Contacts of the strand formed by residues 84 - 90 (chain J) in PDB entry 2BX5
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 ALA 84 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37J GLN* 3.3 37.0 - - + -
38J GLN 3.3 17.3 - - - +
39J LYS* 3.9 5.8 - - + +
40J PRO* 4.6 3.8 - - - -
82J ASP 2.9 6.4 + - - +
83J PHE* 1.3 78.0 - - - +
85J THR* 1.3 61.8 + - - +
86J TYR* 3.3 7.0 - - + -
104J VAL* 3.0 32.8 + - - +
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Residues in contact with THR 85 (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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36J TYR 3.7 0.9 - - - +
37J GLN* 3.6 1.2 - - - -
38J GLN* 2.7 45.5 + - - +
84J ALA* 1.3 74.9 - - - +
86J TYR* 1.3 64.1 + - - +
87J TYR* 4.0 21.6 - - + +
100J GLN 5.1 0.2 - - - +
101J GLY* 3.5 27.4 - - - -
102J THR 3.6 10.1 - - - +
103J LYS* 3.3 35.0 - - + +
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Residues in contact with TYR 86 (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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6J GLN* 3.4 8.9 - - - +
21J ILE* 4.8 8.3 - - + -
35J TRP* 4.9 1.8 - - + -
36J TYR 3.4 4.3 - - - +
37J GLN* 3.2 27.6 + - + -
47J LEU* 3.2 35.2 - - + -
62J PHE* 3.2 24.5 - + - -
73J LEU* 3.8 24.5 - - + -
75J ILE* 4.0 12.3 - - + -
82J ASP* 3.1 27.7 + - - +
84J ALA 3.3 21.8 - - - -
85J THR* 1.3 74.8 - - - +
87J TYR* 1.3 60.6 + - - +
101J GLY* 3.2 2.4 - - - -
102J THR* 3.1 26.7 + - - +
104J VAL* 3.3 28.5 - - + -
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Residues in contact with TYR 87 (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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6J GLN* 3.3 3.6 - - - +
34J ASN 3.4 1.0 - - - +
35J TRP* 3.3 6.4 - - - -
36J TYR* 3.1 36.5 + - + +
38J GLN* 4.2 24.6 + - + -
44J PRO* 5.6 7.0 - - + -
85J THR* 4.0 26.7 - - + +
86J TYR* 1.3 76.9 - - - +
88J CYS* 1.3 61.1 + - - +
89J GLN 3.7 0.3 + - - -
98J PHE* 4.5 23.3 - + + -
99J GLY 4.0 8.5 - - - +
100J GLN* 3.3 34.6 + - - -
101J GLY* 3.3 17.0 - - - -
103J LYS* 5.7 4.5 - - - -
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Residues in contact with CYS 88 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4J MET* 4.0 3.4 - - - +
6J GLN* 3.0 32.3 - - - +
23J CYS* 2.0 54.3 - - + -
33J LEU* 3.6 14.1 - - + -
34J ASN 3.3 4.3 - - - -
35J TRP* 3.8 11.9 - - + -
87J TYR* 1.3 72.8 - - - +
89J GLN* 1.3 57.3 + - - +
98J PHE 3.0 3.6 - - - +
99J GLY* 2.7 31.4 + - - +
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Residues in contact with GLN 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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33J LEU* 3.4 9.0 - - - +
34J ASN* 2.5 53.2 + - - +
36J TYR* 3.3 36.5 + - + -
87J TYR 3.7 0.8 + - - -
88J CYS* 1.3 72.6 - - - +
90J GLN* 1.3 69.0 + - - +
91J SER* 3.6 3.7 + - - -
96J ASN* 3.6 30.2 + - - +
97J THR 3.8 4.0 - - - +
98J PHE* 3.8 35.0 - - + +
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Residues in contact with GLN 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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2J ILE* 3.1 18.0 - - + +
4J MET* 3.5 22.6 - - + +
29J ILE* 4.2 11.2 - - + -
32J TYR 3.9 3.8 - - - -
33J LEU* 4.1 5.1 - - - +
88J CYS 4.1 0.6 + - - -
89J GLN* 1.3 73.5 - - - +
91J SER* 1.3 59.6 + - - +
92J TYR* 3.6 14.1 - - + +
93J SER* 2.7 46.5 + - - +
95J PRO 3.6 6.6 + - - +
96J ASN* 2.8 29.6 - - - +
97J THR* 2.6 53.7 + - - +
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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