Contacts of the helix formed by residues 115 - 134 (chain A) in PDB entry 2LCK
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 115 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A SER* 4.7 4.0 - - - -
114A ALA* 1.3 81.8 - - - +
116A ILE* 1.3 56.9 + - - +
117A GLY 3.1 3.1 - - - -
118A SER* 2.4 40.1 + - - -
119A ARG* 2.7 27.0 + - - -
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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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107A TYR* 5.3 0.4 - - - +
114A ALA* 5.3 2.9 - - + -
115A GLY* 1.3 79.5 - - - +
117A GLY* 1.3 71.8 + - - +
119A ARG* 3.2 31.1 + - - +
120A LEU* 3.1 23.2 + - + +
194A LEU* 3.5 35.7 - - + +
198A ASP* 5.3 11.2 - - + +
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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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115A GLY* 3.1 0.6 - - - -
116A ILE* 1.3 84.2 - - - +
118A SER* 1.3 63.9 + - - +
120A LEU* 3.0 16.5 + - - +
121A LEU* 2.9 32.8 + - - +
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Residues in contact with SER 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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111A SER* 5.2 2.3 + - - -
115A GLY* 2.4 35.4 + - - -
117A GLY* 1.3 74.9 - - - +
119A ARG* 1.3 57.4 + - - +
121A LEU* 3.2 11.7 + - - +
122A ALA* 2.7 37.6 + - - +
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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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106A PHE 4.5 4.7 - - - +
107A TYR* 2.8 72.1 + - + +
108A THR* 5.6 1.8 - - - +
109A LYS* 5.5 5.4 - - + -
111A SER* 6.3 0.6 - - - -
114A ALA* 4.1 13.6 + - - +
115A GLY* 2.7 24.0 + - - +
116A ILE* 3.2 40.7 - - - +
117A GLY 3.1 0.2 - - - -
118A SER* 1.3 78.5 + - - +
120A LEU* 1.3 53.6 + - - +
122A ALA* 4.3 5.6 - - - -
123A GLY* 2.6 33.8 + - - -
190A ASN* 5.7 0.2 - - - +
197A TYR* 4.8 13.5 + - - -
201A LYS* 5.7 4.2 - - - +
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TYR* 5.4 2.2 - - + -
116A ILE* 3.1 10.1 + - + +
117A GLY* 3.0 14.9 + - - +
119A ARG* 1.3 76.2 - - - +
121A LEU* 1.3 56.8 + - + +
123A GLY* 5.1 0.4 - - - -
124A SER* 2.5 44.9 + - - +
190A ASN* 3.8 24.2 - - - +
191A CYS* 5.4 4.0 - - - -
194A LEU* 3.5 50.5 - - + -
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Residues in contact with LEU 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* 2.9 22.8 + - - +
118A SER* 3.6 10.5 - - - +
120A LEU* 1.3 79.1 - - + +
122A ALA* 1.3 55.2 + - - +
124A SER* 4.4 4.3 - - - -
125A THR* 2.6 41.2 + - - +
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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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106A PHE* 3.6 42.8 - - + +
118A SER 2.7 21.5 + - - +
119A ARG* 3.8 3.8 - - - +
121A LEU* 1.3 72.1 - - - +
123A GLY* 1.3 59.4 + - - +
125A THR* 4.0 3.5 - - - -
126A THR* 2.8 36.0 + - - +
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Residues in contact with GLY 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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103A VAL* 5.4 5.5 - - - +
106A PHE* 5.4 2.4 + - - -
107A TYR* 5.3 7.6 - - - -
119A ARG 2.6 22.2 + - - -
120A LEU* 3.9 0.4 - - - -
122A ALA* 1.3 73.1 - - - +
124A SER* 1.3 60.2 + - - +
126A THR* 3.4 8.8 - - - +
127A GLY* 3.1 22.9 + - - -
190A ASN* 4.7 15.2 - - - +
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Residues in contact with SER 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 LEU* 2.5 33.2 + - - +
121A LEU* 3.9 5.2 - - - -
123A GLY* 1.3 73.9 - - - +
125A THR* 1.3 61.9 + - - +
128A ALA* 3.4 22.5 + - - +
190A ASN* 4.6 11.9 + - - +
