Contacts of the helix formed by residues 115 - 128 (chain A) in PDB entry 2BV1
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 LEU 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A THR* 3.8 12.8 - - + -
112A GLU* 2.9 40.1 + - + +
114A ASP* 1.3 85.0 - - + +
116A LEU* 1.3 59.4 + - - +
117A PRO* 3.4 1.8 - - - -
118A CYS* 3.5 17.2 + - + +
119A LYS* 3.0 29.3 + - - +
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Residues in contact with LEU 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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108A TYR* 3.6 43.9 - - + +
111A THR* 3.6 30.1 - - + +
112A GLU 3.8 3.6 - - - +
113A SER* 3.2 26.2 + - - +
115A LEU* 1.3 74.8 - - - +
117A PRO* 1.3 72.1 - - + +
119A LYS* 4.5 0.2 - - - -
120A ALA* 2.8 26.7 + - - +
153A PRO* 4.0 13.2 - - + +
154A THR 4.1 2.0 - - - -
155A PRO* 4.0 37.2 - - + -
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Residues in contact with PRO 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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113A SER 3.8 5.8 - - - +
114A ASP* 3.6 13.2 - - - +
115A LEU 3.6 2.9 - - - -
116A LEU* 1.3 92.5 - - + +
118A CYS* 1.3 57.1 + - - +
120A ALA* 3.8 1.9 - - - +
121A GLU* 3.0 29.9 + - - +
150A ILE 5.0 3.6 - - - +
153A PRO* 3.7 24.6 - - + +
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Residues in contact with CYS 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 ASP 6.0 0.9 - - - -
115A LEU* 3.5 19.6 + - + +
116A LEU 3.2 0.6 - - - -
117A PRO* 1.3 79.1 - - - +
119A LYS* 1.3 59.7 + - - +
121A GLU* 3.4 6.8 + - - +
122A GLU* 2.9 27.9 + - - +
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Residues in contact with LYS 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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104A ALA* 4.6 1.1 - - - -
107A ASP* 3.2 37.2 - - - -
108A TYR* 3.7 24.7 - - + +
111A THR* 4.3 15.5 - - + +
115A LEU* 3.0 18.8 + - + +
116A LEU* 4.0 0.4 - - - +
118A CYS* 1.3 72.8 - - - +
120A ALA* 1.3 66.7 + - - +
122A GLU* 3.2 26.0 + - - +
123A ILE* 2.9 41.2 + - + +
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Residues in contact with ALA 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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108A TYR* 3.8 13.8 - - + -
116A LEU 2.8 21.5 + - - +
117A PRO 3.8 3.1 - - - +
119A LYS* 1.3 73.3 - - - +
121A GLU* 1.3 57.8 + - - +
123A ILE 3.3 0.2 + - - -
124A TYR* 2.9 32.6 + - - +
150A ILE* 4.3 12.1 - - + +
153A PRO* 3.9 20.4 - - + -
158A PHE* 3.6 25.0 - - + -
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Residues in contact with GLU 121 (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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117A PRO 3.0 18.4 + - - +
118A CYS* 3.7 7.4 - - - +
119A LYS 3.3 0.2 - - - -
120A ALA* 1.3 74.8 - - - +
122A GLU* 1.3 57.4 + - - +
124A TYR* 3.5 7.4 + - - +
125A LYS* 3.1 29.6 + - - +
150A ILE* 4.4 12.2 - - + +
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Residues in contact with GLU 122 (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 ALA* 6.1 0.5 - - - +
118A CYS 2.9 15.0 + - - +
119A LYS* 3.2 31.8 + - - +
121A GLU* 1.3 74.6 - - - +
123A ILE* 1.3 69.2 + - - +
125A LYS* 3.5 4.3 + - - +
126A ALA* 3.0 28.4 + - + +
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Residues in contact with ILE 123 (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 PHE* 3.6 33.4 - - + -
104A ALA* 3.6 40.4 - - + +
105A CYS* 4.6 0.9 - - - +
108A TYR* 3.6 19.5 - - + -
119A LYS* 2.9 34.5 + - + +
120A ALA 3.8 2.9 - - - +
122A GLU* 1.3 80.6 - - - +
124A TYR* 1.3 64.9 + - - +
126A ALA* 3.4 0.6 + - - -
127A PHE* 3.1 34.1 + - + +
128A VAL* 3.8 0.6 + - + +
158A PHE* 3.7 23.3 - - + -
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Residues in contact with TYR 124 (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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120A ALA 2.9 19.3 + - - +
121A GLU* 3.7 7.0 - - - +
123A ILE* 1.3 77.1 - - - +
125A LYS* 1.3 61.6 + - + +
128A VAL* 3.0 39.8 + - + -
129A HIS* 2.7 68.9 + + + +
130A SER* 5.3 1.0 + - - -
143A ARG* 5.0 3.5 - - + +
146A THR* 4.7 1.3 - - + -
147A ALA* 3.6 35.0 - - + +
150A ILE* 3.7 32.3 - - + -
158A PHE* 4.9 0.9 - - - -
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Residues in contact with LYS 125 (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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121A GLU 3.1 17.9 + - - +
122A GLU* 4.2 4.3 - - - +
124A TYR* 1.3 79.8 - - + +
126A ALA* 1.3 62.9 + - - +
127A PHE 3.5 0.5 + - - -
129A HIS* 4.1 10.5 - - + +
131A ASP 4.8 1.2 - - - +
132A ALA* 3.5 20.8 + - - +
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Residues in contact with ALA 126 (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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122A GLU* 3.0 24.5 + - + +
125A LYS* 1.3 77.7 - - - +
127A PHE* 1.3 79.1 + - + +
132A ALA* 3.5 7.4 - - - +
133A ALA* 4.3 2.0 + - - +
134A LYS* 3.2 25.7 + - + +
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Residues in contact with PHE 127 (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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97A GLU* 4.0 12.6 - - - -
100A GLU* 3.9 25.1 - - + -
101A PHE* 3.7 48.5 - + + -
104A ALA* 4.1 20.2 - - + -
123A ILE* 3.1 26.7 + - + +
125A LYS 3.3 1.0 - - - -
126A ALA* 1.3 92.5 - - + +
128A VAL* 1.3 62.5 + - + +
129A HIS 3.7 0.7 - - - -
132A ALA* 3.8 5.6 - - - -
134A LYS* 3.7 29.6 - - + -
135A GLN* 3.2 7.1 - - - -
136A ILE* 2.8 32.7 + - + +
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Residues in contact with VAL 128 (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 PHE* 3.9 27.8 - - + -
123A ILE 4.3 0.9 - - - +
124A TYR* 3.0 43.7 + - + +
127A PHE* 1.3 76.9 - - - +
129A HIS* 1.3 68.8 + - - +
130A SER 3.5 0.7 + - - -
135A GLN* 3.4 13.0 - - - +
136A ILE* 3.9 12.9 - - + +
138A ILE* 4.2 12.3 - - + +
143A ARG* 3.6 26.4 + - + +
146A THR* 4.3 12.6 - - + -
158A PHE* 4.6 8.7 - - + -
161A ALA* 5.4 0.4 - - + -
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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