Contacts of the helix formed by residues 125 - 133 (chain A) in PDB entry 3BRU
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 CYS 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A THR* 4.7 0.2 - - - -
82A TYR* 3.5 20.4 - - - +
86A PHE* 5.6 2.5 - - - -
124A GLY* 1.3 71.4 - - - -
126A LEU* 1.3 61.6 + - - +
127A VAL* 3.5 19.7 - - - -
128A GLY* 3.7 2.2 - - - -
129A ASN* 2.9 35.1 + - - +
152A TRP* 3.9 9.6 - - - -
183A TRP* 6.3 0.2 - - - -
187A GLU* 3.1 39.0 - - - +
190A ILE* 3.7 21.6 - - + +
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Residues in contact with LEU 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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36A GLY 5.4 0.4 - - - +
37A LEU* 4.3 8.7 - - + -
40A LEU* 3.5 45.5 - - + +
41A THR* 3.9 12.6 - - + +
78A LEU* 3.7 22.7 - - + +
79A ILE* 4.1 12.8 - - + +
82A TYR* 3.7 47.9 - - + -
124A GLY 3.7 3.4 + - - -
125A CYS* 1.3 74.4 - - - +
127A VAL* 1.3 59.5 + - + +
129A ASN* 3.4 4.0 + - - +
130A LEU* 3.0 39.8 + - + +
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Residues in contact with VAL 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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79A ILE* 5.2 4.3 - - + +
82A TYR* 4.0 13.0 - - + -
125A CYS* 3.3 10.1 - - - -
126A LEU* 1.3 77.9 - - + +
128A GLY* 1.3 61.4 + - - +
131A GLY* 2.9 26.9 + - - -
145A LEU* 4.1 27.9 - - + +
148A VAL* 3.9 20.0 - - + -
149A LEU* 3.6 42.7 - - + +
152A TRP* 3.9 19.3 - - + -
187A GLU* 5.0 0.2 - - - +
191B LEU* 5.5 0.3 - - - +
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Residues in contact with GLY 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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125A CYS* 3.4 6.0 + - - -
126A LEU 3.3 0.2 - - - -
127A VAL* 1.3 77.4 - - - +
129A ASN* 1.3 64.9 + - - +
131A GLY* 4.9 0.4 - - - -
132A GLN* 3.0 20.6 + - - +
187A GLU* 3.3 27.6 + - - -
132B GLN* 3.1 20.1 + - - -
191B LEU* 3.7 11.1 - - - +
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Residues in contact with ASN 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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40A LEU 2.7 28.5 + - - +
41A THR* 3.1 25.3 + - - +
43A LYS 3.4 15.7 + - - +
44A GLY* 4.9 0.2 - - - -
125A CYS 2.9 21.4 + - - +
126A LEU 3.7 4.0 - - - +
128A GLY* 1.3 76.6 - - - +
130A LEU* 1.3 62.6 - - + +
132A GLN* 3.7 3.5 + - - +
133A GLU* 3.2 28.1 + - - +
190A ILE* 6.0 0.2 - - - +
194A LYS* 3.4 15.9 + - - +
132B GLN* 3.3 29.4 - - + +
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Residues in contact with LEU 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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40A LEU* 4.0 15.9 - - + -
45A TYR* 3.4 37.0 - - + +
75A GLY 5.0 2.0 - - - +
79A ILE* 3.8 33.0 - - + -
126A LEU* 3.0 33.3 + - + +
129A ASN* 1.3 76.9 - - + +
131A GLY* 1.3 65.6 + - - +
133A GLU* 3.1 19.5 + - - +
134A MSE 3.2 10.2 + - - -
137A LEU* 3.4 15.8 - - + +
141A PHE* 4.4 12.1 - - + -
145A LEU* 3.8 19.5 - - + +
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Residues in contact with GLY 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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127A VAL 2.9 20.0 + - - -
128A GLY 3.8 0.7 - - - -
130A LEU* 1.3 76.8 - - - +
132A GLN* 1.3 59.9 + - - +
134A MSE 3.3 19.2 - - - +
145A LEU* 3.8 13.8 - - - +
191B LEU* 4.1 16.6 - - - +
194B LYS* 4.9 2.1 + - - -
195B LEU* 4.2 20.3 + - - +
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Residues in contact with GLN 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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128A GLY 3.0 17.2 + - - +
129A ASN 3.9 1.6 - - - +
131A GLY* 1.3 76.0 - - - +
133A GLU* 1.3 56.2 + - - +
134A MSE 3.3 0.4 - - - -
191A LEU* 3.8 14.3 - - - +
43B LYS 4.3 4.3 - - - +
128B GLY* 3.0 30.1 + - - -
129B ASN* 3.3 23.4 + - + +
132B GLN* 3.7 26.2 - - + -
133B GLU* 6.5 0.2 - - + -
187B GLU* 4.9 4.6 + - - -
190B ILE* 5.0 1.3 - - - +
191B LEU* 3.4 32.0 + - + +
194B LYS* 2.8 48.2 + - - +
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Residues in contact with GLU 133 (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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44A GLY* 3.5 10.9 - - - -
45A TYR* 3.0 26.3 + - - -
46A SER* 2.9 37.6 + - - +
47A SER 4.9 0.2 + - - -
129A ASN* 3.2 16.3 + - - +
130A LEU* 3.1 23.5 + - - +
132A GLN* 1.3 76.4 - - - +
134A MSE 1.3 64.3 + - - +
135A GLY 3.2 3.6 - - - -
136A ALA* 2.8 17.8 + - + +
137A LEU* 3.6 15.6 - - + +
43B LYS 4.1 14.1 - - - +
46B SER* 5.5 0.3 - - - -
47B SER* 5.6 0.4 - - - +
133B GLU* 5.2 15.5 - - + +
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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