Contacts of the strand formed by residues 83 - 88 (chain B) in PDB entry 2RIO
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 PHE 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B PHE* 3.7 38.4 - + + -
29B GLY 5.9 1.8 - - - -
46B ARG* 3.7 39.7 - - + -
47B MET 3.3 19.3 - - - +
48B LEU* 3.8 21.3 - - + -
49B ILE* 3.7 8.5 - - - +
79B THR* 3.5 2.9 - - - -
80B THR* 3.0 31.3 + - - -
82B ARG* 1.3 106.3 - - + +
84B LEU* 1.3 58.7 + - - +
85B TYR* 3.6 24.4 - - + -
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LYS 3.2 3.5 - - - +
46B ARG* 3.4 2.3 - - - +
47B MET* 2.8 51.4 + - + +
48B LEU 5.0 0.4 - - - +
49B ILE* 4.0 15.7 - - + +
52B CYS* 4.4 11.4 - - + -
55B ALA* 3.3 34.5 - - + -
56B LEU* 4.3 14.6 - - + -
59B ILE* 5.7 0.4 - - + -
77B SER* 3.9 21.3 - - - +
78B GLU 3.6 4.9 - - - +
79B THR* 3.9 21.5 - - + -
83B PHE* 1.3 72.9 - - - +
85B TYR* 1.3 64.1 + - - +
86B ILE* 3.9 20.9 - - + -
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Residues in contact with TYR 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PHE 3.3 4.5 + - - -
10B GLU* 2.5 41.7 + - + -
13B LEU* 3.7 35.2 - - + -
16B LEU* 3.9 12.4 - - + +
18B VAL* 4.3 2.7 - - + -
33B PHE* 5.4 0.4 - + - -
44B VAL* 3.7 26.9 - - + -
45B LYS 3.3 4.9 - - - -
46B ARG* 3.6 26.3 - - + -
76B CYS 4.0 0.2 - - - +
77B SER* 3.2 8.7 + - - -
78B GLU 2.7 46.0 + - - +
80B THR* 4.1 1.8 - - + -
82B ARG* 3.3 22.7 + - - -
83B PHE* 3.6 21.4 - - + -
84B LEU* 1.3 76.4 - - - +
86B ILE* 1.3 61.2 + - - +
87B ALA 4.0 0.6 + - - -
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ALA 3.6 1.0 - - - +
44B VAL* 3.6 2.0 - - - -
45B LYS* 2.8 42.5 + - + +
47B MET* 3.6 29.4 - - + -
55B ALA* 4.4 0.7 - - + -
58B GLU* 4.2 12.6 - - - +
59B ILE* 3.7 26.2 - - + -
74B TYR* 3.8 15.0 - - + -
76B CYS 3.8 2.7 - - - -
77B SER* 4.8 3.4 - - - +
84B LEU* 3.9 25.4 - - + -
85B TYR* 1.3 75.5 - - - +
87B ALA* 1.3 61.4 + - - +
88B LEU* 3.6 30.2 + - + +
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 3.6 33.5 - - + +
37B PHE* 5.1 0.2 - - + -
42B VAL* 4.1 15.5 - - + -
43B ALA 3.4 5.2 - - - +
44B VAL* 4.5 2.7 - - + +
74B TYR* 3.7 2.1 - - - -
75B TYR* 2.8 38.0 + - + +
76B CYS* 2.8 23.3 + - - +
85B TYR 4.0 1.6 + - - -
86B ILE* 1.3 71.6 - - - +
88B LEU* 1.3 60.7 + - - +
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B VAL* 3.3 9.7 - - - +
43B ALA* 2.8 25.4 + - + +
45B LYS* 4.3 22.7 - - + +
62B LEU* 3.8 28.3 - - + -
72B ILE* 3.8 23.1 - - + -
73B ARG 3.4 11.4 - - - +
74B TYR* 4.1 4.0 - - + -
75B TYR* 3.7 6.5 - - - -
86B ILE* 3.6 28.0 - - + +
87B ALA* 1.3 82.4 - - - +
89B GLU* 1.3 68.5 + - - +
90B LEU 3.3 1.0 + - - -
170B SER* 5.9 2.2 - - - -
171B ASP 6.3 0.2 - - - +
2101B ADP 4.0 17.5 - - - +
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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