Contacts of the helix formed by residues 60 - 71 (chain E) in PDB entry 3ZO7
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 SER 60 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1E MET* 5.6 2.2 - - - -
3E TYR* 3.5 9.1 + - - -
58E VAL* 3.5 10.7 + - - +
59E ASN* 1.3 82.0 - - - +
61E HIS* 1.3 63.7 + - - +
62E ASP* 3.3 11.9 + - - +
63E GLU* 2.9 25.1 + - - +
64E LEU* 3.1 17.2 + - - +
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Residues in contact with HIS 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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1E MET* 5.7 4.7 - - - -
3E TYR* 2.8 39.7 + + - -
60E SER* 1.3 72.6 - - - +
62E ASP* 1.3 69.0 + - - +
64E LEU* 3.1 7.7 + - - +
65E HIS* 2.9 24.2 + - - +
83E PRO* 5.7 6.1 - - + -
47F THR* 3.8 24.1 - - + +
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Residues in contact with ASP 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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60E SER* 3.2 9.1 + - - +
61E HIS* 1.3 80.5 - - - +
63E GLU* 1.3 61.3 - - - +
65E HIS* 3.3 7.8 + - - +
66E GLU* 3.1 24.4 + - - +
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Residues in contact with GLU 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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39E GLN* 3.5 24.0 + - - +
58E VAL* 3.6 22.4 - - + +
59E ASN* 2.9 36.9 + - - +
60E SER* 2.9 20.9 + - - +
62E ASP* 1.3 76.4 - - - +
64E LEU* 1.3 63.1 + - - +
66E GLU* 3.4 10.3 + - - +
67E ILE* 3.1 27.7 + - + +
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Residues in contact with LEU 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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3E TYR* 3.4 40.2 - - + -
5E VAL* 4.7 1.3 - - + -
56E PHE* 3.9 37.5 - - + -
58E VAL* 3.8 14.5 - - + +
60E SER 3.1 11.1 + - - +
61E HIS* 3.1 10.6 + - - +
63E GLU* 1.3 77.8 - - - +
65E HIS* 1.3 63.1 + - - +
67E ILE* 3.2 8.3 + - + +
68E LEU* 3.0 48.1 + - + +
81E VAL* 3.8 17.9 - - + -
47F THR* 4.0 8.1 - - + -
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Residues in contact with HIS 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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61E HIS 2.9 12.7 + - - +
62E ASP* 3.7 10.8 - - - +
64E LEU* 1.3 75.7 - - - +
66E GLU* 1.3 58.5 + - + +
68E LEU* 3.2 2.9 + - - +
69E TRP* 2.7 73.5 + + + +
45F ARG* 3.4 46.4 + - + +
47F THR* 4.1 15.7 - - + +
48F GLY* 3.5 21.3 + - - +
49F LYS 3.9 6.5 - - - -
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Residues in contact with GLU 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 ASP 3.1 13.5 + - - +
63E GLU* 3.7 10.0 - - - +
64E LEU 3.3 0.2 - - - -
65E HIS* 1.3 84.2 - - + +
67E ILE* 1.3 64.4 + - + +
69E TRP* 3.4 8.8 + - + +
70E SER* 3.2 24.1 + - - -
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Residues in contact with ILE 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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30E ARG* 4.7 5.6 - - - +
34E LEU* 4.2 27.4 - - + -
39E GLN* 3.9 27.6 - - + +
56E PHE* 4.1 26.7 - - + -
58E VAL* 3.8 29.6 - - + -
63E GLU* 3.1 16.2 + - + +
64E LEU* 3.4 8.7 - - - +
66E GLU* 1.3 78.7 - - + +
68E LEU* 1.3 65.7 + - + +
70E SER* 2.7 24.8 + - - -
71E LEU* 3.3 10.8 + - + +
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Residues in contact with LEU 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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5E VAL* 4.4 5.8 - - + -
7E MET* 3.9 28.9 - - + -
56E PHE* 4.1 17.3 - - + -
64E LEU* 3.0 40.7 + - + +
65E HIS 3.8 2.5 - - - +
67E ILE* 1.3 75.2 - - - +
69E TRP* 1.3 63.9 + - - +
71E LEU* 3.1 28.0 + - + +
74E PHE* 3.3 15.9 - - + -
79E ILE* 4.4 14.6 - - + -
81E VAL* 4.2 14.1 - - + -
48F GLY* 3.5 32.1 - - - +
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Residues in contact with TRP 69 (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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65E HIS* 2.7 55.2 + + - +
66E GLU* 3.5 9.9 - - + +
67E ILE 3.3 0.2 - - - -
68E LEU* 1.3 73.9 - - - +
70E SER* 1.3 61.0 + - - +
71E LEU 3.7 0.9 + - - +
74E PHE* 3.5 53.0 - + - +
45F ARG* 4.2 15.3 - - - -
49F LYS 4.2 0.4 - - - -
50F TYR* 3.9 48.2 - + - -
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Residues in contact with SER 70 (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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30E ARG* 3.5 29.9 + - - -
66E GLU* 3.2 12.2 + - - -
67E ILE* 2.7 19.5 + - - -
69E TRP* 1.3 78.0 - - - +
71E LEU* 1.3 67.5 + - - +
72E PRO* 3.3 6.6 - - - +
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Residues in contact with LEU 71 (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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7E MET* 3.9 35.4 - - + -
27E ALA 6.1 0.2 - - - +
30E ARG* 4.0 11.4 - - + -
34E LEU* 4.0 17.0 - - + -
40E TRP* 3.9 25.8 - - + -
56E PHE* 5.1 0.7 - - + -
67E ILE* 3.3 13.7 + - + +
68E LEU* 3.1 29.3 + - + +
69E TRP 4.1 0.5 - - - +
70E SER* 1.3 77.4 + - - +
72E PRO* 1.3 74.3 - - + +
73E PHE* 4.4 2.7 - - + +
74E PHE* 3.0 26.1 + - + +
75E PRO* 4.2 1.6 - - - +
77E LEU* 4.4 9.2 - - + -
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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