Contacts of the helix formed by residues 73 - 81 (chain E) in PDB entry 6NRB
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 ASP 73 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72E ASN* 1.3 85.9 - - - +
74E GLY* 1.3 53.4 + - - +
75E ALA 2.8 2.1 + - - -
76E THR* 2.5 35.3 + - - +
77E ILE* 4.6 0.2 - - - +
103E GLY 5.1 2.5 - - - +
104E ASP* 5.3 1.4 - - - +
106E THR* 3.8 8.7 - - + +
107E THR* 4.6 15.2 + - - +
176E LYS* 3.0 33.2 + - - -
400E ARG* 2.3 52.9 + - + +
404E ASP* 3.8 5.3 - - - +
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Residues in contact with GLY 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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48E MET* 3.5 26.2 - - - -
73E ASP* 1.3 69.3 - - - +
75E ALA* 1.3 51.9 + - - +
77E ILE* 2.8 16.4 + - - -
78E LEU* 2.1 45.9 + - - +
106E THR* 3.5 9.6 - - - +
107E THR* 3.7 10.1 - - - +
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Residues in contact with ALA 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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73E ASP 2.8 3.4 + - - -
74E GLY* 1.3 70.6 - - - +
76E THR* 1.3 49.6 + - - +
78E LEU* 4.0 7.6 - - - -
79E SER* 2.5 44.5 + - - +
91E MET 4.5 1.1 - - - -
92E VAL* 4.2 8.1 - - - +
95E SER* 3.5 29.8 - - - +
96E LYS* 3.9 8.5 - - + +
99E ASP* 5.2 5.4 - - + +
106E THR* 3.1 23.0 - - + +
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Residues in contact with THR 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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71E THR* 5.1 4.0 - - + -
72E ASN 3.4 10.1 - - - +
73E ASP* 2.5 16.8 + - + -
75E ALA* 1.3 72.8 - - - +
77E ILE* 1.3 58.9 + - - +
79E SER* 3.0 8.6 + - - -
80E MET* 2.8 47.3 + - + +
99E ASP* 4.6 0.5 + - - -
400E ARG* 3.2 35.5 + - + +
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Residues in contact with ILE 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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521B ILE* 3.5 25.8 - - + -
59E LYS* 3.6 34.1 - - + +
61E MET* 3.6 23.1 - - + -
71E THR* 3.0 27.4 - - - +
72E ASN 3.3 15.7 + - - +
74E GLY* 2.8 28.8 + - - +
76E THR* 1.3 78.4 - - - +
78E LEU* 1.3 53.7 + - + +
80E MET* 3.6 10.3 - - + -
81E MET* 2.5 34.0 + - - +
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Residues in contact with LEU 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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18B GLU* 4.6 2.7 - - - +
521B ILE* 5.5 1.1 - - + -
44E VAL* 3.6 26.7 - - + -
48E MET* 3.5 25.1 - - + -
59E LYS* 4.9 2.9 - - - +
74E GLY* 2.1 41.7 + - - +
75E ALA* 3.9 3.1 - - - +
77E ILE* 1.3 68.7 - - + +
79E SER* 1.3 55.1 + - - +
81E MET* 2.6 42.2 - - + +
83E VAL* 4.0 3.9 - - + +
88E ALA* 5.7 0.9 - - + +
91E MET* 3.4 39.5 - - + +
92E VAL* 3.1 28.3 - - + +
95E SER* 4.4 0.9 - - - +
110E VAL* 3.9 4.7 - - + -
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Residues in contact with SER 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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75E ALA* 2.5 28.6 + - - +
76E THR* 3.3 7.2 - - - -
78E LEU* 1.3 71.8 - - - +
80E MET* 1.3 65.3 + - - +
81E MET 3.3 6.2 - - - +
82E ASP* 4.6 2.4 - - - +
92E VAL* 3.4 21.0 - - - +
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Residues in contact with MET 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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61E MET* 3.1 45.8 - - + +
63E ASP* 5.1 2.9 - - - +
69E THR* 4.3 4.0 - - + +
71E THR* 3.4 38.8 - - + -
76E THR* 2.8 28.9 + - + +
77E ILE* 3.5 15.5 - - + +
79E SER* 1.3 73.7 - - - +
81E MET* 1.3 64.3 + - - +
82E ASP* 3.2 12.0 + - - +
396E GLU* 4.8 10.5 - - - +
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Residues in contact with MET 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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16B ALA* 3.4 27.4 - - - +
18B GLU* 3.3 29.6 - - + +
521B ILE* 3.9 11.3 - - + +
40E ALA* 5.5 5.8 - - + -
44E VAL* 3.6 25.1 - - + -
77E ILE 2.5 20.9 + - - +
78E LEU* 2.6 41.4 - - + +
79E SER 3.3 5.2 - - - +
80E MET* 1.3 73.7 - - - +
82E ASP* 1.3 75.7 + - - +
83E VAL* 3.5 5.8 + - + +
84E ASP 6.1 0.2 - - - +
88E ALA* 4.9 11.0 - - + -
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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