Contacts of the helix formed by residues 54 - 61 (chain B) in PDB entry 5BXD
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 SER 54 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B LEU 4.8 0.3 + - - -
51B TYR* 2.4 37.4 + - - +
53B GLU* 1.3 80.4 - - - +
55B ARG* 1.3 53.2 + - - +
56B ILE* 3.4 5.4 - - - +
57B GLY* 3.0 14.7 + - - -
58B ARG* 2.7 40.2 + - - +
115B PHE 3.2 15.7 - - - -
116B GLN* 3.4 15.7 - - - -
117B LEU* 3.8 6.1 - - - -
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Residues in contact with ARG 55 (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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54B SER* 1.3 69.7 - - - +
56B ILE* 1.3 59.0 + - - +
58B ARG* 3.2 27.4 + - - +
59B LEU* 2.8 38.1 + - + +
64B GLU* 3.5 32.7 + - - +
113B LYS 4.9 1.2 + - - -
114B TYR* 2.7 68.4 + - + +
115B PHE* 3.2 11.7 + - + -
116B GLN* 3.4 27.8 + - - +
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Residues in contact with ILE 56 (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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48B LEU* 3.8 13.4 - - + +
54B SER* 3.4 11.7 - - - +
55B ARG* 1.3 79.6 - - - +
57B GLY* 1.3 65.0 + - - +
59B LEU* 3.4 8.3 + - + -
60B PHE* 3.4 34.7 + - + +
84B PHE* 3.9 31.6 - - + -
87B ILE* 4.1 11.9 - - + -
91B LEU* 3.9 24.5 - - + -
115B PHE* 3.5 39.7 + - + +
117B LEU* 3.9 12.8 - - + -
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Residues in contact with GLY 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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48B LEU 3.5 13.9 - - - -
49B THR* 3.8 7.4 - - - +
51B TYR 3.6 8.5 - - - -
52B PRO* 5.1 1.1 - - - -
54B SER* 3.0 22.5 + - - -
56B ILE* 1.3 78.3 - - - +
58B ARG* 1.3 58.1 + - - +
60B PHE 3.3 1.2 + - - -
61B ASP* 2.9 38.3 + - - +
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Residues in contact with ARG 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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52B PRO 4.0 11.7 - - - +
53B GLU* 3.8 15.4 + - - +
54B SER 2.7 31.3 + - - +
55B ARG* 3.2 40.6 + - - +
57B GLY* 1.3 72.7 - - - +
59B LEU* 1.3 59.4 + - - +
61B ASP* 3.0 10.7 - - - +
63B THR* 2.7 55.3 + - + +
64B GLU* 2.8 22.8 + - + +
116B GLN* 3.7 15.4 + - - +
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Residues in contact with LEU 59 (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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55B ARG* 2.8 18.3 + - + +
56B ILE* 3.7 8.5 - - - +
57B GLY 3.1 0.6 - - - -
58B ARG* 1.3 79.3 - - - +
60B PHE* 1.3 63.2 + - + +
62B GLY* 4.4 3.3 + - - -
64B GLU* 3.4 32.0 - - + +
65B PRO 3.2 27.6 - - - +
66B ILE* 3.5 36.2 - - + +
77B ILE* 4.1 32.3 - - + -
114B TYR* 5.7 5.2 - - + +
115B PHE* 5.0 11.9 - - + -
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Residues in contact with PHE 60 (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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32B VAL* 3.7 26.0 - - + -
34B ILE* 3.5 29.2 - - + -
45B LEU* 3.4 24.5 - - + +
48B LEU* 3.6 36.3 - - + -
49B THR* 4.0 4.7 - - + -
56B ILE* 3.4 30.2 + - + +
57B GLY 3.3 2.0 + - - -
59B LEU* 1.3 83.4 - - + +
61B ASP* 1.3 58.5 + - - +
62B GLY 3.1 5.4 - - - -
66B ILE* 3.7 26.0 - - + -
75B TYR* 4.0 13.0 - + - -
77B ILE* 3.8 24.7 - - + -
84B PHE* 5.2 0.4 - + - -
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Residues in contact with ASP 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 5.3 1.8 - - - -
49B THR* 3.6 18.0 - - + +
52B PRO* 4.7 12.1 - - - +
57B GLY 2.9 27.6 + - - +
58B ARG* 3.0 13.9 - - - +
60B PHE* 1.3 77.1 - - - +
62B GLY* 1.3 62.7 + - - +
63B THR* 2.7 28.3 + - - -
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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