Contacts of the helix formed by residues 104 - 115 (chain A) in PDB entry 5BXD
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 ASP 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A GLN* 4.7 7.3 - - - +
83A MET* 3.4 31.5 - - + +
102A PHE* 3.3 24.9 - - + -
103A LYS* 1.3 80.2 - - - +
105A TYR* 1.3 64.9 + - - +
106A THR 3.6 1.1 - - - -
107A LEU* 3.7 24.8 + - + +
108A LEU 3.3 12.3 + - - -
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Residues in contact with TYR 105 (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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102A PHE* 3.7 20.9 - - + +
103A LYS 3.1 8.5 + - - +
104A ASP* 1.3 76.2 - - - +
106A THR* 1.3 83.2 + - + +
108A LEU* 2.8 25.7 + - - +
109A TYR* 2.9 38.5 + + + -
127A TRP* 3.1 44.9 + + + -
128A LYS* 3.6 39.6 - - + +
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Residues in contact with THR 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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103A LYS 4.9 1.2 + - - -
104A ASP 3.6 0.2 - - - -
105A TYR* 1.3 107.3 - - + +
107A LEU* 1.3 66.6 + - + +
109A TYR* 3.6 4.0 + - + +
110A GLU* 3.1 33.1 + - + +
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Residues in contact with LEU 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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80A ASP* 4.4 14.3 - - - +
83A MET* 4.0 15.0 - - + -
104A ASP* 3.9 34.3 - - + +
105A TYR 3.0 0.6 + - - -
106A THR* 1.3 82.6 - - + +
108A LEU* 1.3 60.5 - - - +
110A GLU* 3.5 8.5 + - + +
111A GLU* 3.2 27.0 + - - +
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Residues in contact with LEU 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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83A MET* 3.2 43.0 - - + +
86A TYR* 3.8 22.9 - - + -
87A ILE* 4.0 16.8 - - + -
98A ILE* 3.9 23.1 - - + -
102A PHE* 4.0 11.7 - - + -
104A ASP 3.3 9.5 + - - +
105A TYR* 2.8 14.3 + - - +
107A LEU* 1.3 72.6 - - - +
109A TYR* 1.3 64.2 + - - +
111A GLU* 3.1 2.8 + - + +
112A ALA* 3.0 21.5 + - - +
120A MET* 4.2 4.3 - - + -
124A MET* 3.6 19.3 - - + -
127A TRP* 5.3 2.7 - - + -
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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 TYR* 2.9 45.3 + + + +
106A THR* 3.9 6.3 - - + +
108A LEU* 1.3 76.2 - - - +
110A GLU* 1.3 59.2 - - + +
112A ALA* 3.5 0.5 + - - +
113A LYS* 3.1 55.0 + - + +
121A LEU* 3.6 21.9 - - + +
124A MET* 3.4 34.0 - - + +
125A GLU* 3.8 25.5 + - + +
127A TRP* 3.6 12.1 - + + -
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Residues in contact with GLU 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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79A ARG* 4.3 12.4 + - - +
106A THR* 3.1 28.5 + - + +
107A LEU* 3.6 10.1 - - + +
108A LEU 3.2 0.4 - - - -
109A TYR* 1.3 80.4 - - + +
111A GLU* 1.3 64.7 + - - +
113A LYS* 3.3 31.8 + - - +
114A TYR* 3.2 22.5 + - - +
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Residues in contact with GLU 111 (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 ARG* 2.8 56.3 + - - +
80A ASP* 3.6 22.1 + - + +
83A MET* 3.9 19.7 - - + -
84A PHE 5.5 0.2 - - - +
87A ILE* 4.1 16.4 - - + -
107A LEU 3.2 16.1 - - - +
108A LEU* 3.1 8.2 + - - +
110A GLU* 1.3 77.8 - - - +
112A ALA* 1.3 60.6 + - - +
114A TYR* 3.3 4.4 + - - +
115A PHE* 3.0 44.3 + - + -
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Residues in contact with ALA 112 (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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87A ILE* 3.7 19.4 - - + +
108A LEU 3.0 9.3 + - - +
109A TYR 3.5 1.1 + - - +
111A GLU* 1.3 74.0 - - - +
113A LYS* 1.3 62.3 + - - +
115A PHE* 3.6 2.6 + - - -
116A GLN 3.0 20.1 + - - -
117A LEU* 3.0 15.1 + - + +
120A MET* 4.1 11.7 - - + -
121A LEU* 3.7 9.9 - - + +
124A MET* 3.5 32.3 - - + -
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Residues in contact with LYS 113 (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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109A TYR* 3.1 45.9 + - + +
110A GLU* 3.3 31.9 + - - +
112A ALA* 1.3 78.1 - - - +
114A TYR* 1.3 61.2 + - - +
116A GLN* 3.0 20.3 + - - +
121A LEU* 3.8 26.4 - - + +
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Residues in contact with TYR 114 (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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55A ARG* 3.4 38.7 + - + -
59A LEU* 4.7 11.4 - - + +
77A ILE* 4.9 6.0 - - + +
79A ARG* 3.2 54.9 - - + +
110A GLU 3.2 7.1 + - - +
111A GLU* 3.3 7.2 + - - +
113A LYS* 1.3 77.8 - - - +
115A PHE* 1.3 90.4 + + - +
116A GLN* 3.0 13.5 + - - +
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Residues in contact with PHE 115 (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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54A SER* 3.3 3.8 - - - -
55A ARG* 2.9 24.9 + - + -
56A ILE* 3.2 42.6 + - + +
59A LEU* 4.3 10.3 - - + -
77A ILE* 4.4 10.8 - - + -
79A ARG* 4.4 12.6 - - + -
80A ASP 6.1 0.2 - - - -
84A PHE* 3.7 34.5 - + + -
87A ILE* 3.8 25.4 - - + -
111A GLU* 3.0 36.3 + - + +
112A ALA* 4.2 4.5 - - - +
114A TYR* 1.3 100.9 - + - +
116A GLN* 1.3 66.4 + - - +
117A LEU* 3.2 5.9 + - + +
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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