Contacts of the helix formed by residues 124 - 131 (chain C) in PDB entry 2BME
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 LYS 124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C GLY 2.9 29.0 + - - -
21C THR 3.6 13.2 - - - +
91C ASP* 3.2 32.6 + - - +
92C ILE* 3.8 8.7 - - - +
93C THR* 4.7 1.3 - - + +
123C ASN* 1.3 92.3 + - - +
125C LYS* 1.3 59.9 + - - +
126C ASP* 3.1 5.4 - - - -
127C LEU* 2.8 44.5 + - + +
152C THR 3.1 0.2 + - - -
1178C GNP 3.2 59.7 + - + +
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Residues in contact with LYS 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ILE* 3.9 10.5 - - - -
122C GLY 5.0 0.2 - - - -
123C ASN 3.3 2.6 - - - -
124C LYS* 1.3 76.4 - - - +
126C ASP* 1.3 57.4 + - - +
128C ASP* 3.0 43.9 + - - +
131C ARG* 3.7 11.1 - - - +
151C GLU* 2.9 45.2 + - + +
152C THR 2.9 23.8 + - - +
153C SER* 4.4 3.1 - - - -
158C GLU* 3.8 29.8 - - - +
1179C TRS 2.9 35.5 + - - -
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Residues in contact with ASP 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C LYS* 3.8 2.6 - - - -
125C LYS* 1.3 78.4 - - - +
127C LEU* 1.3 65.2 + - - +
128C ASP* 3.3 7.6 + - - +
129C ALA 5.1 0.3 + - - -
153C SER* 2.7 29.1 + - - +
155C LEU* 3.4 16.6 - - + +
156C THR* 4.4 14.4 - - + -
1178C GNP 2.8 42.4 + - - +
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Residues in contact with LEU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C THR* 3.5 20.0 - - + +
124C LYS* 2.8 35.9 + - + +
126C ASP* 1.3 90.9 - - - +
128C ASP* 1.3 58.0 + - - +
129C ALA* 3.1 4.5 - - - -
130C ASP* 2.8 36.7 + - - +
1178C GNP 3.5 25.4 - - + +
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Residues in contact with ASP 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ILE* 4.0 19.7 - - + -
125C LYS* 3.0 32.7 + - - +
126C ASP 3.3 5.7 - - - +
127C LEU* 1.3 76.0 - - - +
129C ALA* 1.3 63.1 + - - +
130C ASP 2.9 1.6 - - - -
131C ARG* 3.0 33.6 + - - +
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Residues in contact with ALA 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C ASP 5.1 0.4 + - - -
127C LEU* 2.9 3.2 + - - +
128C ASP* 1.3 81.6 + - - +
130C ASP* 1.3 68.3 - - - +
131C ARG 3.4 1.1 + - - +
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Residues in contact with ASP 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C THR* 3.4 26.2 - - + +
127C LEU* 2.8 22.2 + - - +
129C ALA* 1.3 89.4 - - - +
131C ARG* 1.3 67.1 + - - +
132C GLU* 3.4 9.4 + - - +
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Residues in contact with ARG 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ILE* 3.8 28.5 - - + +
93C THR* 4.4 1.8 - - - +
125C LYS* 3.7 14.5 - - - +
127C LEU 3.7 0.6 + - - -
128C ASP* 3.0 30.9 + - - +
129C ALA 3.4 1.0 + - - +
130C ASP* 1.3 80.8 - - - +
132C GLU* 1.4 60.4 + - - +
133C VAL 2.9 41.1 + - - +
134C THR* 4.2 9.9 - - + +
135C PHE* 3.7 12.7 - - - +
151C GLU* 2.9 42.6 + - - -
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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