Contacts of the helix formed by residues 73 - 86 (chain E) in PDB entry 5X11
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 73 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52E GLY* 2.5 29.8 + - - +
53E PHE 2.8 24.4 + - - +
54E ILE 4.1 11.9 - - - +
55E THR* 4.2 14.6 - - + +
72E LEU* 1.3 77.8 - - - +
74E ASP* 1.3 60.6 + - - +
75E SER* 3.3 4.7 - - - -
76E GLY 2.8 20.4 + - - -
77E LYS* 3.0 16.7 + - - +
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Residues in contact with ASP 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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73E THR* 1.3 73.9 - - - +
75E SER* 1.3 62.2 + - - +
77E LYS* 3.6 8.7 + - - +
78E GLN* 3.2 25.5 + - - +
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Residues in contact with SER 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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51E GLU 4.7 1.7 + - - -
52E GLY 3.5 11.9 + - - -
53E PHE* 3.4 21.3 - - - -
73E THR* 3.3 12.5 - - - -
74E ASP* 1.3 79.9 - - - +
76E GLY* 1.3 54.9 + - - -
78E GLN* 3.8 5.0 - - - +
79E GLU* 3.0 30.7 + - - +
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Residues in contact with GLY 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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9E LEU* 3.9 3.8 - - - +
53E PHE* 3.3 30.5 - - - +
72E LEU* 4.4 11.7 - - - -
73E THR* 2.8 15.0 + - - -
75E SER* 1.3 74.5 - - - +
77E LYS* 1.3 57.4 + - - -
79E GLU* 3.2 4.4 + - - +
80E LEU* 2.9 29.6 + - - +
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Residues in contact with LYS 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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13E ARG 5.6 5.2 - - - -
72E LEU* 3.9 30.8 - - + +
73E THR 3.0 15.6 + - - +
74E ASP* 4.1 9.0 - - - +
76E GLY* 1.3 73.5 - - - +
78E GLN* 1.3 57.6 + - - +
80E LEU* 3.5 6.2 + - - +
81E HIS* 2.9 30.8 + - - +
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Residues in contact with GLN 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 ASP 3.2 17.2 + - - +
75E SER* 3.8 6.1 - - - +
77E LYS* 1.3 79.7 - - - +
79E GLU* 1.3 61.6 + - - +
81E HIS* 3.3 16.6 + - - +
82E ASP* 3.0 62.1 + - - +
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Residues in contact with GLU 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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5E LYS* 2.9 32.7 + - - +
6E TYR* 2.9 35.5 + - + -
9E LEU* 3.9 7.2 - - + -
53E PHE* 3.4 25.5 - - + -
75E SER 3.0 18.2 + - - +
76E GLY 3.4 5.2 - - - +
78E GLN* 1.3 77.4 - - - +
80E LEU* 1.3 61.7 + - - +
82E ASP* 3.5 11.6 + - - +
83E TRP 3.3 16.6 + - - -
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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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6E TYR* 4.1 13.2 - - + +
9E LEU* 3.8 28.4 - - + +
10E GLY* 3.9 25.4 - - - +
13E ARG* 4.0 19.3 - - + -
72E LEU* 4.7 6.1 - - + -
76E GLY 2.9 15.7 + - - +
77E LYS* 3.8 5.8 - - - +
79E GLU* 1.3 73.5 - - - +
81E HIS* 1.3 65.7 - - - +
83E TRP* 3.4 21.1 + - + +
84E LEU* 3.0 46.3 + - + +
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Residues in contact with HIS 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 LYS 2.9 17.8 + - - +
78E GLN* 3.3 17.7 + - - +
80E LEU* 1.3 76.0 - - - +
82E ASP* 1.3 68.9 + - - +
84E LEU* 3.1 21.8 + - - +
85E ILE* 3.2 45.8 + - + +
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Residues in contact with ASP 82 (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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78E GLN* 3.0 46.6 + - - +
79E GLU* 3.7 11.6 - - - +
80E LEU 3.4 0.2 - - - -
81E HIS* 1.3 78.7 - - - +
83E TRP* 1.3 61.1 + - - +
85E ILE* 3.8 10.3 + - - +
86E ARG* 3.3 24.3 + - - +
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Residues in contact with TRP 83 (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* 5.6 5.0 + - - +
3E VAL* 4.8 17.8 - - + +
6E TYR* 3.4 78.5 - + + +
7E ALA* 5.2 1.6 - - - -
79E GLU 3.3 4.2 + - - +
80E LEU* 3.7 20.0 - - + +
81E HIS 3.2 0.2 - - - -
82E ASP* 1.3 77.8 - - - +
84E LEU* 1.3 95.4 + - + +
85E ILE 3.5 0.2 + - - -
86E ARG* 3.5 19.2 + - - +
88E GLN* 4.1 20.4 - - - +
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Residues in contact with LEU 84 (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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13E ARG* 6.3 2.2 - - - -
80E LEU* 3.0 41.5 + - + +
81E HIS* 3.1 11.4 + - - +
83E TRP* 1.3 104.3 - - + +
85E ILE* 1.3 64.5 + - + +
86E ARG 3.6 4.3 + - - +
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Residues in contact with ILE 85 (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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81E HIS* 3.2 45.2 + - + +
82E ASP* 4.0 10.5 - - - +
84E LEU* 1.3 81.0 - - + +
86E ARG* 1.3 64.5 + - - +
87E HIS* 3.5 19.1 + - - -
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Residues in contact with ARG 86 (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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82E ASP 3.3 18.8 + - - +
83E TRP* 3.8 11.3 - - - +
84E LEU 3.4 4.9 - - - +
85E ILE* 1.3 77.9 - - - +
87E HIS* 1.3 62.2 + - - +
88E GLN* 3.1 26.3 + - - -
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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