Contacts of the helix formed by residues 106 - 113 (chain A) in PDB entry 1N0W
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 SER 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A THR* 3.2 4.0 + - - -
105A GLY* 1.3 77.8 - - - +
107A LYS* 1.3 57.0 + - - +
108A GLU* 4.0 1.4 - - - +
109A LEU* 3.0 30.1 + - - +
110A ASP* 2.9 35.1 + - - +
327A PHE* 3.7 10.3 - - - +
334A VAL* 3.9 8.7 - - - -
335A GLY 3.5 18.6 - - - -
336A ASP* 2.9 19.3 + - - -
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Residues in contact with LYS 107 (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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105A GLY 4.2 1.3 - - - +
106A SER* 1.3 71.2 - - - +
108A GLU* 1.3 62.3 - - - +
110A ASP* 3.4 8.9 + - - +
111A LYS* 2.9 45.0 + - - +
336A ASP* 2.8 21.9 + - - +
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Residues in contact with GLU 108 (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 LYS* 1.3 77.7 - - + +
109A LEU* 1.3 64.8 + - - +
111A LYS* 3.3 33.0 + - - +
112A LEU* 3.1 17.5 + - - +
325A ALA* 3.6 17.8 - - + +
326A MSE 3.7 19.1 - - + +
336A ASP* 2.9 20.1 + - + +
337A ALA 6.1 0.2 - - - +
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Residues in contact with LEU 109 (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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104A THR* 3.5 33.0 - - + +
106A SER* 3.0 17.5 + - - +
108A GLU* 1.3 73.8 - - - +
110A ASP* 1.3 66.1 + - - +
112A LEU* 3.2 10.8 + - + +
113A LEU* 3.0 37.3 + - + +
136A ILE* 4.2 24.2 - - + -
300A LEU* 5.3 2.5 - - + -
312A CYS* 3.8 36.1 - - + -
325A ALA* 4.3 6.5 - - + +
326A MSE 4.7 0.2 + - - -
327A PHE* 4.3 23.1 - - + -
334A VAL* 4.6 4.0 - - + -
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Residues in contact with ASP 110 (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 THR* 2.6 28.7 + - - -
104A THR* 2.9 34.5 + - - +
106A SER 2.9 22.7 + - - +
107A LYS* 3.6 8.5 - - - +
109A LEU* 1.3 76.7 - - - +
111A LYS* 1.3 57.8 + - + +
113A LEU* 3.1 3.0 + - - -
114A GLN 3.1 4.7 + - - -
115A GLY* 2.7 50.4 + - - +
116A GLY* 4.0 4.9 - - - +
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Residues in contact with LYS 111 (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 LYS* 2.9 29.8 + - - +
108A GLU* 3.5 32.4 + - - +
109A LEU 3.2 0.2 - - - -
110A ASP* 1.3 77.0 - - + +
112A LEU* 1.3 63.0 + - - +
114A GLN* 3.0 15.8 + - - +
115A GLY* 4.6 2.0 - - - +
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Residues in contact with LEU 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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108A GLU 3.1 12.9 + - - +
109A LEU* 3.2 11.6 + - + +
111A LYS* 1.3 76.3 - - - +
113A LEU* 1.3 57.9 + - + +
114A GLN* 3.2 10.3 + - - +
312A CYS* 3.7 36.8 - - + +
314A ILE* 3.7 31.8 - - + +
323A ALA* 3.5 38.6 - - + +
324A GLU 4.1 6.5 - - - +
325A ALA* 3.7 16.8 - - + +
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Residues in contact with LEU 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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104A THR* 3.7 27.6 - - + -
109A LEU* 3.0 30.2 + - + +
110A ASP 3.1 3.8 + - - +
112A LEU* 1.3 76.4 - - - +
114A GLN* 1.3 69.4 + - - +
115A GLY 3.2 0.7 - - - -
116A GLY* 3.5 15.7 - - - +
117A ILE* 3.8 20.6 - - + -
123A THR* 5.4 0.4 - - + -
298A THR* 4.2 11.9 - - + -
300A LEU* 3.6 36.8 - - + -
314A ILE* 4.0 8.5 - - + -
401A MG 2.2 30.7 - - - -
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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