Contacts of the helix formed by residues 66 - 80 (chain B) in PDB entry 3UXO
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 GLY 66 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B LYS* 4.2 4.7 - - - -
64B GLY 3.4 7.0 + - - -
65B VAL* 1.3 77.7 - - - +
67B THR* 1.3 59.4 + - - -
68B LYS 3.5 2.7 - - - -
69B ILE* 3.5 10.9 + - - +
70B ALA* 3.0 27.0 + - - +
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Residues in contact with THR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LYS* 3.3 34.3 + - - +
66B GLY* 1.3 72.9 - - - -
68B LYS* 1.3 71.7 + - + +
70B ALA* 3.2 4.6 + - - +
71B GLU* 3.0 23.6 + - - +
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Residues in contact with LYS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B GLY 3.5 0.2 - - - -
67B THR* 1.3 84.5 - - + +
69B ILE* 1.3 69.0 + - + +
71B GLU* 3.1 31.1 + - - +
72B LYS* 3.2 42.7 + - - +
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Residues in contact with ILE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 4.0 22.2 - - + -
38B ALA* 3.7 21.3 - - + +
39B TYR* 4.0 25.6 - - + -
42B ALA* 3.7 26.5 - - + -
64B GLY 4.5 9.0 - - - +
65B VAL* 3.9 17.5 - - + -
66B GLY* 3.5 12.2 + - - +
67B THR 3.4 0.4 - - - -
68B LYS* 1.3 77.5 - - + +
70B ALA* 1.3 64.3 + - - +
72B LYS* 3.1 11.3 + - - +
73B ILE* 3.0 28.0 + - + +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B GLY* 3.8 22.8 - - - +
60B LYS* 3.8 23.3 - - + +
65B VAL* 4.4 3.3 - - + +
66B GLY 3.0 15.6 + - - +
67B THR* 3.4 10.3 - - - +
68B LYS 3.2 0.2 - - - -
69B ILE* 1.3 77.8 - - - +
71B GLU* 1.3 59.9 + - - +
73B ILE* 3.4 13.8 + - - +
74B ASP* 3.1 22.3 + - - +
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Residues in contact with GLU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B THR* 3.0 15.1 + - - +
68B LYS* 3.1 27.5 + - - +
70B ALA* 1.3 74.5 - - - +
72B LYS* 1.3 66.3 + - + +
74B ASP* 3.4 7.9 + - + +
75B GLU* 3.3 21.7 + - - +
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Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B MET* 4.1 11.4 - - + -
19B LEU* 5.9 0.7 - - + -
22B LEU* 3.7 24.7 - - + -
39B TYR* 3.3 26.5 + - + +
68B LYS* 3.2 49.2 + - - +
69B ILE* 3.1 10.8 + - + +
71B GLU* 1.3 77.4 - - + +
73B ILE* 1.3 63.4 + - - +
75B GLU* 3.3 6.6 + - - +
76B PHE* 3.1 23.9 + - - +
82B LEU* 3.7 28.4 - - + +
84B LYS* 5.2 16.6 - - + +
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Residues in contact with ILE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 3.6 39.5 - - + -
18B MET* 4.3 9.4 - - + -
19B LEU* 5.2 0.4 - - + -
46B ILE* 3.7 21.3 - - + -
53B ILE* 4.4 12.3 - - + -
55B SER 4.4 5.8 - - - +
56B GLY* 4.4 2.5 - - - +
59B ALA* 3.6 25.4 - - + -
65B VAL* 4.0 6.1 - - + -
69B ILE* 3.0 34.7 + - + +
70B ALA* 3.6 8.3 - - - +
72B LYS* 1.3 76.7 - - - +
74B ASP* 1.3 56.9 + - - +
76B PHE* 3.5 1.9 + - - +
77B LEU* 2.9 33.5 + - + +
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Residues in contact with ASP 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B SER* 3.9 7.3 + - - -
56B GLY* 2.9 30.0 + - - -
57B ALA 5.4 0.5 + - - -
70B ALA 3.1 10.5 + - - +
71B GLU* 3.6 11.9 - - + +
72B LYS 3.3 0.2 - - - -
73B ILE* 1.3 77.3 - - - +
75B GLU* 1.3 58.4 + - - +
77B LEU* 3.3 6.7 + - - +
78B ALA* 3.0 31.2 + - - +
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Residues in contact with GLU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLU 3.3 10.7 + - - +
72B LYS* 3.3 9.4 + - - +
74B ASP* 1.3 76.4 - - - +
76B PHE* 1.3 55.7 + - - +
78B ALA* 4.8 1.6 - - - -
79B THR* 2.3 66.2 + - + +
81B LYS* 3.8 5.3 - - - +
82B LEU* 3.9 11.1 - - + +
83B ARG* 3.0 67.6 + - - +
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Residues in contact with PHE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLY* 3.6 38.4 - - - -
15B ILE* 3.8 19.5 - - + -
18B MET* 3.6 34.5 - - + -
72B LYS 3.1 8.0 + - - +
73B ILE* 3.9 3.8 - - - +
75B GLU* 1.3 78.2 - - - +
77B LEU* 1.3 64.5 + - + +
80B GLY* 2.8 57.5 + - - +
81B LYS* 3.3 18.9 + - - +
82B LEU 4.8 0.4 - - - -
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 4.0 26.2 - - + -
52B LYS* 5.7 4.5 - - - +
53B ILE 3.9 17.0 - - - +
54B LYS* 3.4 35.4 - - + +
55B SER* 4.6 4.7 - - - +
73B ILE* 2.9 20.8 + - + +
74B ASP* 3.4 10.5 - - - +
75B GLU 3.1 0.2 - - - -
76B PHE* 1.3 84.9 - - + +
78B ALA* 1.3 58.1 + - - +
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ASP 3.0 16.3 + - - +
75B GLU* 4.0 1.6 - - - +
77B LEU* 1.3 79.2 - - + +
79B THR* 1.3 68.2 + - + +
80B GLY 3.5 0.4 - - - -
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Residues in contact with THR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B GLU* 2.3 49.8 + - + +
78B ALA* 1.3 81.0 - - + +
80B GLY* 1.3 55.3 + - - +
81B LYS* 2.9 35.4 + - - +
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Residues in contact with GLY 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B PHE* 2.8 44.6 + - - -
77B LEU 4.6 0.4 - - - -
78B ALA 3.5 1.4 - - - -
79B THR* 1.3 77.0 + - - +
81B LYS* 1.3 57.9 + - - +
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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