Contacts of the helix formed by residues 112 - 128 (chain A) in PDB entry 3BRS
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 112 (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* 1.3 76.3 - - - +
113A ASN* 1.3 57.9 + - - +
114A ILE* 3.5 10.0 + - - +
115A GLN* 3.2 39.8 + - + +
116A ALA* 3.0 27.0 + - - +
271A ASP* 3.2 27.2 + - - +
273A GLY* 5.2 1.0 - - - +
274A CYS* 4.8 3.3 - - - -
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Residues in contact with ASN 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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97A ASP* 4.2 7.3 + - - -
110A ALA* 4.7 0.8 - - - +
111A THR* 3.0 41.9 + - - +
112A ASP* 1.3 70.7 + - - +
114A ILE* 1.3 67.9 + - - +
116A ALA* 3.3 6.4 + - - +
117A GLY 2.9 20.1 + - - -
145A THR* 3.7 22.9 - - - +
148A ASP* 3.5 32.2 + - + +
149A ARG* 2.8 46.1 + - + +
223A ILE* 5.5 0.2 - - - +
244A GLN* 4.2 0.7 + - - +
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Residues in contact with ILE 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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112A ASP* 3.3 8.8 + - - +
113A ASN* 1.3 79.9 - - - +
115A GLN* 1.3 63.8 + - + +
117A GLY 3.2 0.3 + - - -
118A ILE* 2.9 39.8 + - + +
148A ASP* 3.6 38.1 - - + +
151A GLU* 3.8 22.4 - - - +
152A GLY* 3.4 17.4 - - - +
155A ILE* 4.2 11.9 - - + -
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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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112A ASP* 3.2 34.3 + - + +
114A ILE* 1.3 80.9 - - + +
116A ALA* 1.3 57.0 + - - +
118A ILE* 3.4 31.1 + - - +
119A ARG* 2.9 46.1 + - - +
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Residues in contact with ALA 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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111A THR* 4.7 5.2 - - + -
112A ASP 3.0 19.6 + - - +
113A ASN* 3.6 10.3 - - - +
114A ILE 3.3 0.2 - - - -
115A GLN* 1.3 74.9 - - - +
117A GLY* 1.4 61.4 + - - +
119A ARG* 3.2 5.7 + - - +
120A ILE* 3.1 23.7 + - - +
223A ILE* 4.1 17.9 - - + -
242A VAL* 3.8 30.4 - - + +
244A GLN* 6.3 0.2 - - + -
274A CYS* 4.4 7.7 - - - -
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Residues in contact with GLY 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 ASN 2.9 15.1 + - - -
114A ILE 3.8 0.9 - - - -
116A ALA* 1.4 72.8 - - - +
118A ILE* 1.3 53.1 + - - +
120A ILE* 3.4 5.9 + - - +
121A GLY 2.7 30.0 + - - -
149A ARG 3.5 22.4 - - - -
153A LEU* 3.2 15.6 - - - -
197A LEU* 5.6 0.2 - - - -
223A ILE* 3.9 12.4 - - - +
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Residues in contact with ILE 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 ILE* 2.9 33.6 + - + +
115A GLN* 3.5 37.0 - - - +
117A GLY* 1.3 76.0 - - - +
119A ARG* 1.3 63.8 + - + +
122A ALA* 3.0 22.4 + - + +
152A GLY* 3.2 22.5 - - - +
155A ILE* 3.9 22.9 - - + -
156A GLY* 3.7 15.0 - - - +
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Residues in contact with ARG 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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115A GLN* 2.9 39.4 + - - +
116A ALA* 3.2 7.1 + - - +
118A ILE* 1.3 74.4 - - + +
120A ILE* 1.3 63.9 + - - +
122A ALA* 3.2 6.6 + - - +
123A VAL* 3.1 26.6 + - - +
242A VAL* 4.6 6.7 - - + +
274A CYS* 4.8 16.9 + - - -
275A ALA* 4.6 4.4 - - - +
276A LEU* 3.8 48.9 + - + +
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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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116A ALA 3.1 13.8 + - - +
117A GLY* 3.7 14.4 - - - +
119A ARG* 1.3 79.5 - - - +
121A GLY* 1.4 63.7 + - - +
123A VAL* 3.3 6.1 + - + +
124A THR* 2.9 29.1 + - - +
153A LEU* 4.2 12.6 - - + -
195A VAL* 4.5 13.2 - - + -
