Contacts of the strand formed by residues 70 - 73 (chain O) in PDB entry 5A0Q
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 70 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68O HIS* 3.0 38.4 - - + -
69O LEU* 1.3 78.7 - - - +
71O LYS* 1.3 61.9 + - - +
72O ILE* 3.8 18.6 - - + -
77O GLY* 3.2 13.3 - - - -
78O CYS* 3.2 17.7 + - - +
80O MET* 4.2 20.4 - - + -
87O SER* 4.7 1.8 - - - -
88O ARG* 3.9 37.2 - - - -
91O VAL* 3.7 37.2 - - + -
95O ARG* 5.2 6.1 - - - -
227O PHE* 3.1 21.4 - - - -
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Residues in contact with LYS 71 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70O PHE* 1.3 73.6 - - - +
72O ILE* 1.3 58.5 + - - +
73O THR 3.2 15.9 - - - +
74O GLU* 4.1 20.6 - - - +
76O ILE 3.7 3.4 - - - -
95O ARG* 3.4 12.6 + - - +
227O PHE* 4.2 24.7 - - + +
67V SER* 4.8 6.3 + - - -
68V ILE* 3.0 54.2 - - + +
71V ASN* 3.8 25.6 + - - +
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Residues in contact with ILE 72 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70O PHE* 3.8 6.3 - - + -
71O LYS* 1.3 71.5 - - - +
73O THR* 1.3 67.7 + - - +
76O ILE* 3.0 13.4 + - + +
77O GLY 4.4 1.1 - - - +
78O CYS* 3.6 41.1 - - + +
91O VAL* 3.7 38.6 - - + +
94O ALA* 3.5 38.8 - - + +
95O ARG* 3.3 21.3 - - + +
98O ALA* 4.1 4.4 - - + +
114O LEU* 5.1 8.5 - - + -
138O MET* 5.1 1.3 - - + -
140O LEU* 6.3 0.9 - - + -
68V ILE* 4.1 6.9 - - - +
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Residues in contact with THR 73 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71O LYS* 3.2 12.0 - - - +
72O ILE* 1.3 78.3 + - - +
74O GLU* 1.3 70.4 + - + +
75O ASN* 4.2 15.9 - - - +
76O ILE* 2.6 48.3 + - + +
98O ALA* 3.2 27.8 - - + +
102O LYS* 6.0 6.1 - - - -
108O GLU* 5.0 5.2 - - + -
109O ILE* 5.7 0.7 - - + -
68V ILE* 4.1 13.9 - - + -
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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