Contacts of the strand formed by residues 81 - 90 (chain E) in PDB entry 3PB1
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 MET 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 TYR* 3.5 9.7 - - - -
68E LEU* 3.0 30.6 + - + +
79E GLY 4.2 3.1 - - - +
80E GLU* 1.3 78.3 - - - +
82E LYS* 1.3 60.5 + - - +
83E PHE* 3.4 35.8 - - + -
110E ARG* 4.7 19.3 - - - +
111E CYS 4.6 1.8 - - - +
112E ALA* 3.6 3.8 - - + -
113E GLN* 3.1 49.8 - - - +
118E ILE* 3.3 32.7 - - + +
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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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36E ARG* 5.0 6.1 - - - +
65E ILE* 3.7 42.1 - - + +
66E VAL 3.8 2.7 - - - -
67E TYR* 3.5 29.4 + - + +
80E GLU* 4.5 0.4 + - - +
81E MET* 1.3 72.7 - - - +
83E PHE* 1.3 68.5 + - - +
84E GLU* 6.5 0.7 - - - -
110E SER* 3.8 21.3 + - - -
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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 ILE* 3.6 9.4 - - - +
66E VAL* 2.8 43.3 + - + +
68E LEU* 3.6 23.1 - - + -
81E MET* 3.4 58.3 - - + -
82E LYS* 1.3 78.4 - - - +
84E GLU* 1.3 62.2 + - - +
108E ILE* 3.7 44.6 - - + -
109E ARG 3.7 7.0 - - - -
110E SER* 3.5 41.7 - + + +
111E CYS 3.9 6.5 - - - -
112E ALA* 3.9 4.3 - - - -
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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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64E TYR 4.4 7.6 - - - +
82E LYS* 6.5 0.9 - - - -
83E PHE* 1.3 77.3 - - - +
85E VAL* 1.3 65.7 + - - +
86E GLU 3.7 0.6 + - - -
108E ILE* 3.4 5.7 - - - +
109E ARG* 2.9 54.3 + - + +
110E SER* 4.0 34.7 + - - +
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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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62E LYS* 3.2 38.4 + - + +
64E TYR* 4.0 23.8 + - + +
66E VAL* 3.7 30.1 - - + -
84E GLU* 1.3 75.8 - - - +
86E GLU* 1.3 58.8 + - - +
87E ASN 3.5 29.8 - - - +
88E LEU* 4.1 14.6 - - + +
106E LEU* 3.9 16.2 - - + -
107E LYS 3.3 10.5 - - - +
108E ILE* 5.0 0.7 - - + -
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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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62E LYS* 3.2 21.3 + - - +
84E GLU* 3.7 1.8 + - - -
85E VAL* 1.3 73.0 - - - +
87E ASN* 1.3 61.5 + - + +
107E LYS* 2.7 54.5 + - + +
108E ILE 4.6 1.6 - - - +
109E ARG* 3.3 43.0 - - + +
244E GLU* 5.3 0.5 - - - +
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Residues in contact with ASN 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* 4.5 3.2 - - + -
62E LYS* 4.2 4.9 - - - +
85E VAL* 3.3 6.5 + - - +
86E GLU* 1.3 82.2 - - + +
88E LEU* 1.3 66.4 + - - +
89E ILE* 3.4 20.0 + - - +
105E LEU 3.6 1.9 - - - +
106E LEU* 3.5 2.9 - - - -
107E LYS* 2.9 43.6 + - + -
244E GLU* 3.9 36.2 - - - +
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Residues in contact with LEU 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* 4.0 22.9 - - + -
60E PRO* 3.6 28.6 - - + +
62E LYS* 4.0 20.7 - - + +
64E TYR* 3.8 33.0 - - + -
85E VAL* 4.1 4.0 - - + +
87E ASN* 1.3 76.8 + - - +
89E ILE* 1.3 63.1 + - - +
90E LEU* 3.7 25.9 + - + +
105E LEU 3.6 2.0 - - - +
106E LEU* 3.8 27.8 - - + -
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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* 3.9 15.5 - - + -
87E ASN* 3.4 20.2 - - - +
88E LEU* 1.3 71.1 - - - +
90E LEU* 1.3 72.6 + - - +
104E ALA* 3.3 7.6 - - - +
105E LEU* 2.8 45.9 + - + +
237E TRP* 3.9 13.3 - - + -
241E HIS* 3.6 56.5 - - + +
244E GLU 3.8 16.4 - - - -
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Residues in contact with LEU 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 THR* 3.6 17.5 - - + +
59E PHE* 3.7 31.0 - - + -
60E ILE* 4.0 58.8 - - + +
88E LEU* 3.7 25.9 + - + +
89E ILE* 1.3 85.4 - - - +
91E HIS* 1.3 66.0 + - - +
92E LYS* 3.5 3.5 + - - +
104E ALA* 4.1 4.5 - - + -
237E TRP* 4.1 3.6 + - - -
241E HIS* 5.8 0.5 + - - -
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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