Contacts of the helix formed by residues 81 - 89 (chain C) in PDB entry 2BP1
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 81 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C ALA 5.4 0.2 - - - -
76C PHE 3.7 8.2 + - - -
78C TYR 2.9 7.8 + - - -
80C ASP* 1.3 75.5 - - - +
82C GLN* 1.3 59.7 + - - +
83C SER 3.4 2.9 - - - -
84C GLU* 3.7 5.1 + - - -
85C THR* 2.9 31.1 + - - -
130C ARG* 3.4 35.9 - - - -
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Residues in contact with GLN 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C MET 4.0 1.8 - - - -
49C GLY* 4.2 16.6 - - - +
79C SER* 3.0 27.2 + - - +
80C ASP 3.3 5.1 + - - -
81C GLY* 1.3 79.6 + - - +
83C SER* 1.3 59.4 + - - +
85C THR* 3.8 19.4 + - - +
86C ILE* 3.0 41.6 + - + +
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Residues in contact with SER 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C THR* 2.7 36.1 + - - -
48C MET* 3.3 17.9 - - - +
74C THR* 2.8 23.2 + - - -
78C TYR* 3.6 19.7 - - - -
79C SER* 2.8 6.4 + - - -
81C GLY 3.4 0.6 - - - -
82C GLN* 1.3 75.9 - - - +
84C GLU* 1.3 63.5 + - - +
86C ILE* 3.2 4.5 + - - +
87C LEU* 3.0 26.4 + - - +
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Residues in contact with GLU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C THR* 3.6 18.4 - - + -
75C ALA 3.3 19.9 - - - +
76C PHE* 3.3 2.4 + - - +
78C TYR 5.0 0.2 + - - -
81C GLY* 3.7 5.3 + - - +
82C GLN 3.5 0.2 - - - -
83C SER* 1.3 78.3 + - - +
85C THR* 1.3 57.9 + - - +
87C LEU* 3.2 1.5 + - - -
88C GLY 2.8 27.2 + - - -
105C THR* 2.5 22.0 + - - -
127C SER* 2.5 31.8 + - - -
130C ARG* 2.9 53.3 + - + +
131C LEU* 3.5 18.1 - - + +
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Residues in contact with THR 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C GLY 2.9 20.5 + - - -
82C GLN* 3.8 24.3 + - - +
84C GLU* 1.3 78.4 - - - +
86C ILE* 1.3 62.7 + - + +
88C GLY* 3.4 2.1 + - - -
89C GLY* 3.2 18.2 + - - -
130C ARG* 3.7 26.6 + - - +
132C GLN* 5.4 0.5 + - - -
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Residues in contact with ILE 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C MET* 4.0 7.2 - - + -
49C GLY* 3.6 33.0 - - - +
52C MET 4.5 0.2 - - - +
53C ASP* 5.1 0.4 - - - -
54C ALA* 4.1 37.2 - - + +
57C SER* 3.7 27.6 - - - +
82C GLN* 3.0 30.0 + - + +
83C SER* 3.2 4.7 + - - +
85C THR* 1.3 74.2 - - + +
87C LEU* 1.3 65.9 + - + +
89C GLY* 3.2 11.5 + - - -
90C LEU* 3.4 21.0 + - + +
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C THR* 3.8 24.0 - - + +
48C MET* 3.6 23.6 - - + -
61C VAL* 3.9 11.2 - - + -
72C LEU* 4.6 9.9 - - + -
74C THR* 3.9 24.0 - - + -
83C SER 3.0 19.2 + - - +
84C GLU 3.7 3.8 - - - +
86C ILE* 1.3 76.0 - - + +
88C GLY* 1.3 60.4 + - - +
89C GLY 3.4 0.7 + - - -
90C LEU* 3.4 37.2 + - + +
91C GLY 5.0 0.2 + - - -
92C LEU* 4.4 4.6 + - + +
94C LEU* 4.0 15.7 - - + +
103C ILE* 4.1 17.3 - - + -
131C LEU* 3.9 8.3 - - + -
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Residues in contact with GLY 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C GLU 2.8 13.3 + - - -
85C THR 3.9 0.9 - - - -
86C ILE 3.2 0.2 - - - -
87C LEU* 1.3 72.6 - - - +
89C GLY* 1.3 58.7 + - - +
90C LEU 3.4 0.7 + - - -
91C GLY* 4.5 4.0 + - - -
92C LEU 5.8 0.2 + - - -
94C LEU* 4.7 1.3 - - - -
130C ARG 3.4 20.0 - - - -
131C LEU* 3.4 20.8 - - - +
132C GLN* 3.0 28.5 + - - +
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Residues in contact with GLY 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C THR 3.2 9.2 + - - -
86C ILE 3.2 10.4 + - - -
88C GLY* 1.3 76.7 - - - +
90C LEU* 1.3 59.7 + - - +
91C GLY 3.3 6.3 + - - -
132C GLN* 3.8 11.2 - - - -
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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