Contacts of the helix formed by residues 62 - 72 (chain E) in PDB entry 2UZC
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 THR 62 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C SER 6.1 0.4 - - - -
21E GLY* 5.0 0.4 - - - -
22E LYS* 3.7 25.5 - - + +
23E ASP* 3.4 24.2 - - + +
28E LEU* 5.6 0.2 - - - -
61E MET* 1.3 76.5 - - - +
63E HIS* 1.3 67.0 + - - +
64E LEU* 3.7 6.3 + - - +
65E GLU* 2.9 40.7 + - - +
66E ALA* 3.1 20.8 + - - +
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Residues in contact with HIS 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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46C ILE* 3.5 42.5 + - + +
18E LEU* 3.1 45.9 + - + +
19E GLN* 3.6 5.8 - - - -
20E GLY 2.7 31.3 + - - +
21E GLY* 4.5 0.4 - - - -
23E ASP* 3.0 8.4 + - - +
24E PHE* 3.9 15.7 - - + -
28E LEU* 4.2 8.3 - - + +
62E THR* 1.3 75.1 - - - +
64E LEU* 1.3 57.2 + - - +
66E ALA* 3.2 2.6 + - - +
67E GLN* 2.9 40.7 + - + +
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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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19C GLN* 3.5 35.0 - - - +
26C MET* 4.5 11.4 - - + -
29C THR* 4.4 8.3 - - + -
31C SER* 3.8 24.7 + - - +
46C ILE* 4.0 21.7 - - + +
47C GLY* 4.2 9.2 - - - +
23E ASP* 5.4 0.2 + - - -
62E THR* 3.3 6.2 + - - +
63E HIS* 1.3 78.7 - - - +
65E GLU* 1.3 57.7 + - + +
67E GLN* 3.4 23.9 + - - +
68E ASN* 2.9 54.6 + - - +
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Residues in contact with GLU 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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22E LYS* 3.4 11.6 + - - -
60E GLY 4.1 0.7 - - - +
61E MET* 3.4 17.7 - - + +
62E THR* 2.9 42.0 + - - +
64E LEU* 1.3 77.6 - - + +
66E ALA* 1.3 56.5 + - - +
68E ASN* 3.2 7.1 + - - +
69E LYS* 2.9 29.4 + - - +
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Residues in contact with ALA 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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18E LEU* 4.9 2.0 - - + -
28E LEU* 3.5 35.0 - - + -
53E ILE* 3.9 9.3 - - + +
61E MET* 3.8 19.9 - - + -
62E THR 3.1 12.5 + - - +
63E HIS 3.6 7.4 - - - +
65E GLU* 1.3 71.8 - - - +
67E GLN* 1.3 66.2 - - - +
69E LYS* 3.2 3.5 + - - +
70E ILE* 3.0 29.7 + - - +
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Residues in contact with GLN 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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46C ILE 3.0 24.2 + - - -
47C GLY* 3.2 22.7 - - - -
84C GLU 4.2 1.3 - - - -
85C SER* 4.0 14.5 + - - +
87C LEU* 3.7 26.1 - - + +
18E LEU* 5.0 3.5 - - + +
63E HIS* 2.9 32.0 + - + +
64E LEU* 3.6 15.9 - - - +
66E ALA* 1.3 75.6 - - - +
68E ASN* 1.3 60.2 + - - +
70E ILE* 3.3 11.4 + - - +
71E LYS* 3.0 45.6 + - + +
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Residues in contact with ASN 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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26C MET* 5.0 10.9 - - - +
64E LEU* 2.9 46.7 + - - +
65E GLU* 3.2 5.0 + - - +
67E GLN* 1.3 75.7 - - - +
69E LYS* 1.3 59.0 + - - +
71E LYS* 3.3 20.0 + - - +
72E GLY* 2.9 27.9 + - - -
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Residues in contact with LYS 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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53E ILE* 3.6 37.0 - - + -
54E ASP* 4.1 18.1 + - - -
56E ILE* 3.1 37.5 - - + +
61E MET* 4.4 12.6 - - + -
65E GLU 2.9 14.6 + - - +
66E ALA* 3.4 11.9 - - - +
68E ASN* 1.3 75.2 - - - +
70E ILE* 1.3 61.8 + - - +
72E GLY* 3.3 10.8 + - - -
73E CYS* 3.3 19.7 + - - -
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Residues in contact with ILE 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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87C LEU* 4.1 19.7 - - + -
14E TRP* 3.8 31.8 + - + +
16E PHE* 4.0 15.9 - - + -
18E LEU* 3.6 29.2 - - + -
50E VAL* 5.9 0.2 - - + -
53E ILE* 3.8 29.2 - - + -
66E ALA 3.0 19.3 + - - +
67E GLN 3.6 6.5 - - - +
69E LYS* 1.3 75.4 - - - +
71E LYS* 1.3 63.1 + - - +
73E CYS* 3.1 19.5 + - - +
77E LEU* 4.1 18.8 - - + -
79E MET* 4.5 4.3 - - - -
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Residues in contact with LYS 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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47C GLY 4.7 1.8 + - - -
84C GLU* 2.7 45.8 + - - +
86C ASP 5.4 1.8 - - - -
87C LEU* 3.8 24.5 - - + -
14E TRP* 5.7 1.1 - - - +
67E GLN* 3.0 32.5 + - - +
68E ASN* 3.3 19.7 + - - +
70E ILE* 1.3 76.3 - - + +
72E GLY* 1.3 59.6 + - - +
73E CYS 3.2 6.0 + - - +
74E THR* 5.7 0.9 - - - +
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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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68E ASN 2.9 16.2 + - - -
69E LYS 3.8 3.6 - - - -
70E ILE 3.2 0.2 - - - -
71E LYS* 1.3 74.0 - - - +
73E CYS* 1.3 64.0 + - - +
74E THR* 3.3 13.7 + - - +
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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