Contacts of the strand formed by residues 70 - 75 (chain F) in PDB entry 2BX5
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 70 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22F THR* 5.5 0.2 - - - +
23F CYS 4.7 1.2 + - - +
24F ARG* 3.6 25.6 + - + +
66F GLY* 3.8 18.5 - - - -
67F SER 3.8 6.5 + - - +
69F THR* 1.3 79.1 - - - +
71F PHE* 1.3 75.6 + - - +
72F THR* 4.1 10.4 + - - -
18G ARG* 2.7 43.1 + - - -
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Residues in contact with PHE 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F MET* 5.0 2.5 - - + -
21F ILE 3.8 0.2 - - - +
22F THR* 3.3 5.4 - - - +
23F CYS* 2.9 47.0 + - + +
29F ILE* 3.7 25.6 - - + -
31F SER* 4.6 7.6 - - - -
33F LEU* 3.4 43.7 - - + -
35F TRP* 4.8 2.0 - - + -
51F ALA* 4.8 9.2 - - - -
65F SER 3.7 8.3 - - - -
66F GLY 3.0 27.6 - - - -
67F SER* 3.9 12.8 - - - -
68F GLY 3.7 22.9 - - - -
69F THR 3.5 14.6 - - - -
70F ASP* 1.3 89.7 - - - +
72F THR* 1.3 66.6 + - - +
73F LEU 4.2 1.1 - - - -
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Residues in contact with THR 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F THR* 3.4 25.1 - - + -
21F ILE 3.1 14.4 - - - +
22F THR* 3.6 15.8 - - + +
35F TRP* 4.6 1.5 - - - +
63F SER 3.3 6.1 - - - +
64F GLY* 4.5 0.4 - - - -
65F SER* 3.1 44.7 + - - +
70F ASP* 4.1 7.6 + - - -
71F PHE* 1.3 80.8 + - - +
73F LEU* 1.3 71.2 + - - +
74F THR* 3.8 6.1 + - - +
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Residues in contact with LEU 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F THR 3.7 0.3 - - - -
21F ILE* 2.9 61.2 + - + +
35F TRP* 3.4 48.2 - - + +
47F LEU* 5.2 3.6 - - + -
48F ILE* 4.1 14.8 - - + -
62F PHE* 4.1 15.9 - - + -
63F SER 3.5 3.6 - - - -
64F GLY* 4.6 1.6 - - - -
72F THR* 1.3 76.4 - - - +
74F THR* 1.3 75.7 + - - +
75F ILE* 4.0 20.6 - - + -
86F TYR* 3.8 26.5 - - + -
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Residues in contact with THR 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ARG* 3.9 26.7 - - - -
19F VAL 3.5 5.8 - - - +
20F THR* 3.9 13.4 - - - +
61F ARG 3.3 4.2 - - - +
62F PHE* 3.4 2.9 - - - -
63F SER* 2.9 51.8 + - - +
65F SER* 5.4 1.0 + - - -
72F THR* 3.8 8.7 + - - +
73F LEU* 1.3 80.7 + - - +
75F ILE* 1.3 61.4 + - - +
76F SER* 4.4 8.5 - - - +
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Residues in contact with ILE 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F ASP 3.4 3.5 - - - +
18F ARG* 3.4 0.7 - - - -
19F VAL* 2.7 58.0 + - + +
21F ILE* 4.9 0.2 - - + -
61F ARG* 3.3 26.0 - - + +
62F PHE* 3.7 24.2 - - + -
73F LEU* 4.0 13.7 - - + -
74F THR* 1.3 75.8 - - - +
76F SER* 1.3 62.1 + - - +
77F SER 3.4 1.0 + - - -
78F LEU* 4.2 28.0 - - + +
82F ASP* 4.5 2.9 - - - +
86F TYR* 3.6 34.1 - - + +
104F VAL* 4.7 2.7 - - + -
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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