Contacts of the helix formed by residues 74 - 82 (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 VAL 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A HIS* 3.9 25.1 - - + +
42A GLN 4.0 2.0 + - - +
43A GLU 3.7 18.2 - - - +
44A GLN 4.4 0.9 - - - -
45A GLY* 3.5 34.3 - - - +
72A LYS 3.9 2.2 - - - +
73A ALA* 1.3 71.1 - - - +
75A GLU* 1.3 61.6 + - - +
76A MSE 3.1 0.2 - - - -
77A LYS* 3.1 23.8 + - - +
78A TRP* 3.5 22.6 - - + +
99A PHE* 4.7 0.9 - - - -
102A GLU* 5.3 2.5 - - - +
103A GLN* 3.7 26.4 + - - +
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Residues in contact with GLU 75 (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* 4.7 6.1 - - - +
45A GLY* 3.2 8.9 - - - -
46A HIS* 2.7 32.8 + - + +
49A LEU* 3.9 17.5 - - + -
67A PHE* 3.7 11.9 - - + -
73A ALA* 3.3 22.5 - - - +
74A VAL* 1.3 77.1 + - - +
76A MSE 1.3 65.8 + - - +
77A LYS 3.2 0.2 - - - -
78A TRP* 3.1 52.5 + - + +
79A PHE* 3.2 18.0 - - - -
150A TRP* 4.4 9.6 + - - +
152A ARG* 6.0 1.9 - - - -
1246A SAH 5.1 2.1 - - - +
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Residues in contact with MSE 76 (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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67A PHE* 3.4 36.5 - - + -
70A CYS* 3.9 32.3 - - + -
71A GLY 4.1 3.1 - - - +
73A ALA 3.6 20.0 - - - +
74A VAL 3.1 1.0 - - - -
75A GLU* 1.3 78.6 - - - +
77A LYS* 1.3 61.8 + - - +
79A PHE 3.4 2.1 + - - -
80A ALA* 3.1 19.2 + - - +
86A VAL* 3.5 24.6 - - + +
88A GLY* 4.5 1.1 - - - -
99A PHE* 3.7 39.3 - - + -
128A ILE* 4.3 6.0 - - + +
130A LEU* 3.6 28.9 - - + -
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Residues in contact with LYS 77 (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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74A VAL 3.1 11.6 + - - +
76A MSE 1.3 76.7 - - - +
78A TRP* 1.3 63.1 + - + +
80A ALA* 4.3 7.0 - - + -
81A ASP* 2.8 67.4 + - - +
99A PHE* 4.5 2.7 - - + -
103A GLN* 3.7 33.0 + - + +
105A LEU* 3.8 43.5 - - + +
128A ILE* 4.5 6.7 - - + -
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Residues in contact with TRP 78 (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 3.7 20.0 - - - -
45A GLY* 3.8 9.4 - - - -
46A HIS 3.5 33.4 - - - -
49A LEU* 3.9 12.8 - - + -
50A LYS* 3.9 30.1 - - + -
53A LEU* 4.2 17.9 - - + -
74A VAL* 3.5 20.2 + - + +
75A GLU* 3.1 34.0 + - + +
77A LYS* 1.3 80.4 - - + +
79A PHE* 1.3 64.5 + - + +
81A ASP* 3.9 3.3 - - - +
82A ARG* 3.0 47.5 + - - +
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Residues in contact with PHE 79 (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* 4.0 24.7 - - + -
53A LEU* 3.7 27.8 - - + -
57A LEU* 4.1 16.4 - - + -
65A VAL* 4.0 17.5 - - + -
67A PHE* 3.7 28.0 - + - -
75A GLU 3.2 21.2 + - - -
76A MSE 3.8 0.4 - - - +
77A LYS 3.2 0.4 - - - -
78A TRP* 1.3 80.7 - - + +
80A ALA* 1.3 65.2 + - - +
82A ARG* 3.1 9.7 + - - +
83A GLY 3.4 0.5 + - - -
84A HIS* 3.1 32.8 + + + -
86A VAL* 3.7 17.5 - - + -
148A MSE 3.5 31.0 - - - -
150A TRP* 4.7 4.0 - - + -
181A LEU* 5.0 3.4 - - + -
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Residues in contact with ALA 80 (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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76A MSE 3.1 16.7 + - - +
77A LYS* 3.9 9.6 - - + +
79A PHE* 1.3 75.6 - - - +
81A ASP* 1.3 62.4 + - - +
83A GLY* 3.1 13.3 + - - -
84A HIS 3.4 13.8 - - - +
86A VAL* 3.8 3.0 - - + +
127A ASN* 4.1 21.9 - - + +
128A ILE* 3.9 28.5 - - + -
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Residues in contact with ASP 81 (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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77A LYS* 2.8 62.9 + - - +
78A TRP* 3.9 7.6 - - - +
80A ALA* 1.3 78.1 - - - +
82A ARG* 1.3 63.9 + - + +
83A GLY 3.3 1.0 + - - -
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Residues in contact with ARG 82 (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* 3.6 23.3 - - - +
54A ASP* 4.7 11.3 + - - -
57A LEU* 3.8 21.8 - - + -
62A GLY 5.6 0.3 + - - -
78A TRP* 3.0 41.7 + - - +
79A PHE 3.1 5.9 + - - +
80A ALA 3.1 1.2 - - - -
81A ASP* 1.3 82.5 - - - +
83A GLY* 1.3 57.6 + - - +
84A HIS* 3.5 25.8 + - + +
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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