Contacts of the helix formed by residues 112 - 122 (chain A) in PDB entry 5NJ8
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 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A GLY* 4.5 12.1 + - - +
110A LEU* 2.9 1.4 + - - +
111A ASN* 1.3 77.5 - - + +
113A GLN* 1.3 55.7 + - + +
114A GLU 2.7 9.6 + - - -
116A GLU* 3.1 8.7 - - - +
161B ASP* 1.9 39.8 - - - +
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Residues in contact with GLN 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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109A GLY 4.6 4.6 + - - +
110A LEU* 2.9 39.5 + - + +
112A LEU* 1.3 78.7 - - + +
114A GLU* 1.3 61.8 + - - +
115A GLY 3.4 0.4 - - - -
116A GLU* 3.4 11.7 + - - +
117A PHE* 2.9 60.9 + - + -
315B TRP* 3.4 9.9 - - - -
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Residues in contact with GLU 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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110A LEU 2.9 8.9 + - - +
111A ASN* 3.3 18.8 - - - +
112A LEU 2.7 6.7 + - - -
113A GLN* 1.3 73.8 - - - +
115A GLY* 1.3 57.5 + - - +
117A PHE* 3.1 3.8 + - - +
118A LEU* 2.8 41.0 + - + +
161B ASP* 4.0 6.1 - - + +
165B LYS* 3.1 39.6 - - + +
176B LEU* 3.5 25.6 - - + -
188B TYR* 2.2 34.8 + - + -
190B SER* 3.1 16.8 - - - -
191B ASP* 5.2 0.3 - - - +
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Residues in contact with GLY 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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114A GLU* 1.3 72.0 - - - +
116A GLU* 1.3 64.5 + - - +
118A LEU* 2.8 18.4 + - - +
119A LEU* 2.9 17.2 + - - +
161B ASP* 2.7 31.9 + - - +
164B LEU* 3.7 23.7 - - - +
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Residues in contact with GLU 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 LEU 3.1 21.9 - - - +
113A GLN* 3.7 10.3 - - - +
115A GLY* 1.3 66.8 + - - +
117A PHE* 1.3 70.4 + - + +
119A LEU* 3.0 12.0 + - + -
120A GLN* 2.5 34.7 + - - +
155B LYS* 3.8 27.0 - - + +
157B SER* 3.9 14.6 + - - -
161B ASP* 3.7 1.9 - - - +
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Residues in contact with PHE 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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110A LEU* 5.2 4.3 - - + -
113A GLN* 2.9 59.3 + - + -
114A GLU* 3.4 6.5 - - - +
116A GLU* 1.3 82.2 - - + +
118A LEU* 1.3 58.3 + - - +
120A GLN* 4.7 3.4 - - - +
121A ALA* 2.8 36.7 + - - +
176B LEU* 3.9 12.6 - - + -
178B ILE* 3.8 24.2 - - + -
188B TYR* 6.1 0.2 - + - -
311B TYR* 4.0 20.4 - - - -
313B LYS* 4.6 18.2 - - + -
315B TRP* 4.1 21.8 - + - -
338B VAL* 3.7 22.4 - - + +
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Residues in contact with LEU 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 GLU* 2.8 46.5 + - + +
115A GLY* 2.8 12.0 + - - +
117A PHE* 1.3 78.1 - - - +
119A LEU* 1.3 63.8 + - + +
121A ALA* 4.3 0.3 - - - +
122A LEU* 3.3 25.5 + - - +
161B ASP 5.3 0.2 - - - +
164B LEU* 3.8 8.3 - - + -
165B LYS* 3.5 37.7 - - + +
168B ILE* 3.8 29.9 - - + +
176B LEU* 3.7 22.7 - - + +
340B ILE* 4.6 14.8 - - + +
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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 GLY 2.9 16.7 + - - +
116A GLU* 3.6 5.2 - - - +
118A LEU* 1.3 78.9 - - + +
120A GLN* 1.3 75.8 + - - +
122A LEU* 3.7 14.3 + - - +
124A GLY 4.2 0.7 - - - +
126A VAL* 5.0 6.7 - - + -
137A TYR* 4.5 2.5 - - - +
139A SER* 3.7 29.6 - - - +
140A SER* 4.5 21.3 - - - +
141A THR* 3.3 27.2 + - + +
157B SER* 6.1 0.9 - - - +
164B LEU* 3.8 31.9 - - + -
168B ILE* 6.1 1.1 - - + -
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Residues in contact with GLN 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 GLU* 2.5 29.4 + - - +
117A PHE 4.4 0.4 - - - +
119A LEU* 1.3 86.1 - - - +
121A ALA* 1.3 67.6 + - - +
122A LEU 3.1 8.0 + - - +
141A THR* 4.8 8.8 - - + +
144A ASP* 5.5 1.0 + - - +
145A TYR* 4.9 1.0 + - - -
260B ARG* 3.1 18.8 + - - -
311B TYR* 4.3 25.6 - - + +
151D ASP* 3.9 38.1 + - + +
152D GLY* 4.4 12.1 - - - +
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Residues in contact with ALA 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 PHE 2.8 24.8 + - - +
120A GLN* 1.3 73.0 - - - +
122A LEU* 1.3 55.6 + - - +
123A ASN 3.5 0.2 + - - -
176B LEU* 4.6 1.6 - - + -
260B ARG* 2.7 18.6 + - - +
309B THR 3.0 20.6 - - - +
310B GLY* 3.2 9.2 - - - -
311B TYR* 4.4 3.4 - - - -
338B VAL* 3.8 23.1 - - + +
339B ALA* 3.9 6.5 - - - -
340B ILE* 3.8 22.4 - - + -
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Residues in contact with LEU 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 LEU 3.3 16.7 + - - +
119A LEU* 3.7 5.8 - - - +
120A GLN 3.1 11.6 - - - +
121A ALA* 1.3 78.6 - - - +
123A ASN* 1.3 67.0 + - - +
124A GLY 2.9 39.6 + - - +
125A PHE 4.2 0.7 - - - +
126A VAL* 4.2 15.3 - - + -
145A TYR* 3.5 5.5 + - - -
268A ILE* 3.6 46.9 - - + -
168B ILE* 4.4 6.7 - - + -
260B ARG* 3.2 1.4 + - - -
309B THR* 4.1 2.7 - - - +
340B ILE* 4.2 16.5 - - + +
342B ARG* 4.1 21.5 - - - +
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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