Contacts of the helix formed by residues 54 - 58 (chain B) in PDB entry 3BSQ
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 54 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B THR* 1.3 78.3 - - - +
55B ALA* 1.3 64.3 + - - +
56B HIS* 3.3 23.6 - - + -
57B CYS* 3.1 22.9 - - - +
98B ASP* 3.5 24.0 - - - +
100B MET* 3.5 10.6 - - - +
192B GLY* 3.6 18.4 - - - -
204B LEU* 4.8 2.0 - - + -
205B VAL 4.0 6.5 - - - +
206B SER* 5.1 0.2 - - - -
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ALA* 1.3 67.7 - - - +
56B HIS* 1.3 55.5 + - - +
57B CYS 3.0 5.2 - - - -
58B LYS* 2.9 30.3 + - - +
86B ARG* 3.4 27.1 + - + -
90B TYR* 3.5 24.6 - - + -
98B ASP* 2.6 13.7 + - - +
99B LEU* 3.5 21.2 - - - +
100B MET* 3.7 11.1 - - - +
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Residues in contact with HIS 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B SO4 3.7 14.3 + - - -
40B HIS* 5.0 3.8 - - - -
41B CYS* 5.3 1.1 - - - -
54B ALA* 3.6 16.6 - - + -
55B ALA* 1.3 75.3 - - - +
57B CYS* 1.3 58.8 + - - +
58B LYS* 3.1 9.4 + - - +
90B TYR* 3.0 24.8 + - - +
95B HIS* 4.1 14.3 + + + -
98B ASP* 2.7 31.5 + - - -
191B SER* 3.2 28.2 + - - -
206B SER* 3.2 26.3 + - - -
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Residues in contact with CYS 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 4.8 1.3 - - + -
40B HIS* 3.9 14.7 + - - -
41B CYS* 2.0 54.1 - - + -
53B THR* 3.7 17.7 - - + -
54B ALA* 3.1 22.8 + - - +
55B ALA 2.9 0.6 + - - -
56B HIS* 1.3 77.7 - - - +
58B LYS* 1.3 65.6 + - - +
62B TYR* 3.5 16.8 + - - -
100B MET* 4.0 4.7 - - + -
191B SER* 3.8 12.6 - - - -
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Residues in contact with LYS 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B SO4 2.4 39.8 + - - -
11B SO4 2.8 19.9 + - - -
40B HIS* 4.4 3.3 - - - -
55B ALA 2.9 15.8 + - - +
56B HIS* 3.1 6.4 - - - +
57B CYS* 1.3 81.4 - - - +
59B MET* 1.3 80.3 + - - +
62B TYR* 3.1 8.5 - - - +
84B SER* 2.8 27.7 + - - +
85B PHE* 4.8 0.2 - - - +
86B ARG* 3.8 28.7 - - - +
100B MET* 3.9 7.6 - - - +
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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