Contacts of the helix formed by residues 125 - 133 (chain B) in PDB entry 2C47
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 125 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B PRO* 1.3 73.5 - - - +
126B LEU* 1.3 59.6 + - - +
127B GLU* 3.2 8.1 + - - +
128B ASP* 2.8 36.6 + - - +
129B LEU* 3.0 32.1 + - - +
168B PRO 3.6 5.4 - - - -
169B GLU* 3.5 17.2 - - - +
171B PHE 3.2 6.7 - - - -
172B LEU* 3.4 19.3 - - - +
1300B 5ID 3.8 7.3 + - - -
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B SER* 1.3 73.2 - - - +
127B GLU* 1.3 57.2 + - - +
129B LEU* 3.8 9.3 - - + -
130B PHE* 2.8 29.5 + - - +
137B PHE* 3.9 5.5 - - + -
145B ILE* 4.0 25.4 - - + -
149B LEU* 4.4 2.9 - - + -
168B PRO* 3.2 8.9 + - + +
171B PHE* 2.9 46.7 + - + +
173B VAL* 4.8 2.7 - - + -
184B ILE* 4.2 20.6 - - + -
245B PHE* 3.9 28.5 - - + -
329B TRP* 4.1 26.2 - - + -
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Residues in contact with GLU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B SER* 3.1 8.2 + - - +
126B LEU* 1.3 75.7 - - - +
128B ASP* 1.3 64.8 + - - +
130B PHE* 3.3 4.9 + - - +
131B ASP* 3.1 36.5 + - - +
135B ARG* 2.8 27.9 + - - -
168B PRO* 3.4 25.9 + - + +
169B GLU* 3.4 30.7 - - + +
217B ARG* 5.3 1.5 + - - -
218B TYR* 5.3 0.4 - - - -
244B TYR* 2.8 25.0 + - - -
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Residues in contact with ASP 128 (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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124B PRO* 3.7 15.5 - - + +
125B SER* 2.8 41.1 + - - +
127B GLU* 1.3 78.3 - - - +
129B LEU* 1.3 56.0 + - - +
131B ASP* 3.4 8.9 + - - +
132B LEU* 3.2 30.2 + - - +
335B PRO* 4.8 13.5 - - + +
1300B 5ID 3.8 10.3 + - - -
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Residues in contact with LEU 129 (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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124B PRO* 4.0 16.8 - - + +
125B SER 3.0 24.2 + - - +
126B LEU* 3.9 7.0 - - + +
128B ASP* 1.3 71.7 - - - +
130B PHE* 1.3 66.7 + - - +
132B LEU* 3.3 11.0 + - + +
133B CYS* 3.0 29.5 + - - -
137B PHE* 4.0 2.5 - - - -
173B VAL* 3.6 36.8 - - + -
329B TRP* 3.6 50.3 - - + -
334B LEU* 3.9 24.5 - - + -
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Residues in contact with PHE 130 (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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126B LEU 2.8 20.0 + - - +
127B GLU* 3.3 9.6 + - - +
129B LEU* 1.3 76.3 - - - +
131B ASP* 1.3 58.9 + - - +
133B CYS* 3.2 8.1 + - - +
135B ARG* 2.8 90.3 + - + -
136B THR* 3.4 12.3 - - - -
137B PHE* 3.6 18.1 - + + -
244B TYR* 3.5 49.1 - + - -
245B PHE* 3.7 32.3 - + + -
248B GLY* 3.9 3.6 - - - -
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Residues in contact with ASP 131 (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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127B GLU* 3.1 29.2 + - - +
128B ASP* 3.5 11.0 - - - +
130B PHE* 1.3 77.1 - - - +
132B LEU* 1.3 60.7 + - - +
134B ASP* 3.3 15.1 + - - +
135B ARG* 3.3 34.4 + - - +
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Residues in contact with LEU 132 (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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128B ASP 3.2 21.9 + - - +
129B LEU* 3.3 21.5 - - + +
131B ASP* 1.3 79.0 - - - +
133B CYS* 1.3 60.7 + - - +
134B ASP* 3.3 8.4 + - - +
329B TRP* 5.2 1.6 - - + -
332B LYS* 3.6 53.3 + - + -
333B PRO* 3.9 14.4 - - + +
334B LEU* 4.6 6.1 - - + -
335B PRO* 3.7 30.5 - - + -
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Residues in contact with CYS 133 (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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129B LEU 3.0 20.1 + - - +
130B PHE 3.2 3.1 + - - +
132B LEU* 1.3 78.0 - - - +
134B ASP* 1.3 71.5 + - - +
135B ARG 3.2 1.8 - - - -
136B THR* 3.2 28.1 + - - +
137B PHE* 4.0 10.1 - - + -
328B ASP* 3.8 24.2 - - + +
329B TRP* 3.8 29.6 - - - -
332B LYS* 4.3 10.3 - - - +
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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