Contacts of the strand formed by residues 88 - 90 (chain J) in PDB entry 2VTX
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 88 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49J THR* 4.1 13.7 - - + -
50J VAL 3.2 12.3 - - - +
51J CYS* 3.4 8.3 - - + +
81J LEU* 4.2 6.3 - - - -
86J LEU* 3.4 23.4 + - - +
87J PRO* 1.3 79.7 - - - +
89J ALA* 1.3 64.9 + - - +
90J THR* 4.3 9.0 - - - +
78K ILE 3.6 11.9 - - - +
79K ALA* 3.0 37.2 - - + -
80K THR 3.4 19.1 - - - +
81K LEU* 4.1 2.2 - - - -
86K LEU* 3.6 13.3 - - + +
89K ALA* 3.7 25.4 - - + -
91K MET* 4.0 6.1 - - + -
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Residues in contact with ALA 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88I MET* 3.5 36.1 - - + -
90I THR* 4.9 2.0 - - - +
49J THR* 3.6 3.5 - - - -
50J VAL* 2.9 33.8 + - + +
81J LEU* 4.3 4.5 - - + +
86J LEU* 5.1 1.1 - - + -
88J MET* 1.3 78.1 - - - +
90J THR* 1.3 62.4 + - - +
91J MET* 3.6 15.3 + - + +
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Residues in contact with THR 90 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I THR* 2.8 32.0 + - - +
48J ARG 3.7 10.5 - - - +
49J THR* 4.6 5.2 - - + +
88J MET* 4.3 12.6 - - - +
89J ALA* 1.3 72.2 - - - +
91J MET* 1.3 70.3 + - - +
92J VAL* 4.0 5.4 - - + -
89K ALA* 4.9 1.0 - - - +
90K THR* 2.7 31.9 + - - +
91K MET* 4.7 0.7 - - - -
92K VAL* 3.7 34.5 - - + +
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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
------------------------------------------------------------
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