Contacts of the helix formed by residues 46 - 58 (chain A) in PDB entry 2BZG
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 HIS 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A GLN* 3.5 20.4 + - - +
45A GLY* 1.3 70.5 - - - -
47A GLN* 1.3 58.4 + - - +
48A LEU* 3.2 42.1 + - + -
49A LEU* 3.3 11.2 + - + +
50A LYS* 3.0 27.4 + - - +
75A GLU* 2.7 19.8 + - - +
78A TRP* 3.5 6.5 - - - -
150A TRP* 3.6 18.0 - + + -
152A ARG* 3.7 22.2 - - + -
183A CYS* 3.5 14.3 - - - -
237A GLU* 2.6 40.8 + - - -
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Residues in contact with GLN 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLN* 5.0 0.6 + - - -
44A GLN* 3.6 20.4 + - - +
45A GLY 2.9 24.3 + - - +
46A HIS* 1.3 73.7 + - - +
48A LEU* 1.3 64.6 + - + +
50A LYS* 3.6 28.0 + - - +
51A LYS* 3.0 26.7 + - - +
78A TRP* 5.1 0.2 - - - -
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A HIS* 3.2 22.6 + - + -
47A GLN* 1.3 77.0 - - + +
49A LEU* 1.3 66.0 + - - +
51A LYS* 3.3 8.6 + - + +
52A HIS* 3.1 29.5 + - - +
218A GLU* 3.9 33.4 - - + -
220A VAL* 4.0 40.6 - - + -
237A GLU* 4.5 11.7 - - - +
239A LEU* 4.0 31.4 - - + +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A HIS* 3.3 13.1 + - + +
48A LEU* 1.3 77.2 - - - +
50A LYS* 1.3 59.7 + - - +
52A HIS 3.1 0.7 + - - +
53A LEU* 2.8 48.0 + - + +
56A PHE* 3.9 23.1 - - + -
75A GLU* 3.9 29.2 - - + -
78A TRP* 3.9 14.1 - - + -
79A PHE* 4.0 16.6 - - + -
150A TRP* 3.6 42.7 - - + -
181A LEU* 4.1 7.2 - - + -
239A LEU* 5.2 0.7 - - - -
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Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A GLN 5.6 0.7 - - - +
46A HIS 3.0 17.9 + - - +
47A GLN* 3.6 31.4 + - - +
49A LEU* 1.3 77.9 - - - +
51A LYS* 1.3 64.1 + - - +
52A HIS 3.4 0.2 + - - -
53A LEU* 3.5 13.5 + - - +
54A ASP 5.0 0.7 + - - -
78A TRP* 3.9 21.1 - - + -
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Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLN 3.0 14.7 + - - +
48A LEU* 3.5 15.0 - - + +
49A LEU 3.2 0.2 - - - -
50A LYS* 1.3 79.4 - - - +
52A HIS* 1.3 71.4 + - + +
54A ASP* 5.0 2.4 + - - +
55A THR* 5.4 1.2 + - - -
218A GLU* 2.7 34.4 + - - +
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Residues in contact with HIS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 3.1 22.7 + - + +
51A LYS* 1.3 91.3 - - + +
53A LEU* 1.3 65.1 + - - +
54A ASP 3.3 2.2 - - - -
55A THR* 3.0 20.7 + - + -
56A PHE* 3.0 51.4 + + + -
217A LEU* 4.4 22.0 + - + +
218A GLU* 2.7 45.2 + - + +
239A LEU* 3.9 7.0 - - + +
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 2.8 27.6 + - + +
50A LYS* 3.5 8.7 + - - +
51A LYS 3.5 2.4 - - - -
52A HIS* 1.3 77.3 - - - +
54A ASP* 1.3 66.8 + - - +
56A PHE* 3.3 9.3 + - + +
57A LEU* 3.0 33.9 + - + +
78A TRP* 4.2 23.3 - - + -
79A PHE* 3.7 37.9 - - + -
82A ARG* 3.6 40.8 - - - +
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Residues in contact with ASP 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LYS 5.0 0.8 + - - -
51A LYS 5.0 2.3 + - - +
52A HIS 3.3 0.4 - - - -
53A LEU* 1.3 83.1 - - - +
55A THR* 1.3 58.6 + - - +
57A LEU* 3.2 5.3 + - - +
58A LYS* 2.8 31.7 + - - +
82A ARG* 4.7 11.8 + - - -
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Residues in contact with THR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LYS 5.4 1.0 + - - -
52A HIS* 3.0 22.6 + - + -
54A ASP* 1.3 75.9 - - - +
56A PHE* 1.3 72.4 + - + +
57A LEU 3.2 0.5 + - - -
58A LYS* 3.2 21.5 + - + +
179A GLN* 5.4 0.2 - - - +
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Residues in contact with PHE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 3.9 16.6 - - + -
52A HIS* 3.0 46.3 + + + -
53A LEU* 3.6 7.0 - - + +
55A THR* 1.3 85.2 - - + +
57A LEU* 1.3 60.4 + - + +
58A LYS 3.7 0.3 + - - +
60A LYS* 3.9 7.1 + - - +
148A MSE 3.8 18.0 - - + +
179A GLN* 3.1 36.9 + - - +
181A LEU* 3.5 44.0 - - + -
217A LEU* 3.7 30.1 - - + -
239A LEU* 4.1 13.9 - - + -
241A LEU* 4.3 9.0 - - + -
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 3.0 35.5 + - + +
54A ASP* 3.5 4.7 - - - +
56A PHE* 1.3 76.7 - - + +
58A LYS* 1.3 66.3 + - - +
59A GLY 3.1 0.7 + - - -
60A LYS* 2.9 23.7 + - - +
63A LEU* 3.8 24.2 - - + -
79A PHE* 4.1 17.3 - - + -
82A ARG* 3.8 26.7 - - - -
84A HIS* 3.6 36.6 - - + +
148A MSE 4.1 6.5 - - + -
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Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ASP 2.8 13.1 + - - +
55A THR* 3.2 20.1 + - + +
56A PHE 4.8 0.2 - - - +
57A LEU* 1.3 75.7 - - - +
59A GLY* 1.3 63.9 + - - +
60A LYS* 3.2 18.1 + - - +
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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