Contacts of the helix formed by residues 106 - 113 (chain B) in PDB entry 5H1C
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104B THR* 3.4 1.1 + - - -
105B GLY* 1.3 82.7 - - - +
107B LYS* 1.3 63.4 + - - +
108B GLU* 4.8 1.6 - - - -
109B LEU* 3.2 34.1 + - - +
110B ASP* 3.0 28.7 + - - +
327B PHE* 5.0 1.1 - - - +
334B VAL* 3.3 11.4 - - - +
335B GLY* 3.5 27.6 - - - -
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Residues in contact with LYS 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B SER* 1.3 72.6 - - - +
108B GLU* 1.3 65.5 + - + +
110B ASP* 2.8 28.2 + - - +
111B LYS* 2.9 24.8 + - - +
336B ASP* 4.9 11.2 + - - +
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Residues in contact with GLU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B SER* 3.6 2.1 + - - +
107B LYS* 1.3 80.1 - - + +
109B LEU* 1.3 58.1 + - + +
111B LYS* 3.2 16.8 + - + +
112B LEU* 2.9 32.4 + - - +
325B ALA* 4.2 10.2 - - + +
326B MET* 2.7 40.3 + - - +
327B PHE* 5.0 0.8 - - + -
336B ASP* 4.3 23.1 + - - +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B THR* 3.1 31.2 - - + +
106B SER* 3.2 20.7 + - - +
107B LYS 3.2 0.4 - - - -
108B GLU* 1.3 76.4 - - + +
110B ASP* 1.3 59.8 + - - +
112B LEU* 3.7 23.6 - - + -
113B LEU* 2.9 41.7 + - + +
136B ILE* 5.0 10.3 - - + -
312B CYS* 3.9 20.6 - - + -
325B ALA* 5.5 1.1 - - + +
326B MET 5.6 0.4 - - - +
327B PHE* 4.0 28.0 - - + -
334B VAL* 3.7 17.0 - - + -
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Residues in contact with ASP 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B THR* 3.7 22.2 - - - +
104B THR* 3.2 29.0 + - - +
105B GLY* 5.5 0.2 - - - -
106B SER 3.0 23.1 + - - +
107B LYS* 2.8 16.6 + - - +
109B LEU* 1.3 78.1 - - - +
111B LYS* 1.3 56.6 + - + +
114B GLN* 3.1 4.2 + - - +
115B GLY* 2.4 40.6 + - - +
116B GLY 4.2 5.1 + - - +
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Residues in contact with LYS 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LYS* 2.9 23.9 + - - +
108B GLU* 3.5 16.9 - - + +
109B LEU 3.1 0.2 - - - -
110B ASP* 1.3 79.1 - - + +
112B LEU* 1.3 67.1 + - + +
114B GLN* 3.2 18.7 + - - +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B GLU 2.9 16.5 + - - +
109B LEU* 3.7 29.2 - - + +
111B LYS* 1.3 80.8 - - + +
113B LEU* 1.3 66.0 + - + +
114B GLN 3.1 2.6 + - - -
312B CYS* 3.7 22.9 - - + +
314B ILE* 3.7 15.5 - - + +
320B LEU* 3.3 17.2 - - - +
323B ALA* 3.7 16.6 - - + +
324B GLU* 3.5 35.4 - - - +
325B ALA* 3.5 22.4 - - + +
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B GLN* 4.6 1.4 - - - +
104B THR* 3.7 29.6 - - + -
109B LEU* 2.9 25.0 + - + +
112B LEU* 1.3 82.6 - - + +
114B GLN* 1.3 72.2 + - - +
116B GLY* 3.5 23.2 - - - +
117B ILE* 4.1 20.9 - - + -
298B THR* 6.5 0.9 - - - -
300B LEU* 4.0 37.0 - - + -
312B CYS* 5.5 0.9 - - - -
314B ILE* 4.9 5.2 - - + -
320B LEU* 3.7 15.4 - - + +
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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