Contacts of the helix formed by residues 96 - 109 (chain A) in PDB entry 1BUO
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 ALA 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A ALA 4.3 0.2 + - - -
95A LYS* 1.3 73.1 - - - +
97A GLU* 1.3 57.0 + - - +
98A ASP 3.1 5.0 + - - -
99A LEU* 3.3 32.3 + - + +
100A ASP 5.0 0.3 + - - -
122A LEU* 5.8 0.3 - - - +
125A ILE* 6.5 1.1 - - + -
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Residues in contact with GLU 97 (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* 3.8 17.0 + - - -
95A LYS* 3.9 24.4 + - + +
96A ALA* 1.3 77.0 - - - +
98A ASP* 1.3 68.3 + - - +
99A LEU 3.5 0.4 - - - -
100A ASP* 3.3 8.1 - - - +
101A ASP* 3.3 12.5 - - - +
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Residues in contact with ASP 98 (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* 2.6 33.0 + - - -
79A THR* 5.8 1.8 - - - +
82A GLN* 2.9 27.7 + - - +
94A ALA* 4.0 10.5 - - + -
95A LYS* 2.9 32.4 + - - +
97A GLU* 1.3 88.1 - - - +
99A LEU* 1.3 57.3 + - - +
100A ASP 3.3 2.5 - - - -
101A ASP* 3.3 14.7 + - + +
102A LEU* 2.9 33.4 + - + +
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Residues in contact with LEU 99 (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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92A LEU* 6.4 0.2 - - + -
94A ALA* 6.1 1.1 - - + -
95A LYS 4.7 2.2 - - - +
96A ALA* 3.3 27.7 + - + +
97A GLU 3.5 0.2 - - - -
98A ASP* 1.3 73.4 - - - +
100A ASP* 1.3 60.6 + - - +
102A LEU* 3.2 10.8 + - + +
103A LEU* 2.8 31.4 + - - +
118A CYS* 4.1 33.0 - - + +
121A MET* 3.8 40.8 - - + -
122A LEU* 4.0 29.2 - - + +
125A ILE* 4.9 7.2 - - + -
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Residues in contact with ASP 100 (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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96A ALA 5.0 0.2 + - - -
97A GLU 3.3 12.0 - - - +
99A LEU* 1.3 75.3 - - - +
101A ASP* 1.3 91.4 + - - +
103A LEU* 3.5 4.3 + - - +
104A TYR* 3.1 23.9 + - - +
122A LEU* 4.4 15.5 - - + +
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Residues in contact with ASP 101 (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 LEU* 5.5 1.1 - - + +
76A SER* 5.4 1.9 + - - -
79A THR* 3.6 22.8 + - + +
97A GLU 3.3 13.0 - - - +
98A ASP* 3.3 11.2 + - + +
100A ASP* 1.3 107.9 + - - +
102A LEU* 1.3 58.2 + - - +
104A TYR* 3.6 5.9 + - - +
105A ALA* 3.1 29.3 + - - +
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Residues in contact with LEU 102 (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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79A THR* 3.8 16.4 - - + -
82A GLN* 3.4 21.5 - - + +
83A ILE* 4.0 14.4 - - + +
92A LEU* 3.8 32.8 - - + -
94A ALA* 3.6 30.7 - - + -
98A ASP* 2.9 23.4 + - + +
99A LEU* 3.6 12.3 - - + +
101A ASP* 1.3 75.8 - - + +
103A LEU* 1.3 59.3 + - - +
105A ALA* 3.3 1.7 + - - +
106A ALA* 2.8 31.9 + - - +
114A LEU* 5.8 1.3 - - + -
118A CYS* 3.7 18.6 - - - -
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Residues in contact with LEU 103 (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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99A LEU 2.8 20.4 + - - +
100A ASP* 3.7 6.3 - - - +
102A LEU* 1.3 74.0 - - - +
104A TYR* 1.3 58.8 + - - +
106A ALA* 3.3 3.4 + - - +
107A GLU* 2.8 58.7 + - - +
115A GLU* 3.7 31.0 - - + +
118A CYS* 4.0 11.8 - - + -
119A LEU* 3.9 30.1 - - + +
122A LEU* 3.9 19.5 - - + -
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Residues in contact with TYR 104 (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* 4.1 22.4 - - + +
100A ASP 3.1 14.6 + - - +
101A ASP* 3.9 6.1 - - - +
103A LEU* 1.3 78.7 - - - +
105A ALA* 1.3 66.6 + - + +
107A GLU* 3.4 17.6 + - - +
108A ILE* 3.1 58.0 + - + +
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Residues in contact with ALA 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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74A PHE* 4.1 12.1 - - + -
75A LEU* 3.9 19.1 - - + -
79A THR* 3.8 11.7 - - + -
83A ILE* 3.7 22.7 - - + -
101A ASP 3.1 19.4 + - - +
102A LEU 3.8 0.7 - - - +
104A TYR* 1.3 78.2 - - + +
106A ALA* 1.3 53.2 + - - +
108A ILE* 3.5 1.7 + - - +
109A LEU* 2.8 41.2 + - + +
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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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83A ILE* 4.5 5.7 - - + +
102A LEU 2.8 18.5 + - - +
103A LEU* 3.6 4.3 - - - +
105A ALA* 1.3 71.1 - - - +
107A GLU* 1.3 60.1 + - - +
109A LEU* 3.5 4.4 + - - -
110A GLU* 2.8 23.9 + - - -
111A ILE* 3.0 16.4 + - + +
114A LEU* 3.7 20.0 - - + -
115A GLU* 3.5 32.9 - - + +
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Residues in contact with GLU 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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103A LEU* 2.8 47.7 + - + +
104A TYR* 3.6 21.7 - - + +
106A ALA* 1.3 75.0 - - - +
108A ILE* 1.3 67.9 + - + +
110A GLU* 3.3 12.6 + - - +
115A GLU* 3.8 21.8 - - + +
119A LEU* 5.3 5.2 - - - +
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Residues in contact with ILE 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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58A MET* 3.4 22.2 - - + +
74A PHE* 3.5 51.1 - - + -
104A TYR* 3.1 50.6 + - + +
105A ALA 3.8 3.4 - - - +
107A GLU* 1.3 79.9 - - + +
109A LEU* 1.4 61.6 + - - +
110A GLU* 3.4 2.4 + - - +
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Residues in contact with LEU 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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56A SER* 2.7 34.9 + - - +
58A MET* 3.3 17.8 + - + -
59A PHE* 4.0 25.8 - - + -
62A LEU* 6.5 0.4 - - + -
72A LEU* 4.8 4.0 - - + -
74A PHE* 3.8 25.8 - - + -
75A LEU* 4.7 6.5 - - + -
80A PHE* 5.1 3.8 - - + -
83A ILE* 3.9 36.3 - - + -
105A ALA 2.8 21.4 + - - +
106A ALA 4.1 0.7 - - - +
108A ILE* 1.4 74.4 - - - +
110A GLU* 1.3 71.1 + - - +
111A ILE* 3.9 14.6 - - + -
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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