197A LEU* 4.8 1.3 - - + -
221A VAL* 3.5 34.3 - - + -
222A CYS 3.6 19.7 - - - +
223A ILE* 4.1 13.0 - - + -
240A ALA* 4.0 20.6 - - + +
242A VAL* 3.4 23.3 - - + +
276A LEU* 4.3 3.8 - - + -
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Residues in contact with GLY 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 GLY 2.7 21.7 + - - -
118A ILE 3.7 2.2 - - - -
119A ARG 3.3 0.4 - - - -
120A ILE* 1.4 72.7 - - - +
122A ALA* 1.3 57.9 + - - +
124A THR* 3.2 3.6 + - - -
125A LYS* 2.8 29.1 + - - +
153A LEU* 3.5 29.8 - - - -
156A GLY 3.6 9.0 - - - +
157A LEU* 3.6 5.5 - - - +
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Residues in contact with ALA 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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118A ILE* 3.0 17.0 + - + +
119A ARG* 3.2 6.9 + - - +
121A GLY* 1.3 73.4 - - - +
123A VAL* 1.3 64.7 + - - +
125A LYS* 3.5 7.3 + - + +
126A ASN* 3.3 19.4 + - - +
156A GLY* 3.6 12.7 + - - +
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Residues in contact with VAL 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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119A ARG 3.1 16.3 + - - +
120A ILE* 3.3 10.5 + - + +
122A ALA* 1.3 77.7 - - - +
124A THR* 1.3 60.2 + - - +
126A ASN* 3.1 9.5 + - - +
127A LEU* 3.1 28.0 + - + +
221A VAL* 4.1 15.7 - - + -
239A GLU* 5.0 3.4 - - - +
240A ALA* 3.8 22.4 - - + -
276A LEU* 3.6 34.3 - - + -
278A THR* 4.5 5.8 - - - +
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Residues in contact with THR 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 ILE 2.9 22.3 + - - -
121A GLY* 3.6 6.4 - - - -
123A VAL* 1.3 72.7 - - - +
125A LYS* 1.3 65.7 + - - +
127A LEU* 3.0 18.2 + - - +
128A VAL* 3.1 13.2 + - - +
134A ILE* 3.8 38.1 - - + -
153A LEU* 4.5 2.3 - - - +
157A LEU* 4.0 6.1 - - + -
193A VAL* 3.8 20.6 - - + -
195A VAL* 4.1 6.6 - - + +
221A VAL* 3.6 19.2 - - - +
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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 GLY 2.8 16.8 + - - +
122A ALA* 3.6 8.5 - - + +
124A THR* 1.3 76.2 - - - +
126A ASN* 1.3 62.6 + - - +
128A VAL* 3.5 7.2 + - - +
129A ARG* 3.4 20.0 + - - +
156A GLY 3.7 11.3 + - - +
157A LEU* 3.4 32.0 - - + +
158A SER* 2.8 27.9 + - - -
159A ASP* 3.9 9.8 + - - -
160A ASP* 3.2 23.8 - - - +
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Residues in contact with ASN 126 (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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122A ALA 3.3 8.7 + - - +
123A VAL* 3.1 12.2 + - - +
125A LYS* 1.3 79.9 - - - +
127A LEU* 1.3 66.4 + - - +
129A ARG* 3.3 53.2 + - - +
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Residues in contact with LEU 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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123A VAL* 3.1 18.7 + - + +
124A THR* 3.0 9.1 + - - +
126A ASN* 1.3 83.2 - - - +
128A VAL* 1.3 58.9 + - - +
129A ARG* 3.3 3.2 + - - +
130A LYS 4.9 1.0 + - - -
131A SER 3.9 5.9 - - - +
192A SER* 5.3 0.9 + - - -
193A VAL* 3.8 28.8 - - + +
219A LYS* 4.3 24.4 + - + +
221A VAL* 4.0 14.1 - - + -
239A GLU* 3.3 39.7 - - - +
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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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124A THR 3.1 13.4 + - - +
125A LYS* 3.8 9.0 - - - +
127A LEU* 1.3 74.6 - - - +
129A ARG* 1.3 62.7 + - - +
130A LYS 3.3 3.3 + - - -
131A SER 3.3 8.4 + - - +
132A GLY 3.7 15.9 - - - +
134A ILE* 4.0 24.9 - - + -
160A ASP* 4.9 7.4 - - + +
163A LYS* 3.0 40.6 + - + -
192A SER* 4.0 11.4 - - - +
193A VAL* 3.6 27.6 - - + -
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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