Contacts of the helix formed by residues 54 - 68 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48F SER* 4.3 1.1 - - - -
53F LEU* 1.3 75.3 - - - +
55F GLU* 1.3 59.2 + - - +
56F SER* 3.1 11.2 - - - +
57F THR* 2.9 35.4 + - - +
58F ILE* 3.1 11.5 + - - +
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Residues in contact with GLU 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F LEU* 3.7 41.8 - - + +
45F ARG* 3.4 39.0 + - - +
48F SER* 3.9 9.3 + - - -
53F LEU 3.6 1.8 + - - -
54F ALA* 1.3 72.4 - - - +
56F SER* 1.3 59.4 + - - +
57F THR 3.4 0.2 - - - -
58F ILE* 4.0 9.6 - - - -
59F HIS* 3.4 22.9 + - - +
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Residues in contact with SER 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F ALA* 3.1 7.3 - - - +
55F GLU* 1.3 78.7 - - - +
57F THR* 1.3 60.3 + - - +
59F HIS* 3.7 6.7 + - - +
60F GLU* 3.2 28.6 + - - +
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Residues in contact with THR 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F ILE* 5.9 2.5 - - + -
53F LEU* 3.8 24.5 - - + -
54F ALA* 2.9 26.8 + - - +
56F SER* 1.3 76.4 - - - +
58F ILE* 1.3 64.3 - - - +
60F GLU* 3.5 4.9 + - + +
61F ARG* 3.1 32.0 + - + +
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Residues in contact with ILE 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F ILE* 4.1 16.2 - - + -
44F LEU* 3.7 22.0 - - + +
47F ILE* 3.6 29.6 - - + -
48F SER* 4.3 9.4 - - - +
51F THR* 3.4 32.3 - - + -
53F LEU* 3.8 14.1 - - + -
54F ALA 3.1 13.6 + - - +
55F GLU* 4.0 9.4 - - - +
56F SER 3.4 0.2 - - - -
57F THR* 1.3 76.3 - - - +
59F HIS* 1.3 61.1 + - - +
61F ARG* 3.2 7.2 + - - +
62F ILE* 3.0 41.9 + - + +
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Residues in contact with HIS 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F LEU* 3.8 26.4 - - + +
55F GLU 3.4 17.6 + - - +
56F SER* 3.8 8.0 + - - +
57F THR 3.3 0.4 - - - -
58F ILE* 1.3 78.8 - - - +
60F GLU* 1.3 67.7 + - - +
62F ILE* 3.4 6.5 + - + +
63F ARG* 3.3 31.4 + - + +
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Residues in contact with GLU 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F SER 3.2 16.5 + - - +
57F THR* 3.9 5.4 - - + +
58F ILE 3.3 0.2 - - - -
59F HIS* 1.3 81.2 + - - +
61F ARG* 1.3 66.4 + - + +
63F ARG* 2.6 54.0 + - - +
64F LYS* 3.1 24.3 + - - +
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Residues in contact with ARG 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F ASP* 2.7 36.7 + - - -
28F ILE* 3.3 20.4 - - + +
29F ASP* 3.4 23.3 + - - +
32F ILE* 3.7 23.8 - - + -
53F LEU* 5.8 0.9 - - + -
57F THR* 3.1 28.8 + - + +
58F ILE 3.2 5.6 + - - +
60F GLU* 1.3 75.4 - - - +
62F ILE* 1.3 57.6 + - - +
64F LYS* 3.3 25.5 + - - +
65F LEU* 3.0 33.3 + - + +
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Residues in contact with ILE 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E LYS* 5.5 7.4 - - - +
32F ILE* 3.8 20.0 - - + -
36F LEU* 3.9 18.2 - - + -
44F LEU* 4.2 12.8 - - + -
47F ILE* 4.4 7.2 - - + -
58F ILE* 3.0 36.6 + - + +
59F HIS* 3.8 5.8 - - + +
60F GLU 3.3 0.4 - - - -
61F ARG* 1.3 76.8 - - - +
63F ARG* 1.3 57.5 + - - +
65F LEU* 3.2 9.6 + - - +
66F ARG* 2.9 51.8 + - + +
71F ILE* 4.3 9.2 - - + -
74F PHE* 4.3 10.3 - - + -
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Residues in contact with ARG 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F HIS* 3.3 19.0 + - + +
60F GLU* 2.6 61.9 + - - +
62F ILE* 1.3 78.4 - - - +
64F LYS* 1.3 61.8 + - - +
66F ARG* 3.9 12.8 - - - +
67F GLU* 2.8 69.1 + - - +
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Residues in contact with LYS 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F LEU* 5.7 2.3 - - - +
29F ASP* 4.0 14.8 - - - +
60F GLU* 3.1 15.9 + - - +
61F ARG* 3.3 33.9 - - - +
62F ILE 3.2 0.2 - - - -
63F ARG* 1.3 86.6 - - + +
65F LEU* 1.3 80.3 + - + +
67F GLU* 3.3 8.1 + - - +
68F SER* 2.9 61.8 + - - -
70F VAL* 4.5 3.8 - - - +
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Residues in contact with LEU 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F LEU* 4.6 2.9 - - + -
29F ASP* 3.9 30.1 - - + +
32F ILE* 4.7 9.9 - - + -
33F ILE* 4.0 23.8 - - + -
61F ARG* 3.0 22.4 + - + +
62F ILE* 3.2 7.6 + - - +
64F LYS* 1.3 97.0 - - + +
66F ARG* 1.3 60.6 + - - +
68F SER* 3.2 3.8 + - - -
69F GLY 3.0 5.7 + - - -
70F VAL* 2.9 51.4 + - + -
71F ILE* 3.2 25.0 + - + -
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Residues in contact with ARG 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E ASP* 4.6 15.4 + - - -
41E LYS* 3.8 22.8 - - - +
62F ILE* 2.9 31.1 + - - +
63F ARG* 3.9 10.0 - - - +
65F LEU* 1.3 75.2 - - - +
67F GLU* 1.3 63.0 + - - +
69F GLY* 3.4 10.2 + - - -
71F ILE* 3.8 30.6 - - + +
73F LYS* 6.3 0.4 - - - +
74F PHE* 3.7 30.6 - - + +
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Residues in contact with GLU 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F ARG* 2.8 51.2 + - - +
64F LYS* 3.3 6.9 + - - +
66F ARG* 1.3 76.1 - - - +
68F SER* 1.3 64.6 + - - +
69F GLY* 3.5 0.9 + - - -
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Residues in contact with SER 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F LYS* 2.9 40.1 + - - -
65F LEU 3.2 9.0 + - - -
67F GLU* 1.3 78.5 - - - +
69F GLY* 1.3 58.9 + - - +
70F VAL* 3.4 13.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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