Contacts of the strand formed by residues 45 - 49 (chain N) 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 LYS 45 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36N TYR* 3.2 5.4 - - - -
37N GLN* 2.8 57.7 + - + +
38N GLN* 5.5 2.9 - - + -
42N LYS* 4.3 27.7 - - + +
43N ALA* 2.8 10.9 + - + +
44N PRO* 1.3 74.0 - - - +
46N LEU* 1.3 59.6 + - - +
47N LEU* 3.3 7.3 + - + +
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Residues in contact with LEU 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N ASN* 4.0 8.5 - - - +
36N TYR* 3.1 51.7 - - + +
44N PRO 4.4 0.2 + - - -
45N LYS* 1.3 68.6 - - - +
47N LEU* 1.3 71.9 + - - +
48N ILE 4.2 8.1 - - - +
49N TYR* 2.9 62.6 - - + +
55N GLN* 3.9 13.9 + - - +
58N VAL* 5.0 0.5 - - - +
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Residues in contact with LEU 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N TRP* 2.7 19.4 + - + +
36N TYR 4.5 0.7 - - - -
37N GLN* 3.3 36.3 - - + +
45N LYS* 3.3 7.2 + - + +
46N LEU* 1.3 80.0 - - - +
48N ILE* 1.3 67.1 + - + +
55N GLN* 3.1 24.4 - - - +
58N VAL* 3.6 26.1 - - + +
62N PHE* 3.9 27.8 - - + -
73N LEU* 5.4 4.5 - - + -
86N TYR* 3.3 32.8 - - + -
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Residues in contact with ILE 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N ASN* 3.1 4.4 - - - +
35N TRP* 2.9 58.5 + - + +
46N LEU* 4.2 6.5 - - - +
47N LEU* 1.3 81.4 - - + +
49N TYR* 1.3 71.6 + - - +
51N ALA 3.1 25.1 - - - +
52N SER 3.8 6.1 - - - +
53N SER 3.4 17.9 - - - +
54N LEU* 3.9 10.3 - - + +
62N PHE* 4.8 7.2 - - + -
63N SER* 3.8 15.3 - - - +
64N GLY* 3.2 28.7 - - - +
73N LEU* 4.1 10.5 - - + -
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Residues in contact with TYR 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M SER* 4.4 10.1 - - - +
32M TYR* 3.7 19.7 - + - +
92M TYR* 5.1 19.3 - + - -
33N LEU 3.5 1.8 - - - -
34N ASN* 3.6 14.1 - - + -
36N TYR* 5.5 0.7 - - - -
46N LEU* 2.9 45.3 - - + +
47N LEU 4.1 0.4 + - - -
48N ILE* 1.3 74.9 - - - +
50N ALA* 1.3 52.7 + - - +
51N ALA 2.7 18.2 + - - -
53N SER 3.0 30.3 + - - +
55N GLN* 2.5 35.0 - - - +
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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