Contacts of the strand formed by residues 81 - 90 (chain E) in PDB entry 5BRR
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67E ILE* 3.8 0.4 - - - -
68E LEU* 2.9 40.1 + - + +
79E GLU 4.2 6.3 + - - +
80E GLU* 1.3 81.5 - - - +
82E LYS* 1.3 60.1 + - - +
83E PHE* 3.5 23.5 - - + -
111E CYS 4.6 0.3 - - - +
112E ALA* 3.4 8.0 - - - -
113E GLN* 2.9 51.2 + - - +
115E SER* 4.1 8.7 + - - -
118E VAL* 3.2 26.0 - - + +
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Residues in contact with LYS 82 (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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65E THR* 5.3 4.9 - - - +
66E VAL 3.5 4.5 - - - +
67E ILE* 3.1 32.8 - - + -
70E ARG* 4.6 3.4 - - - +
76E PRO* 5.5 3.4 - - - +
80E GLU* 4.2 20.0 + - + +
81E GLN* 1.3 70.9 - - - +
83E PHE* 1.3 75.2 + - - +
304E GOL 3.9 22.0 + - - +
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Residues in contact with PHE 83 (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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65E THR* 3.3 8.9 - - - -
66E VAL* 2.8 40.1 + - - +
68E LEU* 4.0 14.4 - - + -
81E GLN* 3.5 36.6 - - + -
82E LYS* 1.3 82.0 - - - +
84E GLU* 1.3 63.8 - - - +
108E LEU* 3.8 40.6 - - + -
109E LYS 4.2 11.4 - - - -
110E SER* 4.8 4.3 - - - -
111E CYS* 3.4 28.0 - - + -
112E ALA* 3.2 22.4 - - - -
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Residues in contact with GLU 84 (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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36E LYS* 5.3 3.8 - - - +
62E HIS* 3.8 26.3 - - - +
64E LEU 4.1 8.1 - - - +
65E THR* 4.9 3.6 - - + +
83E PHE* 1.3 78.1 - - - +
85E VAL* 1.3 56.1 + - - +
108E LEU 3.7 0.7 - - - -
109E LYS* 2.7 77.2 + - + +
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Residues in contact with VAL 85 (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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33E ILE* 5.8 0.2 - - + -
61E PRO* 3.9 25.6 - - + +
64E LEU* 3.4 39.0 + - + +
66E VAL* 3.9 26.0 - - + -
84E GLU* 1.3 73.9 - - - +
86E GLU* 1.3 62.9 + - - +
87E LYS 3.5 29.8 - - - +
88E TYR 4.4 0.2 - - - +
106E LEU* 4.1 21.1 - - + -
107E GLN 3.7 6.7 - - - +
108E LEU* 4.6 2.5 - - + +
109E LYS* 3.3 17.3 + - - -
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Residues in contact with GLU 86 (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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61E PRO* 3.6 14.3 - - - +
85E VAL* 1.3 72.8 - - - +
87E LYS* 1.3 66.3 + - + +
107E GLN* 2.8 35.7 + - - +
108E LEU 4.1 1.7 - - - +
109E LYS* 3.4 51.9 + - + +
110E SER 4.4 8.3 + - - +
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Residues in contact with LYS 87 (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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51E TRP* 4.6 9.9 - - + -
61E PRO* 4.0 9.6 - - + -
85E VAL* 3.5 7.4 - - - +
86E GLU* 1.3 86.3 - - + +
88E TYR* 1.3 65.1 + - - +
89E ILE* 4.0 28.5 - - + +
107E GLN* 2.8 54.7 + - + +
241E ASN 5.6 0.4 + - - -
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Residues in contact with TYR 88 (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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59E PHE* 3.6 40.5 - + + +
60E PHE* 2.3 64.7 + + - +
61E PRO* 4.1 19.6 - - + +
64E LEU* 3.7 21.8 - - + -
85E VAL* 4.8 0.2 - - + -
87E LYS* 1.3 78.0 - - - +
89E ILE* 1.3 65.8 + - - +
90E VAL* 4.1 15.7 + - + -
104E ALA* 5.6 0.9 - - + -
105E LEU 3.2 10.3 - - - +
106E LEU* 3.5 19.1 - - + -
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Residues in contact with ILE 89 (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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51E TRP* 4.5 7.9 - - + -
87E LYS* 4.0 29.2 - - + +
88E TYR* 1.3 77.4 - - - +
90E VAL* 1.3 72.2 + - - +
91E HIS 3.6 0.7 + - - -
104E ALA* 3.5 4.1 - - - -
105E LEU* 2.8 40.5 + - + +
237E TRP* 3.7 11.5 - - + -
241E ASN* 3.5 46.4 - - + +
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Residues in contact with VAL 90 (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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56E ALA* 4.2 23.6 - - + +
59E PHE* 4.1 26.2 - - + -
60E ARG* 3.7 40.6 - - + +
88E TYR* 4.0 12.7 + - + -
89E ILE* 1.3 83.5 - - - +
91E HIS* 1.3 78.6 + - - +
92E LYS* 3.5 3.1 + - - -
94E PHE* 4.2 9.0 - - + -
103E ILE 4.3 3.6 - - - -
104E ALA* 4.4 4.0 - - + -
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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