Contacts of the helix formed by residues 54 - 68 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48E SER* 4.1 0.7 - - - -
53E LEU* 1.3 77.1 - - - +
55E GLU* 1.3 59.0 + - - +
56E SER* 3.3 14.4 - - - +
57E THR* 2.8 31.3 + - + +
58E ILE* 3.3 14.2 + - - +
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Residues in contact with GLU 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E LEU* 3.4 45.7 - - + +
45E ARG* 3.5 26.9 + - - +
48E SER* 3.4 17.9 + - - +
54E ALA* 1.3 70.5 - - - +
56E SER* 1.3 64.7 + - - +
57E THR 3.4 0.4 - - - -
58E ILE* 3.9 8.3 - - + -
59E HIS* 3.4 15.4 + - - +
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Residues in contact with SER 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E ALA* 3.3 9.4 - - - +
55E GLU* 1.3 83.3 + - - +
57E THR* 1.3 64.3 + - - +
59E HIS* 3.7 5.3 + - - +
60E GLU* 3.7 18.5 + - - +
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Residues in contact with THR 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E LEU* 3.6 14.3 - - - +
54E ALA* 2.8 32.3 + - + +
56E SER* 1.3 78.3 - - - +
58E ILE* 1.3 57.7 + - - +
60E GLU* 3.2 8.0 + - - +
61E ARG* 2.8 38.5 + - - +
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Residues in contact with ILE 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E ILE* 4.6 11.2 - - + -
44E LEU* 4.2 19.3 - - + +
47E ILE* 3.6 44.2 - - + -
48E SER* 3.5 21.8 - - - +
51E THR* 3.8 13.9 - - + -
53E LEU* 3.9 12.1 - - + -
54E ALA 3.3 18.7 + - - +
55E GLU* 3.9 8.5 - - - -
57E THR* 1.3 80.6 + - - +
59E HIS* 1.3 61.8 + - - +
61E ARG* 3.1 10.6 + - - +
62E ILE* 3.0 31.8 + - + +
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Residues in contact with HIS 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E LEU* 4.0 23.8 - - + -
55E GLU 3.4 15.8 + - - +
56E SER* 3.9 6.5 - - - +
57E THR 3.3 0.6 - - - -
58E ILE* 1.3 79.8 - - - +
60E GLU* 1.3 65.1 + - - +
62E ILE* 3.7 13.4 + - + +
63E ARG* 3.2 45.5 + - + +
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Residues in contact with GLU 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E SER 3.7 9.4 + - - +
57E THR* 3.2 11.0 + - - +
59E HIS* 1.3 78.9 - - - +
61E ARG* 1.3 64.6 + - - +
63E ARG* 3.3 37.7 + - - +
64E LYS* 3.2 33.3 + - - +
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Residues in contact with ARG 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ASP* 3.1 35.9 + - - +
28E ILE* 3.4 36.8 - - + +
29E ASP* 3.2 27.4 + - - +
32E ILE* 3.5 22.7 - - + -
53E LEU* 6.1 0.6 - - + +
57E THR* 2.8 28.5 + - - +
58E ILE* 3.1 10.1 + - - +
60E GLU* 1.3 78.9 - - + +
62E ILE* 1.3 60.7 + - - +
64E LYS* 3.3 15.9 - - - +
65E LEU* 3.2 28.5 + - - +
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Residues in contact with ILE 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E ILE* 3.7 28.7 - - + -
36E LEU* 4.2 14.6 - - + -
44E LEU* 6.0 7.6 - - + -
47E ILE* 5.7 1.8 - - + -
58E ILE* 3.0 22.3 + - + +
59E HIS* 3.9 15.5 - - + +
61E ARG* 1.3 74.1 - - - +
63E ARG* 1.3 60.9 + - - +
65E LEU* 3.6 9.5 - - - +
66E ARG* 2.9 44.3 + - - +
71E ILE* 4.6 3.4 - - + -
74E PHE* 4.2 23.8 - - + -
41F LYS* 4.3 17.0 - - - +
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Residues in contact with ARG 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E HIS* 3.2 40.4 + - + +
60E GLU* 3.3 30.4 + - - +
61E ARG 3.2 0.4 - - - -
62E ILE* 1.3 81.3 - - + +
64E LYS* 1.3 57.3 + - - +
66E ARG* 3.6 8.0 + - - +
67E GLU* 3.1 25.3 + - - +
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Residues in contact with LYS 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E LEU* 5.6 2.0 - - - +
29E ASP* 3.2 26.1 + - - -
60E GLU* 3.2 23.7 + - - +
61E ARG* 3.3 21.0 - - - +
63E ARG* 1.3 74.5 - - - +
65E LEU* 1.3 76.1 + - - +
66E ARG 3.2 0.4 - - - -
67E GLU* 3.6 9.6 - - + +
68E SER* 2.7 42.5 + - - -
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Residues in contact with LEU 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E LEU* 4.6 4.3 - - + -
29E ASP* 4.0 28.3 - - + +
32E ILE* 4.8 10.1 - - + -
33E ILE* 3.8 29.2 - - + -
61E ARG* 3.2 26.0 + - + +
62E ILE* 3.6 11.2 - - - +
64E LYS* 1.3 91.9 - - - +
66E ARG* 1.3 57.8 + - - +
68E SER* 3.2 6.3 + - - +
70E VAL* 3.1 51.9 + - + -
71E ILE* 3.2 22.9 + - + -
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Residues in contact with ARG 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E ILE* 2.9 31.1 + - - +
63E ARG* 3.8 7.4 - - - +
64E LYS 3.2 0.2 - - - -
65E LEU* 1.3 74.0 - - - +
67E GLU* 1.3 65.1 + - - +
69E GLY* 3.6 10.2 + - - -
71E ILE* 4.0 24.1 + - + +
73E LYS* 6.1 2.0 - - - +
74E PHE* 3.5 40.6 - - + +
39F ASP* 4.6 10.7 + - - -
41F LYS* 4.2 29.9 - - - +
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Residues in contact with GLU 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ARG* 5.0 12.8 - - - +
49A LYS* 4.1 9.0 + - - -
63E ARG 3.1 17.8 + - - +
64E LYS* 3.2 11.2 + - + +
66E ARG* 1.3 78.4 - - - +
68E SER* 1.3 64.5 + - - +
69E GLY* 3.4 0.9 + - - -
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Residues in contact with SER 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LYS* 3.0 29.7 + - - +
64E LYS* 2.7 29.7 + - - -
65E LEU* 3.2 13.0 + - - +
67E GLU* 1.3 77.0 - - - +
69E GLY* 1.3 58.2 + - - +
70E VAL* 3.5 19.4 - - - +
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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