Contacts of the strand formed by residues 40 - 48 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B THR* 4.0 7.0 - - - +
11B CYS* 4.0 1.0 - - - -
38B ARG* 3.6 16.4 + - - +
39B ARG* 1.3 80.9 + - - +
41B CYS* 1.3 65.0 + - - +
59B CYS* 3.6 5.4 - - - +
60B TRP* 2.8 41.3 + - + +
62B ASP 4.7 4.3 - - - -
63B ASP* 5.8 0.4 - - - -
64B ILE* 3.5 36.6 + - + -
66B CYS* 3.5 25.4 - - + -
85B CYS* 4.6 1.8 - - + -
86B CYS 3.3 11.9 + - - +
87B GLU* 3.4 38.6 - - + +
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Residues in contact with CYS 41 (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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8B THR* 3.6 14.6 - - - -
10B GLU 3.7 2.9 - - - -
11B CYS* 2.1 48.7 - - - -
40B HIS* 1.3 74.5 - - - +
42B PHE* 1.3 61.9 + - - +
58B GLY 3.3 6.1 - - - -
60B TRP* 4.8 0.4 - - - -
85B CYS* 3.2 7.8 - - - +
86B CYS* 2.9 31.0 + - - -
88B GLY 3.9 3.4 - - - -
91B CYS* 3.6 22.7 - - - -
92B ASN* 3.5 19.7 - - + -
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Residues in contact with PHE 42 (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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29B GLU* 5.5 0.2 - - - -
41B CYS* 1.3 76.4 - - - +
43B ALA* 1.3 67.0 + - - +
44B THR* 4.0 10.3 - - + -
56B LYS* 4.0 37.9 - - + -
57B GLN* 3.4 1.4 - - - -
58B GLY* 2.9 51.1 + - - -
59B CYS 3.5 23.1 - - - -
60B TRP* 3.8 30.1 - + + -
72B CYS* 4.5 0.9 - - - -
83B PHE* 3.8 26.9 - + + -
84B CYS 3.2 15.0 - - - +
85B CYS* 4.2 3.4 - - + +
92B ASN* 2.9 25.0 + - - -
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Residues in contact with ALA 43 (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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42B PHE* 1.3 79.6 - - - +
44B THR* 1.3 59.6 + - - +
45B TRP* 3.6 11.2 - - + -
54B ILE* 6.1 0.2 - - + -
56B LYS 3.4 7.2 - - - -
57B GLN* 3.9 16.2 - - + -
72B CYS* 4.2 2.4 - - - -
83B PHE* 3.4 4.5 - - - -
84B CYS* 3.0 46.8 + - - +
92B ASN 4.6 3.1 - - - +
95B PHE* 4.0 17.3 - - + -
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Residues in contact with THR 44 (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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42B PHE* 4.0 9.6 - - + -
43B ALA* 1.3 75.3 - - - +
45B TRP* 1.3 63.4 + - - +
54B ILE* 3.9 2.8 - - - +
55B VAL* 2.9 34.9 + - + +
56B LYS* 2.9 43.4 + - + +
81B VAL* 3.4 18.0 - - - +
82B TYR 2.9 17.6 + - - -
83B PHE* 4.4 11.6 - - + +
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Residues in contact with TRP 45 (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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43B ALA* 3.6 23.1 - - + -
44B THR* 1.3 80.7 + - - +
46B LYS* 1.3 83.3 + - - +
47B ASN* 4.3 2.0 - - + -
52B ILE* 3.9 13.0 - - + -
53B GLU 3.3 18.4 - - - +
54B ILE* 4.1 3.8 - - - -
55B VAL* 4.0 4.9 - - - +
74B GLU* 4.0 17.7 - - + -
81B VAL* 3.8 3.7 - - - +
82B TYR* 2.8 61.1 + + + +
83B PHE 4.0 3.1 - - - -
84B CYS* 3.7 26.0 - - - -
95B PHE* 3.5 38.6 - + + -
96B SER 4.1 14.1 - - - -
147B NAG 2.9 34.2 + - + +
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Residues in contact with LYS 46 (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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45B TRP* 1.3 84.0 - - - +
47B ASN* 1.4 60.9 + - - +
48B ILE* 4.1 15.5 - - + -
51B SER 4.2 0.9 - - - +
52B ILE* 3.4 3.8 - - - -
53B GLU* 2.8 59.9 + - + +
55B VAL* 4.2 16.8 - - + -
80B GLU 4.6 12.3 - - - +
81B VAL* 4.9 15.3 - - + -
82B TYR* 4.5 2.2 - - - -
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Residues in contact with ASN 47 (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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45B TRP* 4.3 2.7 - - + -
46B LYS* 1.4 76.1 - - - +
48B ILE* 1.3 63.2 + - - +
49B SER 3.5 2.6 + - - -
50B GLY* 3.0 26.0 + - - -
51B SER 3.5 5.4 - - - -
52B ILE* 5.1 2.5 - - - -
80B GLU 5.2 1.2 + - - -
82B TYR* 3.5 35.4 + - + -
147B NAG 1.4 70.8 + - - +
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Residues in contact with ILE 48 (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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46B LYS* 4.6 13.2 - - + -
47B ASN* 1.3 77.6 - - - +
49B SER* 1.3 75.1 + - - +
50B GLY 3.3 0.2 - - - -
51B SER* 3.1 33.2 + - - +
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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