Contacts of the helix formed by residues 54 - 69 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C SER* 3.8 0.9 - - - -
52C GLY 4.0 0.6 + - - -
53C LEU* 1.3 82.5 - - + +
55C GLU* 1.3 58.5 + - - +
56C SER* 3.3 11.2 - - - +
57C THR* 2.6 31.6 + - + +
58C ILE* 3.2 11.1 + - - +
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Residues in contact with GLU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 3.6 46.6 - - + +
45C ARG* 3.8 15.6 + - - +
48C SER* 3.7 15.6 + - - +
54C ALA* 1.3 71.3 - - - +
56C SER* 1.3 61.5 + - - +
57C THR 3.5 0.7 - - - -
58C ILE* 3.9 10.5 - - + -
59C HIS* 3.4 21.8 + - - +
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Residues in contact with SER 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ALA* 3.3 6.1 - - - +
55C GLU* 1.3 79.8 + - - +
57C THR* 1.3 66.3 + - - +
59C HIS* 3.9 4.2 + - - +
60C GLU* 3.4 22.9 + - - +
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Residues in contact with THR 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C LEU* 3.4 28.3 - - + +
54C ALA* 2.6 31.9 + - + -
56C SER* 1.3 77.6 - - - +
58C ILE* 1.3 54.1 + - - -
60C GLU* 3.0 8.1 + - - +
61C ARG* 2.7 43.8 + - - +
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Residues in contact with ILE 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ILE* 6.0 0.4 - - + -
32C ILE* 4.5 13.7 - - + -
44C LEU* 3.8 23.3 - - + +
47C ILE* 3.7 37.5 - - + -
48C SER* 3.4 26.5 - - - +
51C THR* 3.7 10.5 - - + -
53C LEU* 3.5 15.5 - - + +
54C ALA 3.2 13.4 + - - +
55C GLU* 3.9 7.0 - - - -
56C SER 3.5 0.2 - - - -
57C THR* 1.3 80.8 + - - +
59C HIS* 1.3 61.6 + - - +
61C ARG* 3.3 10.0 + - - +
62C ILE* 3.1 32.3 + - + +
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Residues in contact with HIS 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 4.2 26.9 - - + -
55C GLU 3.4 18.9 + - - +
56C SER* 4.0 6.7 + - - +
57C THR 3.2 0.6 - - - -
58C ILE* 1.3 78.6 - - - +
60C GLU* 1.3 64.3 + - - +
62C ILE* 3.5 6.4 + - + +
63C ARG* 3.0 38.8 + - + +
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Residues in contact with GLU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C SER 3.4 12.6 + - - +
57C THR* 3.0 10.3 + - - +
59C HIS* 1.3 80.2 + - - +
61C ARG* 1.3 65.6 + - - +
63C ARG* 3.0 42.6 + - - +
64C LYS* 3.1 35.4 + - - +
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Residues in contact with ARG 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ILE* 3.4 47.1 - - + +
29C ASP* 3.4 29.2 + - - +
32C ILE* 3.6 22.9 - - + -
53C LEU* 4.8 7.0 - - + +
57C THR* 2.7 35.6 + - - +
58C ILE* 3.3 8.9 + - + +
60C GLU* 1.3 72.5 - - - +
62C ILE* 1.3 61.1 + - - +
64C LYS* 3.3 16.6 - - - +
65C LEU* 3.0 30.3 + - - +
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Residues in contact with ILE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ILE* 4.0 13.2 - - + -
36C LEU* 3.9 25.1 - - + -
44C LEU* 4.1 23.6 - - + -
47C ILE* 4.6 7.0 - - + -
58C ILE* 3.1 24.1 + - + +
59C HIS* 3.8 6.5 - - + +
61C ARG* 1.3 73.9 - - - +
63C ARG* 1.3 57.6 + - - +
65C LEU* 3.2 8.9 + - - +
66C ARG* 2.8 53.9 + - + +
71C ILE* 4.5 1.8 - - + -
74C PHE* 4.3 15.7 - - + -
41D LYS* 5.2 10.1 - - - +
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Residues in contact with ARG 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C HIS* 3.0 31.9 + - + +
60C GLU* 3.0 33.3 + - - +
61C ARG 3.3 0.2 - - - -
62C ILE* 1.3 77.6 - - - +
64C LYS* 1.3 61.6 + - - +
66C ARG* 3.5 9.0 + - - +
67C GLU* 3.0 50.3 + - - +
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Residues in contact with LYS 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ASP* 2.8 42.5 + - - -
60C GLU* 3.1 26.8 + - - +
61C ARG* 3.3 27.3 - - - +
63C ARG* 1.3 78.5 - - - +
65C LEU* 1.3 68.3 + - + +
66C ARG 3.3 0.4 - - - -
67C GLU* 3.9 4.2 - - - +
68C SER* 2.7 40.1 + - - +
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Residues in contact with LEU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ASP* 4.1 18.2 - - + +
32C ILE* 4.6 12.6 - - + -
33C ILE* 4.0 25.6 - - + -
61C ARG* 3.0 29.6 + - + +
62C ILE* 3.4 6.7 - - - +
64C LYS* 1.3 97.6 - - + +
66C ARG* 1.3 62.3 + - - +
68C SER* 3.1 13.5 + - - +
70C VAL* 3.1 47.0 + - + -
71C ILE* 3.2 24.1 + - + -
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Residues in contact with ARG 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ILE* 2.8 32.9 + - + +
63C ARG* 3.7 8.5 - - - +
65C LEU* 1.3 77.7 - - - +
67C GLU* 1.3 64.2 - - + +
69C GLY* 3.5 9.4 + - - -
71C ILE* 3.7 23.4 + - + +
73C LYS* 5.9 1.4 - - - +
74C PHE* 3.4 42.3 - - + +
39D ASP* 4.5 14.8 + - - -
41D LYS* 4.2 23.2 - - - +
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Residues in contact with GLU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ARG* 3.0 47.4 + - - +
64C LYS* 4.5 3.6 - - - +
66C ARG* 1.3 77.9 - - + +
68C SER* 1.3 62.8 + - - +
69C GLY 3.4 0.2 - - - -
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Residues in contact with SER 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C LYS* 2.7 24.2 + - - +
65C LEU* 3.1 15.1 + - - +
67C GLU* 1.3 77.4 - - - +
69C GLY* 1.3 57.8 + - - +
70C VAL* 3.5 16.4 - - - +
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Residues in contact with GLY 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C LEU 3.2 4.9 + - - -
66C ARG 3.5 8.0 + - - -
67C GLU 3.4 2.4 - - - -
68C SER* 1.3 80.6 + - - +
70C VAL* 1.3 66.4 + - - +
71C ILE 3.4 10.8 + - - -
72C LYS* 3.9 7.4 - - - +
79D ASP* 3.6 18.8 - - - +
82D ALA* 5.6 0.7 - - - -
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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