - - - +
49E PHE* 3.5 38.9 - - + +
68E GLU 2.9 16.9 + - - +
69E ILE* 4.0 3.4 - - - +
71E ALA* 1.3 77.0 - - - +
73E LEU* 1.3 62.9 + - + +
75E ALA* 3.1 20.9 + - + +
76E GLY* 3.4 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E LEU* 4.9 3.4 - - + -
49E PHE* 4.5 11.9 - - + -
56E VAL* 4.0 32.1 - - + -
58E THR* 4.4 5.2 - - + -
69E ILE* 3.0 41.7 + - + +
70E ALA* 4.3 2.7 - - - +
72E LEU* 1.3 80.4 - - + +
74E ALA* 1.3 62.1 + - - +
76E GLY* 3.2 14.2 + - - +
80E THR* 5.8 4.0 - - + -
82E LEU* 3.8 36.6 - - + -
100E LEU* 4.5 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E ALA 3.2 19.6 + - - +
71E ALA* 3.6 6.5 - - - +
73E LEU* 1.3 76.8 - - - +
75E ALA* 1.3 59.9 + - - +
76E GLY 3.6 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E GLU 5.2 6.5 - - - +
48E ALA* 5.9 4.5 - - + -
71E ALA 3.2 10.7 + - - +
72E LEU* 3.1 16.7 + - + +
74E ALA* 1.3 76.1 - - - +
76E GLY* 1.3 64.7 + - - +
77E THR* 5.5 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E PHE* 6.0 6.3 - - - -
72E LEU 3.4 5.3 + - - -
73E LEU* 3.2 16.4 + - - -
74E ALA 4.3 3.1 - - - +
75E ALA* 1.3 84.5 - - - +
77E THR* 1.3 67.4 + - - -
78E PRO* 3.9 1.7 - - - +
80E THR* 4.7 7.6 - - - -
----------------------------------------------------------
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