Contacts of the helix formed by residues 124 - 131 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A GLY 2.8 28.4 + - - -
21A THR 3.6 10.3 - - - +
91A ASP* 3.0 36.3 + - - +
92A ILE* 3.6 8.5 - - + +
93A THR* 4.5 0.9 + - - +
123A ASN* 1.3 90.1 + - - +
125A LYS* 1.3 58.3 + - - +
126A ASP* 3.1 9.6 - - - -
127A LEU* 2.8 48.2 + - + +
152A THR 3.1 1.0 + - - -
1180A GNP 3.2 58.2 + - + +
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Residues in contact with LYS 125 (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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92A ILE* 4.0 10.7 - - + +
122A GLY 4.6 0.9 - - - +
123A ASN 3.3 1.4 - - - -
124A LYS* 1.3 77.2 - - - +
126A ASP* 1.3 62.3 + - - +
127A LEU 3.3 0.5 + - - -
128A ASP* 3.3 21.7 + - - +
131A ARG* 5.2 2.1 + - - +
151A GLU* 3.6 53.2 - - + +
152A THR 3.0 15.9 + - - +
153A SER* 4.1 4.5 - - - -
158A GLU* 3.0 47.3 + - + +
1181A TRS 4.0 21.7 + - - -
12C LYS* 5.5 0.6 - - - +
81C ARG* 4.5 16.8 + - - +
82C GLY* 4.8 4.9 - - - -
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Residues in contact with ASP 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 LYS 3.6 2.9 - - - -
125A LYS* 1.3 80.7 - - + +
127A LEU* 1.3 63.7 + - - +
128A ASP 3.2 5.6 + - - -
129A ALA 5.1 0.2 + - - -
153A SER* 2.8 26.5 + - - +
155A LEU* 3.6 13.7 - - + +
156A THR* 3.9 17.0 - - + -
1180A GNP 2.8 41.1 + - - +
81C ARG* 3.4 25.5 + - - +
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Residues in contact with LEU 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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92A ILE* 4.5 0.7 - - - -
93A THR* 3.7 18.3 - - + +
124A LYS* 2.8 39.3 + - + +
126A ASP* 1.3 84.5 - - - +
128A ASP* 1.3 55.8 + - - +
129A ALA* 3.1 3.4 - - - -
130A ASP* 2.9 39.2 + - + +
131A ARG* 3.5 3.3 + - - -
1180A GNP 3.4 32.5 - - + +
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Residues in contact with ASP 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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92A ILE* 4.3 8.7 - - - -
125A LYS 3.3 16.3 + - - +
126A ASP 3.2 3.8 + - - -
127A LEU* 1.3 76.1 - - - +
129A ALA* 1.3 61.3 + - - +
130A ASP 3.1 0.7 - - - -
131A ARG* 2.8 53.4 + - - +
81C ARG* 3.4 37.7 + - - +
82C GLY* 5.9 1.9 + - - -
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Residues in contact with ALA 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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127A LEU 3.0 1.8 + - - -
128A ASP* 1.3 79.3 + - - +
130A ASP* 1.3 68.1 + - - +
131A ARG 3.5 0.2 - - - -
81C ARG* 4.8 4.7 - - - +
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Residues in contact with ASP 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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93A THR* 3.4 28.5 - - + +
127A LEU* 2.9 24.6 + - + +
129A ALA* 1.3 86.7 - - - +
131A ARG* 1.3 65.6 + - - +
132A GLU* 3.4 8.1 + - - +
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Residues in contact with ARG 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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92A ILE* 3.7 31.9 - - + +
93A THR* 4.5 0.2 - - - +
125A LYS* 5.2 4.2 + - - +
127A LEU 3.5 1.8 + - - -
128A ASP* 2.8 44.3 + - - +
129A ALA 3.5 0.8 - - - -
130A ASP* 1.3 77.6 - - - +
132A GLU* 1.3 61.7 + - - +
133A VAL 2.8 48.5 + - - +
134A THR* 4.4 9.4 - - + +
135A PHE* 3.5 13.9 - - - +
151A GLU* 2.8 42.2 + - - -
82C GLY* 6.0 4.6 - - - -
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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