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Residues in contact with THR 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 LEU* 2.6 28.5 + - - +
122A ALA* 4.0 3.8 - - - -
124A SER* 1.3 80.2 - - - +
126A THR* 1.3 63.7 + - - +
128A ALA* 3.9 3.5 - - - +
129A LEU* 3.1 27.8 + - + +
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Residues in contact with THR 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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102A SER 5.7 0.2 - - - -
103A VAL* 4.0 31.5 - - + +
106A PHE* 3.9 28.2 - - + -
122A ALA 2.8 26.3 + - - +
123A GLY* 3.4 12.3 - - - +
125A THR* 1.3 74.8 - - - +
127A GLY* 1.3 67.5 + - - +
129A LEU* 3.1 8.6 + - - +
130A ALA* 2.7 34.2 + - - +
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Residues in contact with GLY 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 VAL* 5.3 4.9 - - - -
123A GLY 3.1 10.5 + - - -
126A THR* 1.3 83.3 - - - +
128A ALA* 1.3 67.4 + - - +
130A ALA* 3.0 17.8 + - - +
131A VAL* 3.1 19.8 + - - +
186A ASN* 6.3 2.5 - - - -
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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 SER 3.4 19.9 + - - +
125A THR* 3.9 4.5 - - - +
127A GLY* 1.3 76.6 - - - +
129A LEU* 1.3 60.5 + - - +
131A VAL* 2.7 29.9 - - - +
132A ALA* 3.6 4.9 + - - +
183A VAL* 5.6 9.4 - - + -
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Residues in contact with LEU 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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125A THR* 3.1 19.5 + - + +
126A THR* 3.2 15.3 - - - +
127A GLY 3.1 0.2 - - - -
128A ALA* 1.3 81.5 - - - +
130A ALA* 1.3 55.4 + - - +
132A ALA* 2.7 36.9 - - + +
133A VAL* 3.7 11.8 + - + +
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Residues in contact with ALA 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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99A LEU* 3.7 38.8 - - + +
103A VAL* 5.3 4.0 - - + -
126A THR 2.7 16.8 + - - +
127A GLY* 3.0 12.7 + - - +
129A LEU* 1.3 69.3 - - - +
131A VAL* 1.3 62.5 + - + +
132A ALA 2.9 6.2 + - - -
133A VAL* 3.1 17.4 + - - +
134A ALA* 3.3 12.5 + - - +
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Residues in contact with VAL 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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127A GLY 3.1 9.0 + - - +
128A ALA* 2.7 35.9 - - - +
130A ALA* 1.3 73.7 - - + +
132A ALA* 1.3 61.7 + - - +
134A ALA 2.7 26.1 - - - +
135A GLN* 3.4 30.7 + - + +
183A VAL* 4.6 19.1 - - + -
186A ASN* 3.7 24.7 - - - +
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Residues in contact with ALA 132 (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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128A ALA 4.1 4.5 - - - +
129A LEU* 2.7 31.8 + - + +
131A VAL* 1.3 83.9 - - - +
133A VAL* 1.3 61.1 + - + +
135A GLN* 5.5 1.3 - - - +
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Residues in contact with VAL 133 (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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129A LEU* 4.3 17.0 - - + +
130A ALA* 3.1 8.5 + - - +
132A ALA* 1.3 82.6 - - + +
134A ALA* 1.3 62.1 + - + +
135A GLN 4.2 1.0 + - - -
136A PRO* 4.6 5.7 - - - +
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Residues in contact with ALA 134 (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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95A VAL* 5.9 7.4 - - + -
130A ALA 3.3 6.2 + - - +
131A VAL* 2.7 27.5 - - - +
133A VAL* 1.3 81.7 - - + +
135A GLN* 1.3 61.2 + - - +
136A PRO* 4.4 0.9 - - - -
138A ASP* 5.0 4.1 - - - +
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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