Contacts of the strand formed by residues 33 - 38 (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 LEU 33 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4J MET* 3.2 35.4 - - + -
23J CYS* 3.9 8.1 - - + -
29J ILE* 3.7 9.0 - - + -
31J SER 2.9 6.9 + - - -
32J TYR* 1.3 74.6 - - - +
34J ASN* 1.3 73.1 + - - +
35J TRP* 3.8 19.1 - - + +
48J ILE 4.8 0.3 - - - -
49J TYR 3.5 1.2 - - - -
50J ALA 3.2 1.0 + - - -
51J ALA* 2.9 23.1 + - - -
71J PHE* 3.6 50.0 - - + -
88J CYS* 3.6 21.5 - - + -
89J GLN 3.4 15.3 - - - +
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Residues in contact with ASN 34 (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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32I TYR* 4.1 7.3 + - - -
32J TYR 4.7 0.9 - - - -
33J LEU* 1.3 92.1 + - - +
35J TRP* 1.3 62.2 + - - +
36J TYR* 4.0 8.8 + - + -
46J LEU* 3.5 15.7 - - + +
48J ILE 3.1 13.7 - - - +
49J TYR* 3.1 23.1 - - - +
50J ALA 3.2 3.6 + - - -
87J TYR 3.4 0.7 - - - +
88J CYS* 3.3 3.0 - - - -
89J GLN* 2.5 65.2 + - - +
91J SER* 3.8 17.1 + - - -
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Residues in contact with TRP 35 (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* 2.6 31.9 - - - -
21J ILE* 3.7 12.6 - - + -
22J THR 4.1 3.1 - - - -
23J CYS* 3.6 36.6 - - + -
33J LEU* 3.8 17.5 - - + +
34J ASN* 1.3 78.0 - - - +
36J TYR* 1.3 61.3 + - - +
46J LEU* 3.5 4.3 - - - +
47J LEU* 3.0 22.7 + - + -
48J ILE* 3.0 42.1 + - + +
51J ALA* 4.5 8.4 + - - +
63J SER 5.6 0.2 - - - -
64J GLY* 5.3 0.6 - - - -
71J PHE* 4.0 8.2 - - + +
72J THR* 4.0 5.8 - - - -
73J LEU* 3.3 67.6 - - + +
86J TYR* 4.9 0.4 - - + -
87J TYR 3.3 8.7 - - - -
88J CYS* 3.8 12.8 - - + -
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Residues in contact with TYR 36 (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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34J ASN* 4.0 6.3 + - + -
35J TRP* 1.3 75.3 - - - +
37J GLN* 1.3 60.5 + - - +
38J GLN 3.8 0.2 + - - -
44J PRO* 3.0 44.0 - - + -
45J LYS 3.9 2.9 - - - -
46J LEU* 3.3 43.3 - - + +
47J LEU* 4.4 1.1 - - - -
85J THR 3.7 1.0 - - - +
86J TYR* 3.4 6.1 - - - -
87J TYR* 3.1 38.4 + - + +
89J GLN* 3.3 49.5 + - + -
98J PHE* 4.1 13.5 - + + -
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Residues in contact with GLN 37 (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* 1.3 72.5 - - - +
38J GLN* 1.3 60.3 + - - +
39J LYS* 3.1 33.3 - - - +
43J ALA 3.6 1.0 - - - +
44J PRO* 3.5 0.2 - - - +
45J LYS* 3.1 33.8 + - + +
47J LEU* 3.4 34.1 - - + +
62J PHE* 4.0 11.9 - - - -
81J GLU 4.1 7.0 + - - +
84J ALA* 3.3 25.1 - - + -
85J THR 3.6 3.4 - - - -
86J TYR* 3.2 30.9 + - + -
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Residues in contact with GLN 38 (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 3.8 0.4 + - - -
37J GLN* 1.3 73.9 - - - +
39J LYS* 1.3 75.4 + - - +
40J PRO 4.0 0.2 - - - -
41J GLY* 5.6 2.6 + - - -
42J LYS 4.0 9.2 + - - +
43J ALA* 3.9 15.5 - - - +
44J PRO* 3.1 43.5 - - + +
84J ALA* 3.6 3.8 - - - -
85J THR* 2.7 42.4 + - - +
87J TYR* 4.2 23.5 + - + -
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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