Contacts of the helix formed by residues 125 - 132 (chain A) in PDB entry 1BIK
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 GLU 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A TRP* 3.4 55.6 - - + +
107A CYS* 4.6 8.0 - - + +
124A SER* 1.3 72.2 - - - +
126A LYS* 1.3 63.6 + - - +
128A CYS* 3.0 5.7 + - - +
129A ARG* 2.8 63.9 + - + +
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Residues in contact with LYS 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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124A SER* 3.9 8.5 - - - +
125A GLU* 1.3 79.2 - - - +
127A GLU* 1.3 52.3 + - - +
129A ARG* 3.0 21.2 + - - +
130A GLU* 2.7 46.6 + - + +
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Residues in contact with GLU 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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74A GLN* 3.4 31.6 + - - +
77A ARG* 2.5 34.4 + - - +
122A PHE* 3.8 4.5 - - + -
123A TYR* 2.8 35.4 + - - +
124A SER* 2.9 19.7 + - - +
126A LYS* 1.3 75.0 - - - +
128A CYS* 1.3 63.9 + - - +
130A GLU* 3.2 17.0 + - - +
131A TYR* 3.0 35.5 + - + -
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Residues in contact with CYS 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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98A TRP* 4.1 5.4 - - + -
99A ALA 4.0 11.9 - - - -
100A PHE* 4.1 4.5 - - - -
107A CYS* 2.0 52.4 - - + -
122A PHE* 3.5 43.9 - - + +
124A SER 3.2 6.0 + - - +
125A GLU 3.0 7.5 + - - +
127A GLU* 1.3 78.9 - - - +
129A ARG* 1.3 61.2 + - - +
131A TYR* 4.0 0.7 - - - +
132A CYS* 3.0 22.7 + - - +
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Residues in contact with ARG 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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107A CYS* 4.1 13.2 - - + -
125A GLU* 2.8 55.5 + - + +
126A LYS* 3.4 23.5 - - - +
128A CYS* 1.3 78.3 - - - +
130A GLU* 1.3 56.5 + - + +
133A GLY* 2.8 38.0 + - - +
134A VAL* 3.7 38.8 - - + +
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Residues in contact with GLU 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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126A LYS* 2.7 32.7 + - + +
127A GLU* 3.3 25.7 - - - +
129A ARG* 1.3 76.2 - - + +
131A TYR* 1.3 68.4 + - + +
133A GLY* 4.3 1.9 + - - -
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Residues in contact with TYR 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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74A GLN 3.9 17.3 + - - -
77A ARG* 3.6 61.0 + - - +
78A THR* 4.0 17.9 - - - -
79A VAL* 3.5 29.6 - - + +
82A CYS* 3.8 2.8 - - - -
122A PHE* 3.5 26.5 - + + -
127A GLU* 3.0 26.9 + - + +
130A GLU* 1.3 86.2 - - + +
132A CYS* 1.3 62.6 + - - +
133A GLY 3.9 0.3 + - - -
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Residues in contact with CYS 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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82A CYS* 2.0 50.9 - - + -
100A PHE* 3.6 42.9 - - + -
122A PHE* 3.7 24.7 - - - -
128A CYS 3.0 11.4 + - - +
129A ARG 3.8 0.2 - - - -
131A TYR* 1.3 76.9 - - - +
133A GLY* 1.3 65.6 + - - +
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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