Contacts of the strand formed by residues 49 - 52 (chain R) in PDB entry 2X86
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 ASP 49 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94Q TYR* 2.4 33.8 + - - -
98Q LYS* 3.0 29.6 + - - +
146Q LEU* 4.6 2.7 - - - -
150Q TYR* 4.5 9.4 - - + -
1R MET* 6.1 1.1 - - + -
27R ILE 3.3 3.0 + - - +
28R LEU* 3.6 21.4 - - + +
29R VAL 3.0 22.3 + - - -
47R ILE* 3.6 12.1 - - - +
48R ALA* 1.3 85.0 - - + +
50R TYR* 1.3 72.2 + - - +
51R MET* 4.3 7.4 - - - +
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Residues in contact with TYR 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87Q LYS* 5.9 0.6 - - - -
90Q MET* 4.1 35.4 - - + -
94Q TYR* 3.6 13.3 + + + -
95Q GLN* 4.0 9.0 - - - +
98Q LYS* 4.2 0.9 + - - -
142Q TYR* 5.7 1.1 - + - -
146Q LEU* 3.6 22.7 - - + -
8R ALA* 5.0 1.3 - - + -
28R LEU* 4.1 1.3 - - - -
29R VAL* 3.4 24.7 - - + -
31R ASP* 3.2 42.6 + - + +
33R LEU* 3.3 36.0 + - + +
42R LEU* 4.7 8.3 - - + -
47R ILE* 4.8 2.7 - - + -
49R ASP* 1.3 91.3 + - - +
51R MET* 1.3 80.9 + - - +
52R ASP* 3.9 7.3 + - + -
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Residues in contact with MET 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95Q GLN* 5.4 6.5 - - - +
98Q LYS* 5.2 4.5 - - - +
28R LEU* 4.0 23.1 - - + -
29R VAL 2.9 7.7 + - - +
30R VAL* 3.2 11.1 - - + -
31R ASP 3.1 23.2 + - - +
49R ASP* 4.3 11.2 - - - +
50R TYR* 1.3 82.7 - - - +
52R ASP* 1.3 73.9 + - - +
55R ASP* 4.0 7.4 - - + +
56R PHE* 4.0 32.8 - - - +
59R GLN* 4.1 25.6 - - - +
66R PHE* 4.3 15.0 - - + -
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Residues in contact with ASP 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87Q LYS* 3.6 37.9 + - + +
91Q ASP* 5.1 6.1 - - - +
30R VAL* 4.2 0.4 - - - -
31R ASP 3.3 10.9 - - - +
32R ASN* 3.8 13.7 - - - +
33R LEU 4.6 0.9 + - - -
50R TYR* 3.9 10.3 + - + -
51R MET* 1.3 77.0 - - - +
53R LYS* 1.3 70.4 + - - +
54R GLU* 2.9 33.7 + - - +
55R ASP* 3.1 21.5 + - - +
56R PHE* 3.0 20.6 + - - +
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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