Contacts of the helix formed by residues 54 - 68 (chain H) in PDB entry 2ZNZ
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 ALA 54 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H SER* 4.0 0.7 - - - -
52H GLY 4.0 0.8 + - - -
53H LEU* 1.3 74.7 - - - +
55H GLU* 1.3 65.4 + - - +
56H SER* 4.2 11.0 - - - +
57H THR* 3.0 28.8 + - - +
58H ILE* 3.3 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H LEU* 3.6 28.6 - - + +
45H ARG* 3.3 37.3 + - - +
48H SER* 3.2 23.1 + - - +
54H ALA* 1.3 71.1 - - - +
56H SER* 1.3 56.9 + - - +
58H ILE* 3.5 7.1 + - - +
59H HIS* 3.1 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 56 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H ALA* 4.2 8.2 - - - +
55H GLU* 1.3 76.2 - - - +
57H THR* 1.3 70.5 + - - +
59H HIS* 3.6 7.7 + - - +
60H GLU* 3.2 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 57 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H ILE* 5.5 0.2 - - + -
53H LEU* 4.3 21.8 - - + +
54H ALA* 3.0 26.9 + - - +
56H SER* 1.3 78.7 + - - +
58H ILE* 1.3 66.9 + - - +
60H GLU* 3.1 7.3 + - - +
61H ARG* 2.9 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 58 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H ILE* 4.3 15.3 - - + -
44H LEU* 3.7 18.8 - - + +
47H ILE* 3.8 29.2 - - + +
48H SER* 3.3 46.0 - - - +
53H LEU* 3.8 27.1 - - + -
54H ALA 3.3 12.5 + - - +
55H GLU* 3.7 6.3 - - - +
57H THR* 1.3 73.4 - - - +
59H HIS* 1.3 58.3 + - - +
61H ARG* 3.2 2.4 + - - +
62H ILE* 3.0 47.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 59 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H LEU* 3.9 28.9 - - + +
55H GLU 3.1 17.2 + - - +
56H SER* 3.8 9.1 + - - +
57H THR 3.3 0.2 - - - -
58H ILE* 1.3 77.2 - - - +
60H GLU* 1.3 62.3 + - - +
62H ILE* 3.6 6.3 + - + +
63H ARG* 3.1 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H SER 3.2 13.3 + - - +
57H THR* 3.1 10.6 + - - +
59H HIS* 1.3 78.6 + - - +
61H ARG* 1.3 66.2 + - + +
63H ARG* 2.6 50.4 + - - +
64H LYS* 3.0 44.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H ASP* 2.9 43.8 + - - -
28H ILE* 3.4 30.9 - - + +
29H ASP* 3.3 22.7 + - - +
32H ILE* 3.7 25.6 - - + -
57H THR* 2.9 33.3 + - + +
58H ILE 3.5 7.2 - - - +
60H GLU* 1.3 76.1 - - - +
62H ILE* 1.3 56.3 + - - +
64H LYS* 3.3 28.3 + - - +
65H LEU* 2.9 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G LYS* 5.2 4.0 - - - +
32H ILE* 3.7 20.2 - - + -
36H LEU* 3.9 16.6 - - + -
44H LEU* 4.3 11.4 - - + -
47H ILE* 4.4 6.3 - - + -
58H ILE* 3.0 40.5 + - + +
59H HIS* 3.9 6.5 - - + +
61H ARG* 1.3 72.1 - - - +
63H ARG* 1.3 58.9 + - - +
65H LEU* 3.3 8.5 + - - +
66H ARG* 2.9 45.6 + - - +
71H ILE* 4.2 11.7 - - + -
74H PHE* 4.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H HIS* 3.1 30.9 + - + +
60H GLU* 2.6 57.3 + - - +
62H ILE* 1.3 77.0 - - - +
64H LYS* 1.3 71.0 - - - +
66H ARG* 3.5 9.0 + - - +
67H GLU* 2.8 69.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 64 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H GLU* 3.0 36.3 + - - +
61H ARG* 3.7 29.4 - - - +
63H ARG* 1.3 97.4 - - - +
65H LEU* 1.3 56.6 + - + +
67H GLU* 3.1 8.8 + - - +
68H SER* 2.8 34.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H LEU* 4.3 8.1 - - + -
29H ASP* 4.0 31.9 - - - +
32H ILE* 4.7 10.3 - - + -
33H ILE* 4.1 21.1 - - + -
61H ARG* 2.9 32.0 + - + +
62H ILE* 3.3 9.8 + - - +
64H LYS* 1.3 76.3 - - + +
66H ARG* 1.3 59.4 - - - +
68H SER* 3.4 4.0 + - - +
69H GLY 3.3 1.7 + - - -
70H VAL* 2.9 54.6 + - + -
71H ILE* 3.0 26.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 66 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G ASP* 4.7 8.5 + - - -
41G LYS* 4.1 35.7 - - - +
62H ILE* 2.9 31.2 + - + +
63H ARG* 3.7 7.4 - - - +
65H LEU* 1.3 73.3 - - - +
67H GLU* 1.3 66.2 + - - +
69H GLY* 3.3 10.7 + - - -
71H ILE* 3.8 22.4 - - + +
74H PHE* 3.9 33.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H ARG* 2.8 56.4 + - - +
64H LYS* 3.1 8.4 + - - +
66H ARG* 1.3 78.7 - - - +
68H SER* 1.3 61.8 + - - +
69H GLY* 3.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 68 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H LYS 2.8 21.7 + - - -
65H LEU* 3.4 8.1 + - - +
67H GLU* 1.3 73.4 - - - +
69H GLY* 1.3 58.8 + - - +
70H VAL* 3.4 20.8 + - - +
----------------------------------------------------------
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