Contacts of the helix formed by residues 106 - 120 (chain A) in PDB entry 2BZN
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 GLY 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A GLY 3.4 2.4 - - - -
105A THR* 1.3 83.8 + - - +
107A SER* 1.3 60.4 + - - -
108A SER* 3.2 4.0 - - - -
109A ASP* 3.8 13.5 + - - +
110A PHE* 2.9 28.9 + - - +
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Residues in contact with SER 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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105A THR 3.7 1.2 + - - -
106A GLY* 1.3 72.3 - - - -
108A SER* 1.3 62.4 + - - +
110A PHE* 3.4 7.2 + - - +
111A GLU* 2.9 36.2 + - - +
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Residues in contact with SER 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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106A GLY* 3.2 1.1 - - - -
107A SER* 1.3 80.0 + - - +
109A ASP* 1.3 67.3 + - - +
111A GLU* 3.4 16.4 + - - +
112A GLN* 3.1 37.2 + - - +
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Residues in contact with ASP 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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78A LYS* 3.3 26.4 + - - +
102A SER 5.3 0.5 - - - +
103A SER* 3.2 19.5 + - - +
104A GLY* 3.0 29.8 + - - +
106A GLY* 3.4 17.6 + - - +
108A SER* 1.3 78.7 + - - +
110A PHE* 1.3 65.3 + - - +
112A GLN* 3.2 14.2 + - - +
113A LEU* 3.0 23.0 + - - +
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Residues in contact with PHE 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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103A SER* 3.5 6.0 + - - -
106A GLY 2.9 19.9 + - - +
107A SER* 3.7 7.4 - - - +
109A ASP* 1.3 74.6 - - - +
111A GLU* 1.3 58.1 + - + +
113A LEU* 3.3 12.9 + - + +
114A GLU* 2.9 51.8 + - + +
141A PHE* 4.1 29.6 - + + -
144A ASP* 5.5 2.5 - - + -
145A VAL* 3.9 21.8 - - + -
148A ARG* 4.2 14.8 - - + -
149A PHE* 4.1 26.5 - + - -
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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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107A SER* 2.9 19.4 + - - +
108A SER* 3.4 22.0 + - - +
110A PHE* 1.3 76.4 - - + +
112A GLN* 1.3 59.8 + - + +
114A GLU* 3.0 13.3 + - - +
115A GLN* 2.9 45.3 + - - +
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Residues in contact with GLN 112 (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* 4.5 14.8 + - - +
80A TYR 4.5 12.3 - - - +
81A SER* 5.3 3.6 - - - -
82A LEU 5.9 0.2 + - - -
108A SER* 3.1 26.8 + - - +
109A ASP* 3.5 16.4 + - - +
111A GLU* 1.3 77.7 - - + +
113A LEU* 1.3 65.5 + - - +
115A GLN* 3.3 11.0 + - - +
116A ILE* 3.1 33.7 + - + +
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Residues in contact with LEU 113 (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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101A ALA* 3.4 44.6 - - + +
102A SER 4.3 7.6 - - - +
103A SER* 4.1 17.7 - - - -
109A ASP 3.0 12.9 + - - +
110A PHE* 3.4 28.5 - - + +
112A GLN* 1.3 75.7 - - - +
114A GLU* 1.3 58.3 + - - +
116A ILE* 3.2 10.4 + - - +
117A LEU* 3.0 51.9 + - + +
126A ILE* 3.9 24.2 - - + -
128A LEU* 4.6 4.0 - - + -
145A VAL* 4.9 1.3 - - + -
149A PHE* 4.8 1.8 - - + -
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Residues in contact with GLU 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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110A PHE* 2.9 34.6 + - + +
111A GLU* 3.4 12.2 - - - +
113A LEU* 1.3 76.7 - - - +
115A GLN* 1.3 57.5 + - + +
117A LEU* 3.4 1.6 + - - +
118A GLU* 2.9 55.6 + - - +
148A ARG* 2.9 32.4 + - - +
149A PHE* 4.1 21.3 - - + -
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Residues in contact with GLN 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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82A LEU* 3.3 32.5 - - + +
111A GLU* 2.9 30.4 + - - +
112A GLN* 3.7 10.8 - - - +
113A LEU 3.3 0.2 - - - -
114A GLU* 1.3 78.3 - - + +
116A ILE* 1.3 56.5 + - - +
118A GLU* 4.0 9.7 - - - +
119A ALA* 2.9 32.7 + - - +
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Residues in contact with ILE 116 (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 TYR 5.0 4.9 - - - +
82A LEU* 3.9 17.7 - - + +
85A TRP* 3.4 65.3 - - + +
101A ALA* 4.2 17.0 - - + -
102A SER 6.0 1.3 - - - +
112A GLN* 3.1 26.2 + - + +
113A LEU* 3.2 9.8 + - - +
115A GLN* 1.3 75.6 - - - +
117A LEU* 1.3 61.7 + - + +
119A ALA 3.3 0.2 + - - -
120A ILE* 2.8 35.9 + - + +
123A VAL* 4.8 5.8 - - + -
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Residues in contact with LEU 117 (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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101A ALA* 4.4 11.4 - - + -
113A LEU* 3.0 29.0 + - + +
114A GLU 3.9 3.6 - - - +
116A ILE* 1.3 78.6 - - + +
118A GLU* 1.3 60.1 + - - +
120A ILE 3.7 15.2 - - - +
121A PRO* 3.8 6.8 - - - +
123A VAL* 3.9 28.9 - - + +
125A TYR 4.6 3.4 - - - +
126A ILE* 3.5 31.0 - - + -
149A PHE* 3.7 33.2 - - + -
152A HIS* 3.8 29.2 + - + +
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Residues in contact with GLU 118 (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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114A GLU* 2.9 45.6 + - - +
115A GLN* 4.0 8.6 - - - +
117A LEU* 1.3 76.8 - - + +
119A ALA* 1.3 64.5 + - - +
120A ILE 3.3 0.5 + - - -
121A PRO* 3.9 8.7 - - - +
148A ARG* 3.5 22.3 + - - +
149A PHE* 5.6 1.1 - - + -
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Residues in contact with ALA 119 (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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82A LEU* 3.9 21.3 - - + -
86A GLN* 4.0 17.7 - - - +
115A GLN 2.9 19.7 + - - +
118A GLU* 1.3 77.8 - - - +
120A ILE* 1.3 66.7 + - + +
121A PRO* 3.4 7.6 - - - +
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Residues in contact with ILE 120 (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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82A LEU* 5.1 0.4 - - + -
85A TRP* 3.6 54.1 - - + +
86A GLN* 4.0 9.0 - - + +
89A ALA* 4.0 21.3 - - + -
96A LEU* 4.4 5.6 - - + -
116A ILE* 2.8 19.4 + - + +
117A LEU 3.7 7.2 - - - +
118A GLU 3.2 0.4 - - - -
119A ALA* 1.3 91.3 - - + +
121A PRO* 1.3 57.0 - - - +
122A GLN* 3.1 18.2 - - - +
123A VAL* 3.0 43.7 + - + +
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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