Contacts of the helix formed by residues 69 - 81 (chain E) in PDB entry 1Z6Z
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 69 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66E ASP* 3.3 22.8 + - + +
67E LEU 3.3 1.5 - - - +
68E GLY* 1.3 81.0 - - - +
70E GLU* 1.3 66.1 + - - +
71E ALA* 3.4 8.7 - - + +
72E GLY 4.0 3.1 - - - +
73E LEU* 3.2 23.6 + - - +
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Residues in contact with GLU 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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69E ALA* 1.3 72.8 - - - +
71E ALA* 1.3 59.7 + - - +
73E LEU* 3.1 8.1 + - - +
74E GLN* 2.9 50.6 + - + +
114F SER* 2.5 39.1 + - - -
115F THR* 3.8 21.5 - - + +
118F ASN* 3.4 18.3 + - - +
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Residues in contact with ALA 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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69E ALA* 3.4 4.5 - - + +
70E GLU* 1.3 78.8 - - - +
72E GLY* 1.3 63.5 + - - +
74E GLN* 3.4 6.6 + - - +
75E GLN* 3.1 34.4 + - - +
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Residues in contact with GLY 72 (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 ALA* 3.2 23.8 - - - +
66E ASP* 3.1 33.3 + - - -
67E LEU* 4.3 0.6 - - - +
69E ALA* 3.6 5.5 + - - +
70E GLU 3.3 0.8 - - - -
71E ALA* 1.3 78.6 - - - +
73E LEU* 1.3 61.3 + - - +
75E GLN* 3.3 14.0 + - - +
76E LEU* 3.3 5.0 + - - +
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Residues in contact with LEU 73 (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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66E ASP 3.7 1.4 + - - -
67E LEU* 4.3 21.1 - - + +
69E ALA 3.2 16.9 + - - +
70E GLU* 3.1 7.4 + - - +
72E GLY* 1.3 76.6 - - - +
74E GLN* 1.3 60.8 + - - +
76E LEU* 3.1 4.6 + - + +
77E LEU* 2.9 50.9 + - + +
122E ALA 6.0 0.2 - - - +
126E THR* 4.8 2.9 - - + -
127E SER* 3.9 41.7 - - - +
130E CYS* 4.4 9.6 - - + -
131E LEU* 5.3 4.0 - - + -
114F SER* 3.6 33.2 - - - +
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Residues in contact with GLN 74 (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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70E GLU* 2.9 41.4 + - + +
71E ALA* 3.9 6.3 - - - +
73E LEU* 1.3 75.1 - - - +
75E GLN* 1.3 56.3 + - - +
77E LEU* 3.7 26.4 - - - +
78E GLY* 2.7 31.9 + - - -
112F SER 5.3 3.0 + - - -
114F SER* 3.7 10.1 + - - +
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Residues in contact with GLN 75 (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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63E VAL* 4.0 7.3 - - + +
64E PRO 4.6 12.8 - - - +
65E ALA* 4.3 7.2 - - + -
71E ALA* 3.1 23.3 + - - +
72E GLY* 3.3 15.9 - - - +
73E LEU 3.2 0.2 - - - -
74E GLN* 1.3 76.7 - - - +
76E LEU* 1.3 57.1 + - - +
78E GLY* 3.9 0.9 - - - -
79E ALA* 3.1 26.3 + - - +
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Residues in contact with LEU 76 (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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8E LEU* 4.7 7.9 - - + -
10E THR* 4.2 9.0 - - + -
35E VAL* 4.5 11.2 - - + -
37E SER* 3.8 17.3 - - - +
63E VAL* 3.7 35.6 - - + +
65E ALA* 4.8 0.7 - - + -
67E LEU* 3.7 25.6 - - + -
72E GLY 3.3 7.6 + - - +
73E LEU* 3.1 10.3 + - + +
75E GLN* 1.3 77.1 - - - +
77E LEU* 1.3 64.4 + - + +
79E ALA* 3.1 14.2 + - + +
80E LEU* 3.3 13.8 + - + +
131E LEU* 3.8 35.9 - - + -
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Residues in contact with LEU 77 (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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73E LEU* 2.9 32.8 + - + +
74E GLN* 3.7 34.5 - - - +
76E LEU* 1.3 76.1 - - + +
78E GLY* 1.3 62.7 + - - +
80E LEU* 3.3 26.9 - - + +
81E ARG* 3.6 4.9 + - - +
130E CYS* 4.0 14.1 - - + +
131E LEU* 4.1 17.5 - - + +
134E SER* 3.2 29.6 - - - +
112F SER* 4.6 15.0 - - - +
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Residues in contact with GLY 78 (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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74E GLN 2.7 22.1 + - - -
75E GLN* 3.9 1.8 - - - -
77E LEU* 1.3 71.8 - - - +
79E ALA* 1.3 62.6 + - - +
80E LEU 3.2 0.7 + - - -
81E ARG* 3.2 18.8 + - - +
82E GLU* 3.5 15.3 + - - +
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Residues in contact with ALA 79 (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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35E VAL* 5.8 0.7 - - + -
61E VAL* 5.3 3.4 - - + -
63E VAL* 3.8 27.8 - - + -
75E GLN 3.1 14.5 + - - +
76E LEU* 3.1 10.7 + - + +
78E GLY* 1.3 75.4 - - - +
80E LEU* 1.3 62.6 + - - +
82E GLU* 3.3 9.2 + - - +
83E LEU* 3.1 31.5 + - + +
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Residues in contact with LEU 80 (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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8E LEU* 3.9 17.5 - - + -
35E VAL* 6.0 0.7 - - + -
76E LEU* 3.3 11.8 + - + +
77E LEU* 3.3 20.4 + - + +
78E GLY 3.1 0.2 - - - -
79E ALA* 1.3 74.1 - - - +
81E ARG* 1.3 55.5 + - - +
82E GLU 2.7 5.7 + - - -
83E LEU* 2.7 51.5 + - + +
131E LEU* 4.7 3.6 - - + +
134E SER* 3.7 30.1 - - - +
135E VAL* 3.7 37.0 - - + +
138E ALA* 5.1 10.3 - - + +
139E PHE* 5.4 7.8 - - + -
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Residues in contact with ARG 81 (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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77E LEU 3.6 5.1 + - - +
78E GLY* 3.2 12.6 + - - +
80E LEU* 1.3 77.1 - - - +
82E GLU* 1.3 63.1 + - + +
83E LEU 5.3 0.9 - - - -
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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