Contacts of the helix formed by residues 68 - 76 (chain E) in PDB entry 2RHB
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 GLU 68 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66E VAL 3.5 0.6 + - - -
67E PRO* 1.3 74.8 - - - +
69E ILE* 1.3 68.4 + - - +
70E LYS* 3.2 21.8 - - + -
71E ILE* 2.9 30.9 + - + +
72E LEU* 3.4 4.6 + - - +
157E PRO* 6.1 0.9 - - - +
159E GLN* 3.9 11.9 + - - +
160E ALA* 4.7 4.8 - - - +
161E SER* 4.4 24.6 - - - +
166E THR* 3.4 29.4 + - - +
197E SER* 2.9 31.1 + - - -
272E ASP* 4.3 9.0 - - - +
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Residues in contact with ILE 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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66E VAL* 6.5 0.2 - - + -
67E PRO 5.0 2.2 - - - +
68E GLU* 1.3 72.4 - - - +
70E LYS* 1.3 52.2 + - - +
72E LEU* 3.0 11.9 + - + +
73E ASN* 2.7 59.7 + - - +
85E ILE* 4.2 15.0 - - + -
86E TRP 3.9 21.5 - - - +
87E ASP* 3.9 28.9 - - + +
88E TYR 5.2 0.4 - - - +
94E ALA* 3.7 25.4 - - + +
161E SER* 6.3 2.0 - - - -
271E MET* 5.4 2.0 - - + -
272E ASP* 4.5 15.9 + - + +
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Residues in contact with LYS 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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68E GLU* 3.4 20.6 - - + -
69E ILE* 1.3 77.9 - - - +
71E ILE* 1.3 60.8 + - + +
73E ASN* 4.2 6.5 - - - -
74E ASN* 2.7 43.4 + - - +
195E THR* 2.9 20.7 + - - +
197E SER* 2.8 36.5 + - - +
272E ASP* 3.4 29.5 + - - +
273E SER* 3.7 38.4 + - - +
274E THR* 4.0 7.2 + - - +
323E ASP* 3.7 15.0 - - - +
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Residues in contact with ILE 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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67E PRO* 4.7 1.3 - - + -
68E GLU* 2.9 28.0 + - + +
70E LYS* 1.3 80.8 - - + +
72E LEU* 1.3 56.7 + - - +
74E ASN* 4.0 4.6 - - - +
75E LEU* 3.1 35.0 + - + +
157E PRO* 4.1 26.7 - - + -
178E TYR* 3.4 39.3 - - + +
194E PHE* 4.3 4.7 - - + -
323E ASP* 3.7 36.9 - - + +
324E TYR* 4.2 11.4 - - + -
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Residues in contact with LEU 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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67E PRO* 3.8 27.1 - - + +
68E GLU 3.9 6.3 - - - +
69E ILE* 3.0 20.2 + - + +
71E ILE* 1.3 75.0 - - - +
73E ASN* 1.3 62.9 + - - +
75E LEU* 3.1 2.9 + - + -
76E GLY 2.9 25.8 + - - -
77E VAL* 3.0 31.0 + - + -
85E ILE* 3.9 32.5 - - + -
95E HIS* 4.3 15.3 - - + +
122E LEU* 3.8 32.5 - - + -
141E VAL* 5.6 0.4 - - + -
178E TYR* 5.4 4.7 - - + +
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Residues in contact with ASN 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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69E ILE* 2.7 44.8 + - - +
70E LYS* 3.7 6.1 - - - +
72E LEU* 1.3 74.0 - - - +
74E ASN* 1.3 65.0 + - - +
76E GLY* 3.5 11.1 + - - +
77E VAL 5.0 6.7 - - - +
94E ALA* 5.1 6.2 - - - +
95E HIS* 5.3 3.3 + - - -
271E MET* 4.8 10.7 - - - +
272E ASP 4.2 11.5 + - - -
273E SER* 5.9 1.7 - - - -
36F ASP* 4.3 31.6 + - - +
38F ILE* 5.6 6.2 - - - +
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Residues in contact with ASN 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 LYS* 2.7 25.7 + - - +
71E ILE 4.0 2.0 - - - +
73E ASN* 1.3 79.0 - - - +
75E LEU* 1.3 62.2 + - - +
76E GLY 3.3 0.4 + - - -
180E LYS* 5.4 1.0 + - - -
273E SER* 5.7 2.4 - - - -
274E THR* 2.6 33.9 + - - -
323E ASP* 3.0 32.7 + - - +
324E TYR 3.9 10.4 - - - +
325E ALA* 3.4 26.4 - - + +
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Residues in contact with LEU 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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71E ILE* 3.1 19.8 + - + +
72E LEU* 3.1 8.1 + - + +
74E ASN* 1.3 78.5 - - - +
76E GLY* 1.3 60.9 + - - +
77E VAL* 3.4 2.2 + - + -
120E THR* 4.4 1.6 + - - +
141E VAL* 4.2 25.2 - - + +
178E TYR* 3.5 38.4 - - + -
180E LYS* 3.2 42.6 + - + +
189E LEU* 4.8 10.8 - - + -
324E TYR* 3.2 45.1 - - + +
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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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72E LEU 2.9 4.7 + - - -
73E ASN* 3.5 7.8 + - - -
74E ASN 3.3 4.4 + - - -
75E LEU* 1.3 78.3 - - - +
77E VAL* 1.3 65.1 + - - +
78E ASP* 3.3 14.0 + - - +
120E THR* 3.2 19.4 + - - -
180E LYS* 5.4 0.2 - - - -
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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