Contacts of the strand formed by residues 40 - 48 (chain A) in PDB entry 1BTE
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 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A THR* 4.1 5.6 - - - -
11A CYS* 3.8 1.9 - - - -
31A CYS* 4.3 1.4 - - - -
38A ARG* 3.8 20.0 + - + +
39A ARG* 1.3 78.0 + - - +
41A CYS* 1.3 66.5 + - - +
59A CYS* 3.4 7.4 - - - +
60A TRP* 2.8 43.4 + - + +
62A ASP 5.0 2.9 - - - -
63A ASP* 6.1 0.2 - - - -
64A ILE* 3.7 33.7 + - + -
66A CYS* 3.5 25.2 - - - -
85A CYS* 4.4 4.0 - - + -
86A CYS 3.4 9.8 + - - +
87A GLU* 3.5 34.8 - - + +
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Residues in contact with CYS 41 (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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8A THR* 3.6 11.0 - - - +
10A GLU 3.6 7.4 - - - -
11A CYS* 2.1 48.5 - - - -
40A HIS* 1.3 73.2 - - - +
42A PHE* 1.3 62.0 + - - +
58A GLY 3.3 5.6 - - - +
60A TRP* 4.7 0.4 - - - -
85A CYS* 3.1 9.0 - - - +
86A CYS* 2.9 30.4 + - - -
88A GLY 3.8 12.1 - - - -
91A CYS* 3.6 13.9 - - - -
92A ASN* 3.5 19.3 - - + -
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Residues in contact with PHE 42 (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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41A CYS* 1.3 76.8 - - - +
43A ALA* 1.3 65.6 + - - +
44A THR* 4.0 11.0 - - + -
56A LYS* 3.9 41.1 - - + -
57A GLN* 3.4 1.7 - - - -
58A GLY* 2.9 53.8 + - - -
59A CYS 3.4 24.7 - - - -
60A TRP* 3.8 27.1 - + + -
72A CYS* 4.5 0.9 - - - -
83A PHE* 3.7 27.6 - + + -
84A CYS 3.1 14.8 - - - +
85A CYS* 4.1 0.9 - - + +
92A ASN* 3.0 25.0 + - - -
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Residues in contact with ALA 43 (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 PHE* 1.3 76.9 - - - +
44A THR* 1.4 65.5 + - - +
45A TRP* 3.6 6.0 - - + -
54A ILE* 6.1 0.2 - - + -
56A LYS 3.4 6.7 - - - -
57A GLN* 3.9 15.7 - - + -
72A CYS* 4.1 2.6 - - - -
83A PHE* 3.4 4.3 - - - -
84A CYS* 3.0 43.0 + - - +
92A ASN 4.5 3.1 - - - +
95A PHE* 4.0 25.1 - - + -
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Residues in contact with THR 44 (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 PHE* 4.0 9.6 - - + -
43A ALA* 1.4 73.1 - - - +
45A TRP* 1.3 65.2 + - - +
54A ILE* 3.8 3.5 - - - +
55A VAL* 2.8 33.4 + - - +
56A LYS* 2.8 33.7 + - - +
60A TRP* 5.9 1.1 - - + -
81A VAL* 4.3 11.2 - - + -
82A TYR 3.1 10.5 - - - +
83A PHE* 3.4 32.3 - - + -
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Residues in contact with TRP 45 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ALA* 3.6 14.4 - - + -
44A THR* 1.3 82.0 - - - +
46A LYS* 1.3 77.5 + - - +
47A ASN* 4.2 0.4 - - + -
52A ILE* 3.9 15.9 - - + -
53A GLU 3.4 13.9 - - - +
54A ILE* 4.1 6.3 - - - -
55A VAL* 4.0 4.7 - - - +
74A GLU* 3.9 13.9 - - + -
81A VAL* 3.8 4.3 - - - +
82A TYR* 2.8 65.2 + + + +
83A PHE 4.0 2.5 - - - -
84A CYS* 3.6 32.8 - - - -
95A PHE* 3.5 36.1 - + + -
96A SER 3.9 23.6 - - - -
97A TYR 4.8 0.2 - - - -
147A NAG 3.0 28.5 + - + +
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A TRP* 1.3 82.0 - - - +
47A ASN* 1.3 61.4 + - - +
48A ILE* 4.1 14.8 - - + -
51A SER 3.6 1.1 - - - +
52A ILE* 3.3 4.7 - - - -
53A GLU* 2.9 55.6 + - + +
55A VAL* 4.1 19.3 - - + -
80A GLU* 4.5 16.3 + - - +
81A VAL* 4.1 23.3 - - + +
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Residues in contact with ASN 47 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A TRP* 4.2 1.6 - - + -
46A LYS* 1.3 76.0 - - - +
48A ILE* 1.3 68.4 + - - +
49A SER 4.0 1.2 + - - -
50A GLY* 2.9 23.4 + - - -
51A SER 3.4 3.6 - - - -
52A ILE* 3.4 11.7 - - + -
80A GLU 5.2 0.6 + - - -
82A TYR* 3.7 35.7 + - + -
147A NAG 1.4 68.1 + - - +
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Residues in contact with ILE 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 LYS* 4.9 13.2 - - + -
47A ASN* 1.3 82.8 - - - +
49A SER* 1.3 81.4 + - - +
51A SER* 2.9 30.4 + - - +
80A GLU 5.8 3.8 - - - +
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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