Contacts of the helix formed by residues 104 - 110 (chain A) in PDB entry 2BTO
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 ASN 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ALA 3.1 13.3 + - - +
102A GLY* 3.8 5.8 - - - +
103A GLY* 1.3 75.8 - - - +
105A PHE* 1.3 66.5 + - - +
106A ALA* 2.8 38.0 + - - +
107A VAL* 3.2 26.6 + - + +
108A GLY 3.6 4.0 + - - -
146A GLY* 3.5 13.5 - - - -
188A ASN* 3.9 2.0 - - - -
402A TRP* 3.1 44.1 + - + +
403A TYR* 3.4 12.4 - - + -
406A GLU* 4.9 2.2 + - - +
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Residues in contact with PHE 105 (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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104A ASN* 1.3 71.2 + - - +
106A ALA* 1.3 62.4 + - - +
108A GLY 3.1 2.9 + - - -
109A TYR* 3.0 59.3 + + + -
110A LEU* 6.2 0.4 - - + -
146A GLY* 3.8 2.2 - - - -
149A SER* 3.6 34.1 - - - +
150A GLY* 3.3 19.7 - - - -
153A ALA* 3.9 7.6 - - + -
188A ASN* 2.8 28.5 + - - +
191A PHE* 3.5 59.0 - + + -
192A ALA 3.7 0.9 - - - -
195A THR* 5.5 0.9 - - - -
403A TYR* 4.2 1.1 - - + -
408A MET* 4.2 16.8 - - + -
416A LEU* 5.3 2.9 - - + -
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Residues in contact with ALA 106 (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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104A ASN* 2.8 21.9 + - - +
105A PHE* 1.3 76.7 - - - +
107A VAL* 1.3 56.0 + - - +
109A TYR* 4.4 1.8 - - - +
110A LEU* 2.7 37.0 + - + +
111A GLY 3.2 4.0 + - - -
403A TYR* 4.3 4.4 - - + +
406A GLU* 3.6 27.8 - - + +
408A MET* 4.1 26.7 - - + -
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Residues in contact with VAL 107 (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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73A LEU* 4.7 1.3 - - + -
100A GLY 4.3 3.1 - - - +
101A ALA* 3.8 36.3 - - + +
104A ASN* 3.2 18.7 + - + +
106A ALA* 1.3 76.0 - - - +
108A GLY* 1.3 60.6 + - - +
111A GLY 3.2 8.4 + - - +
112A ALA* 3.0 45.8 + - + +
113A GLY 3.1 6.6 + - - -
406A GLU* 3.7 28.5 - - - +
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Residues in contact with GLY 108 (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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73A LEU* 4.4 9.6 - - - -
101A ALA* 4.5 0.6 - - - +
104A ASN 3.6 3.8 + - - -
105A PHE 3.1 4.4 + - - -
107A VAL* 1.3 81.1 - - - +
109A TYR* 1.3 56.5 + - - +
113A GLY* 3.2 26.6 - - - -
146A GLY 3.5 20.4 + - - -
150A GLY 3.4 6.7 - - - -
151A PHE* 3.3 18.2 + - - -
154A LEU* 4.2 1.2 - - - +
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Residues in contact with TYR 109 (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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105A PHE* 3.0 43.8 + + + +
106A ALA* 4.2 1.6 - - - +
108A GLY* 1.3 79.7 - - - +
110A LEU* 1.3 72.4 - - + +
114A ARG* 2.8 54.6 + - - -
150A GLY 3.5 18.8 - - - +
153A ALA* 4.0 5.8 - - + -
154A LEU* 3.7 26.6 - - + +
157A GLU* 2.5 37.0 + - - -
195A THR* 4.8 0.7 - - - -
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Residues in contact with LEU 110 (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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105A PHE* 6.2 0.4 - - + -
106A ALA* 2.7 18.4 + - + +
109A TYR* 1.3 101.5 - - + +
111A GLY* 1.3 62.9 + - - +
114A ARG* 3.7 25.5 - - - +
406A GLU 3.5 23.6 - - - +
407A GLY* 3.7 25.1 - - - +
408A MET* 4.1 15.3 - - + +
412A GLN* 5.6 1.6 - - - +
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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