Contacts of the strand formed by residues 81 - 90 (chain B) in PDB entry 4BNR
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 GLN 81 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ILE* 3.7 3.6 - - - +
67B VAL* 3.3 4.0 - - - -
68B ALA* 2.8 40.9 + - + +
79B SER 4.0 5.7 + - - +
80B GLU* 1.3 77.4 - - - +
82B ILE* 1.3 62.0 + - - +
83B ILE* 4.0 7.7 + - + +
111B SER 4.6 1.6 - - - +
112B LEU* 3.5 23.1 - - + -
113B THR* 2.8 53.6 + - - -
115B ASN* 3.9 10.1 - - - +
118B VAL* 3.7 16.5 - - - +
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Residues in contact with ILE 82 (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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65B GLN* 3.1 41.5 - - - +
66B ILE 3.5 6.1 - - - +
67B VAL* 4.2 19.1 - - + -
80B GLU* 4.3 9.6 + - + +
81B GLN* 1.3 77.2 - - - +
83B ILE* 1.3 66.8 + - - +
84B THR* 6.3 0.7 - - + -
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Residues in contact with ILE 83 (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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65B GLN* 4.0 3.4 - - - -
66B ILE* 2.9 42.6 + - + +
81B GLN* 4.6 6.7 - - + +
82B ILE* 1.3 85.7 - - - +
84B THR* 1.3 70.3 + - - +
108B LEU* 3.8 7.4 - - + -
109B SER* 3.9 2.9 - - - +
110B GLY* 3.5 33.7 - - - +
111B SER 3.9 10.1 - - - +
112B LEU* 3.7 48.0 - - + +
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Residues in contact with THR 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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36B THR* 5.7 2.5 - - + +
64B LEU 3.3 14.1 - - - +
65B GLN* 3.9 12.8 - - + +
82B ILE* 6.3 0.2 - - + -
83B ILE* 1.3 78.5 - - - +
85B VAL* 1.3 65.4 + - - +
108B LEU* 3.6 2.6 - - - -
109B SER* 2.8 52.0 + - - -
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Residues in contact with VAL 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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33B PHE* 4.0 24.7 - - + -
61B PRO* 3.7 19.9 - - + +
64B LEU* 2.9 25.6 + - + +
65B GLN* 4.2 7.0 - - - -
66B ILE* 4.2 15.0 - - + -
84B THR* 1.3 78.8 + - - +
86B SER* 1.3 62.9 + - - +
87B LYS 3.6 17.5 - - - +
88B ILE* 4.0 18.8 - - + -
106B LEU* 4.1 15.7 - - + -
107B LYS 3.5 13.2 - - - +
108B LEU* 4.4 3.8 - - + +
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Residues in contact with SER 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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60B GLU* 3.6 8.0 - - - +
61B PRO* 3.2 17.3 - - - +
84B THR* 3.8 1.6 + - - -
85B VAL* 1.3 73.7 - - - +
87B LYS* 1.3 64.4 + - - +
107B LYS* 3.0 23.6 + - - +
108B LEU 3.4 12.8 + - - -
109B SER* 3.9 20.8 - - - -
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Residues in contact with LYS 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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51B TYR* 5.5 2.1 + - - -
60B TYR* 3.6 44.9 + - + +
61B PRO* 3.8 1.8 - - - +
85B VAL* 3.6 4.6 - - - +
86B SER* 1.3 85.3 + - - +
88B ILE* 1.3 71.0 + - - +
89B ILE* 4.0 28.4 + - - +
106B LEU 3.7 0.2 - - - -
107B LYS* 2.8 55.4 + - + +
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Residues in contact with ILE 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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59B VAL* 3.7 35.0 - - + -
60B TYR* 2.8 86.2 + - + +
61B PRO* 3.9 20.9 - - + -
64B LEU* 4.0 8.3 - - + -
85B VAL* 4.0 7.4 - - + -
87B LYS* 1.3 81.8 - - - +
89B ILE* 1.3 64.1 + - - +
90B LEU 3.9 5.2 + - - +
104B SER* 4.6 0.4 - - - -
105B LEU 3.5 8.1 - - - +
106B LEU* 4.0 12.8 - - + -
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Residues in contact with ILE 89 (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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51B TYR* 3.8 24.2 - - + +
87B LYS* 4.0 25.8 - - + +
88B ILE* 1.3 73.9 - - - +
90B LEU* 1.3 61.5 + - - +
92B GLU* 5.8 0.7 - - - +
104B SER* 3.2 5.1 - - - -
105B LEU* 2.8 44.7 + - + +
107B LYS* 5.4 0.9 - - + +
238B TRP* 3.6 15.4 - - + -
242B ASN* 3.4 47.8 - - + +
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Residues in contact with LEU 90 (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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56B GLY* 3.6 37.5 - - - +
59B VAL* 3.9 7.9 - - + -
60B TYR* 3.4 54.6 + - + +
88B ILE* 3.8 4.4 + - - +
89B ILE* 1.3 78.3 - - - +
91B HIS* 1.3 80.2 + - - +
92B GLU* 3.1 6.6 + - - +
94B PHE* 3.9 28.3 - - + -
103B ILE 3.8 3.8 - - - +
104B SER* 3.9 3.6 - - - -
238B TRP* 4.3 0.9 - - - -
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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