Contacts of the helix formed by residues 111 - 121 (chain A) in PDB entry 1BQ2
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 GLN 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A GLN 2.6 29.5 + - - +
98A TRP* 2.9 13.1 + - - +
101A TRP* 3.7 17.5 - - + +
109A ILE* 3.4 15.1 + - + +
110A ASP* 1.3 73.6 - - - +
112A ILE* 1.3 61.6 + - - +
114A THR* 3.6 7.6 - - - -
115A VAL* 3.2 27.4 + - - +
129A ILE 4.4 3.9 - - - +
130A VAL* 3.6 18.4 - - + +
131A SER* 2.8 47.1 + - - +
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Residues in contact with ILE 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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63A LEU* 4.0 15.7 - - + -
98A TRP* 3.8 48.7 - - + +
99A ARG* 4.0 12.3 - - - -
110A ASP* 3.2 7.6 + - - +
111A GLN* 1.3 73.7 - - - +
113A THR* 1.3 65.3 + - - +
115A VAL* 3.4 6.5 + - - +
116A LEU* 3.2 21.5 + - - +
130A VAL* 4.2 20.6 - - + -
150A PHE* 4.5 4.3 - - + -
184A LEU* 5.6 1.6 - - + -
188A MET* 3.9 24.9 - - + +
239A ILE* 4.2 9.2 - - + -
240A PHE* 4.0 18.4 - - + -
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Residues in contact with THR 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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110A ASP* 2.8 34.4 + - + -
112A ILE* 1.3 73.7 - - - +
114A THR* 1.3 66.6 + - - +
116A LEU* 3.0 10.5 + - + +
117A ASN* 2.9 47.3 + - - +
240A PHE* 3.5 19.2 - - - -
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Residues in contact with THR 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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109A ILE* 4.6 9.6 - - + +
110A ASP 2.9 19.0 + - - -
111A GLN* 3.6 9.4 - - - +
113A THR* 1.3 74.9 - - - +
115A VAL* 1.3 59.0 + - + +
117A ASN* 3.1 13.2 + - - +
118A GLN* 2.9 47.2 + - + +
129A ILE 6.1 0.4 - - - +
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Residues in contact with VAL 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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111A GLN 3.2 18.3 + - - +
112A ILE* 3.5 5.4 - - - +
114A THR* 1.3 76.3 - - + +
116A LEU* 1.3 58.1 + - - +
118A GLN* 3.1 11.6 + - - +
119A LEU* 2.9 31.6 + - + +
128A ILE* 4.0 14.5 - - + +
129A ILE 3.7 14.6 - - - +
130A VAL* 3.7 19.5 - - + -
152A PHE* 3.5 35.0 - - + -
188A MET* 4.1 17.3 - - + -
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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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112A ILE 3.2 13.6 + - - +
113A THR* 3.0 13.2 + - + +
115A VAL* 1.3 74.5 - - - +
117A ASN* 1.3 65.0 + - - +
119A LEU* 3.8 3.2 - - + +
120A LYS* 3.0 44.0 + - - +
188A MET* 3.9 22.7 - - + -
191A GLN* 4.2 13.7 - - + +
192A CYS* 3.2 32.1 - - - -
238A SER* 6.2 1.1 - - - -
239A ILE* 3.8 35.0 - - + +
240A PHE* 5.8 1.1 - - + -
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Residues in contact with ASN 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 THR* 2.9 38.5 + - - +
114A THR* 3.3 11.0 - - - +
116A LEU* 1.3 79.4 - - - +
118A GLN* 1.3 51.6 + - + +
120A LYS* 3.7 9.2 - - - +
121A ASN* 2.8 54.5 + - - +
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Residues in contact with GLN 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 THR* 2.9 38.0 + - + +
115A VAL* 3.4 12.8 - - - +
117A ASN* 1.3 73.8 - - + +
119A LEU* 1.3 60.5 + - - +
122A ASP* 2.7 47.0 + - + +
125A SER* 3.6 19.9 + - - -
127A ARG* 3.3 30.7 + - - +
128A ILE* 4.0 18.8 - - + +
129A ILE 5.5 0.3 - - - +
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Residues in contact with LEU 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 VAL* 2.9 20.2 + - + +
116A LEU 4.0 3.4 - - - +
118A GLN* 1.3 76.7 - - - +
120A LYS* 1.3 60.6 + - - +
123A PRO* 3.5 20.6 - - - +
128A ILE* 3.6 23.8 - - + -
152A PHE* 4.1 14.4 - - + -
154A VAL* 3.5 28.3 - - + -
159A LEU* 3.6 36.3 - - + -
188A MET* 4.8 11.4 - - - -
192A CYS* 4.2 26.0 - - + +
194A LEU* 4.6 10.6 - - + +
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Residues in contact with LYS 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 LEU* 3.0 38.2 + - - +
117A ASN* 3.8 11.0 - - - +
119A LEU* 1.3 79.7 - - - +
121A ASN* 1.3 71.5 + - - +
123A PRO* 4.2 5.0 - - - +
191A GLN* 3.7 22.0 + - - +
192A CYS* 4.3 17.6 - - + +
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Residues in contact with ASN 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 ASN* 2.8 39.8 + - - +
120A LYS* 1.3 87.4 - - - +
122A ASP* 1.3 58.2 + - + +
123A PRO* 3.5 6.9 - - - +
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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