Contacts of the helix formed by residues 117 - 131 (chain A) in PDB entry 1B54
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 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A SER* 1.3 71.7 - - - +
118A LYS* 1.3 66.3 + - - +
120A ALA* 3.2 3.0 + - + -
121A LYS* 3.0 43.5 + - + +
159A GLU* 5.1 4.2 + - + +
162A GLU* 3.9 29.4 - - + +
163A VAL* 3.8 18.3 - - + +
166A PHE* 3.3 44.2 - - + -
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Residues in contact with LYS 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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96A THR* 3.3 31.6 + - + +
116A SER* 3.7 8.7 - - - +
117A LEU* 1.3 80.1 - - - +
119A LYS* 1.3 55.7 + - - +
121A LYS* 3.6 7.2 + - - +
122A LYS* 3.1 26.7 + - - +
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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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94A LEU* 2.6 51.7 + - + +
95A GLN* 4.7 0.7 - - - +
96A THR* 3.5 27.4 - - - +
99A CYS* 3.9 4.0 - - - -
114A ILE* 4.3 6.3 - - + -
115A ASP* 2.9 37.2 + - - +
116A SER* 3.0 24.5 + - - +
118A LYS* 1.3 74.9 - - - +
120A ALA* 1.3 66.1 + - - +
122A LYS* 3.7 2.8 - - - +
123A LEU* 2.9 26.7 + - - +
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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
----------------------------------------------------------
114A ILE* 4.0 23.4 - - + +
116A SER 3.3 10.7 + - - +
117A LEU* 3.2 10.0 + - - +
119A LYS* 1.3 78.4 - - - +
121A LYS* 1.3 63.6 + - - +
123A LEU* 3.9 0.4 - - - +
124A ASN* 3.0 21.1 + - - +
163A VAL* 4.7 2.9 - - + -
166A PHE* 3.8 23.1 - - + -
167A PHE* 4.1 12.8 - - + -
175A ILE* 3.3 13.2 - - + +
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Residues in contact with LYS 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 LEU* 3.0 40.7 + - + +
118A LYS* 3.9 6.3 - - - +
120A ALA* 1.3 77.0 - - - +
122A LYS* 1.3 57.3 + - - +
124A ASN* 3.8 1.9 + - - +
125A GLU* 2.8 36.9 + - - +
166A PHE* 3.8 32.7 - - + -
171A GLU* 4.2 24.3 + - - +
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Residues in contact with LYS 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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96A THR* 3.4 42.6 - - + +
99A CYS* 3.5 12.1 - - + -
100A LYS* 5.0 4.1 - - - +
118A LYS* 3.1 18.8 + - + +
119A LYS 3.3 4.5 + - - +
121A LYS* 1.3 75.0 - - - +
123A LEU* 1.3 58.5 + - - +
125A GLU* 3.3 35.2 + - - +
126A SER* 2.8 47.5 + - - +
129A LYS* 4.1 7.4 - - - +
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Residues in contact with LEU 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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94A LEU* 5.4 1.6 - - + -
99A CYS* 4.0 33.1 - - + +
102A LEU* 4.6 8.7 - - + -
103A ALA* 4.4 8.3 - - + +
111A VAL* 3.9 21.8 - - + -
114A ILE* 4.0 13.7 - - + -
119A LYS 2.9 18.0 + - - +
120A ALA 3.9 3.1 - - - +
122A LYS* 1.3 72.3 - - - +
124A ASN* 1.3 61.4 + - - +
126A SER* 3.4 1.1 + - - -
127A ARG* 2.8 32.9 + - - +
137A ILE* 4.1 17.3 - - + -
139A CYS* 3.8 19.5 - - - -
175A ILE* 3.8 22.0 - - + -
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Residues in contact with ASN 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 3.0 18.0 + - - +
121A LYS 3.8 3.3 + - - +
123A LEU* 1.3 76.6 - - - +
125A GLU* 1.3 64.2 + - - +
127A ARG* 4.5 1.6 - - - -
128A ALA* 3.1 23.7 + - - +
166A PHE* 4.1 10.6 - - + -
171A GLU* 3.2 26.7 + - - +
172A CYS* 3.7 10.7 - - - +
173A LYS 3.3 3.1 + - - -
174A TYR* 2.8 40.4 + - - +
175A ILE* 3.6 21.5 + - + +
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Residues in contact with GLU 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 LYS* 2.8 28.4 + - - +
122A LYS* 3.3 36.4 + - - +
124A ASN* 1.3 79.0 - - - +
126A SER* 1.3 60.3 + - - +
128A ALA* 3.2 13.2 + - - +
129A LYS* 2.8 34.5 + - + +
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Residues in contact with SER 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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99A CYS 4.0 1.1 - - - -
100A LYS* 3.2 27.5 + - - +
103A ALA* 3.5 18.6 - - - -
122A LYS* 2.8 29.1 + - - -
123A LEU 3.9 1.3 - - - -
125A GLU* 1.3 69.5 - - - +
127A ARG* 1.3 65.4 + - - +
129A LYS* 2.9 29.1 + - - +
130A PHE* 3.0 31.2 + - - +
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Residues in contact with ARG 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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103A ALA* 2.8 39.1 + - + +
105A VAL 2.8 20.2 + - - -
106A PRO 3.0 22.8 + - - -
108A LEU* 4.0 11.1 + - - +
123A LEU 2.8 23.0 + - - +
124A ASN* 3.9 4.5 - - - +
125A GLU 3.3 0.2 - - - -
126A SER* 1.3 72.4 - - - +
128A ALA* 1.3 57.2 + - - +
131A GLN* 2.8 59.3 + - - +
132A PRO* 3.8 0.2 - - - +
134A CYS* 3.3 15.5 - - - +
135A ASN* 3.4 15.9 + - - +
137A ILE* 3.3 31.0 - - + +
174A TYR* 3.7 28.3 - - + +
175A ILE* 4.8 0.2 - - + -
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Residues in contact with ALA 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 ASN* 3.1 13.9 + - - +
125A GLU* 3.4 11.4 - - - +
126A SER 3.2 0.2 - - - -
127A ARG* 1.3 78.2 - - - +
129A LYS* 1.3 57.4 + - + +
132A PRO* 3.1 28.6 - - - +
174A TYR* 3.5 34.3 - - + -
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Residues in contact with LYS 129 (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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100A LYS* 4.2 9.5 - - - +
122A LYS* 4.1 16.0 - - - +
125A GLU* 2.8 31.8 + - + +
126A SER* 2.9 37.4 + - - +
128A ALA* 1.3 78.5 - - + +
130A PHE* 1.3 92.0 + - + +
132A PRO* 4.1 4.0 - - - +
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Residues in contact with PHE 130 (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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100A LYS* 3.3 50.5 - - + -
103A ALA* 4.5 2.2 - - + +
104A LYS* 3.9 37.2 - - + -
126A SER* 3.0 23.6 + - - +
129A LYS* 1.3 109.2 - - + +
131A GLN* 1.3 77.5 + - + +
132A PRO* 3.4 6.8 - - - +
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Residues in contact with GLN 131 (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 ALA 3.3 20.6 - - - +
104A LYS* 3.0 23.8 + - - +
106A PRO* 4.0 11.7 - - - +
127A ARG* 2.8 45.9 + - - +
130A PHE* 1.3 87.1 + - - +
132A PRO* 1.3 66.6 - - - +
133A ASP* 3.1 5.8 - - - +
134A CYS* 3.0 40.9 + - + +
174A TYR* 4.5 0.3 - - - -
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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