Contacts of the helix formed by residues 68 - 81 (chain A) in PDB entry 1BTB
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 GLU 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A PHE* 4.3 21.9 - - + -
60A LYS* 3.2 43.5 + - + +
65A ASN* 4.6 15.4 + - + +
66A GLY 3.7 0.2 - - - -
67A ALA* 1.3 77.0 - - - +
69A SER* 1.3 56.1 + - - +
71A LEU* 4.3 2.8 - - + +
72A GLN* 3.1 34.5 + - - +
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Residues in contact with SER 69 (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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34A LEU* 2.6 39.0 - - - +
65A ASN* 3.7 20.4 + - - +
66A GLY 3.8 4.7 + - - -
67A ALA 2.4 12.5 + - - -
68A GLU* 1.3 71.1 - - - +
70A VAL* 1.3 67.4 + - - -
72A GLN* 2.9 23.6 + - - +
73A VAL* 2.9 10.4 + - - +
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Residues in contact with VAL 70 (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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16A LEU* 3.9 13.5 - - + -
17A HIS* 3.1 37.7 - - + +
20A LEU* 2.9 30.1 - - + -
34A LEU* 3.3 11.9 - - + +
37A LEU* 3.0 18.8 - - + -
53A TRP* 3.9 10.3 - - + -
66A GLY 3.9 3.6 - - - +
67A ALA 2.8 8.1 + - - +
69A SER* 1.3 74.0 - - - +
71A LEU* 1.3 66.3 + - - +
73A VAL* 2.8 14.6 + - - +
74A PHE* 2.9 21.9 + - + -
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Residues in contact with LEU 71 (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 LEU* 3.7 15.3 - - + -
53A TRP* 3.5 18.9 - - + -
56A PHE* 3.2 33.0 - - + -
67A ALA 3.0 11.2 + - - +
68A GLU* 4.3 3.4 - - + +
70A VAL* 1.3 77.6 - - - +
72A GLN* 1.3 60.7 - - - +
74A PHE* 2.8 21.0 + - + +
75A ARG* 2.9 20.0 + - + +
86A ILE* 3.3 31.9 - - + -
88A LEU* 3.6 26.7 - - + -
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Residues in contact with GLN 72 (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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34A LEU* 5.4 2.4 - - - +
68A GLU* 3.1 20.5 + - + +
69A SER* 2.9 22.3 + - - +
71A LEU* 1.3 79.8 - - - +
73A VAL* 1.3 57.8 + - + +
75A ARG* 4.2 5.0 - - - +
76A GLU* 2.9 41.6 + - + +
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Residues in contact with VAL 73 (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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34A LEU* 3.4 44.9 - - + +
37A LEU* 3.6 11.0 - - + -
38A TRP* 3.1 40.7 - - + -
41A LEU* 3.4 17.7 - - + -
69A SER 2.9 6.0 + - - +
70A VAL 2.8 11.0 + - - +
72A GLN* 1.3 78.4 - - + +
74A PHE* 1.3 57.6 + - - +
76A GLU* 4.1 0.9 - - - -
77A ALA* 2.9 27.0 + - - +
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Residues in contact with PHE 74 (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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20A LEU* 3.8 10.1 - - + -
24A LEU* 3.5 33.9 - - + -
37A LEU* 3.9 10.8 - - + -
41A LEU* 3.6 12.1 - - + -
49A LEU* 3.4 25.6 - - + -
51A LEU* 3.3 33.0 - - + -
70A VAL* 2.9 46.6 + - + -
71A LEU* 2.8 8.9 + - + +
73A VAL* 1.3 80.8 - - - +
75A ARG* 1.3 56.5 + - - +
77A ALA* 3.8 1.6 - - - +
78A LYS* 2.9 26.0 + - - +
84A ILE* 3.6 23.3 - - + +
86A ILE* 3.4 19.7 - - + +
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Residues in contact with ARG 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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71A LEU* 2.9 19.5 + - + +
72A GLN* 4.2 4.9 - - - +
74A PHE* 1.3 74.7 - - - +
76A GLU* 1.3 62.8 + - + +
78A LYS* 3.0 20.7 - - - +
79A ALA* 2.7 27.2 + - - +
86A ILE* 3.4 45.4 + - + +
88A LEU* 4.0 21.6 - - - +
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Residues in contact with GLU 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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38A TRP* 3.1 23.4 - - + -
72A GLN* 2.9 31.7 + - + +
73A VAL* 4.1 0.7 - - - -
75A ARG* 1.3 77.4 - - - +
77A ALA* 1.3 58.9 + - - +
79A ALA* 2.7 31.5 + - - +
80A GLU* 2.8 10.6 + - - +
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Residues in contact with ALA 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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38A TRP* 2.8 27.6 - - + -
41A LEU* 3.8 29.8 - - + -
42A THR* 4.7 3.4 - - + +
73A VAL 2.9 16.4 + - - +
76A GLU* 1.3 75.3 - - - +
78A LYS* 1.3 63.3 + - - +
80A GLU* 2.8 19.9 + - - +
82A CYS* 3.4 14.9 - - + +
84A ILE* 3.8 8.1 - - + -
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Residues in contact with LYS 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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74A PHE 2.9 14.2 + - - +
75A ARG* 3.0 36.7 + - - +
77A ALA* 1.3 77.2 - - - +
79A ALA* 1.3 60.3 + - - +
81A GLY* 3.3 5.5 + - - -
82A CYS 3.3 26.4 - - - +
83A ASP* 4.8 5.2 - - - -
84A ILE* 3.0 43.9 - - + +
85A THR* 4.8 5.6 - - - +
86A ILE* 4.1 6.3 - - + +
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Residues in contact with ALA 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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75A ARG 2.7 10.9 + - - +
76A GLU* 2.7 26.2 + - - +
78A LYS* 1.3 75.4 - - - +
80A GLU* 1.3 56.8 + - - +
81A GLY* 2.8 12.7 + - - -
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Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TRP* 3.2 37.5 + - + -
42A THR* 3.2 19.4 - - + +
76A GLU 2.8 6.3 + - - +
77A ALA* 2.8 13.4 + - - +
79A ALA* 1.3 77.6 - - + +
81A GLY* 1.3 56.8 + - - +
82A CYS* 3.5 5.6 - - - +
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Residues in contact with GLY 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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78A LYS 3.3 3.3 + - - -
79A ALA 2.8 8.4 + - - -
80A GLU* 1.3 79.4 - - - +
82A CYS* 1.3 67.9 + - - +
83A ASP* 3.7 1.2 + - - +
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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