Contacts of the helix formed by residues 152 - 160 (chain A) in PDB entry 2B4M
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 HIS 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A GLU* 4.2 16.2 + - + -
130A GLU* 2.2 44.9 + - - -
148A TYR* 2.8 56.5 + + + +
149A VAL 4.1 4.0 - - - -
151A LYS* 1.3 78.6 - - + +
153A LYS* 1.3 63.9 + - - +
154A ASP 3.3 2.7 - - - -
155A GLN* 3.1 25.8 + - + +
156A ILE* 3.4 13.8 - - + +
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Residues in contact with LYS 153 (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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149A VAL 4.1 9.2 + - - +
150A ASN* 4.1 24.0 - - - +
151A LYS 2.9 17.3 + - - +
152A HIS* 1.3 71.9 - - - +
154A ASP* 1.3 68.0 + - - +
156A ILE* 3.6 6.0 + - - +
157A ALA* 3.4 19.1 + - - +
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Residues in contact with ASP 154 (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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152A HIS 3.3 0.8 - - - -
153A LYS* 1.3 82.4 - - - +
155A GLN* 1.3 64.7 + - - +
157A ALA* 3.4 9.3 + - - +
158A GLU* 3.2 28.4 + - - +
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Residues in contact with GLN 155 (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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122A LYS 4.0 3.0 + - - -
123A TRP* 3.9 8.1 - - - +
127A GLU* 2.8 33.6 + - - +
148A TYR* 2.7 34.0 + - - -
152A HIS* 3.1 20.0 + - + +
154A ASP* 1.3 78.6 - - - +
156A ILE* 1.3 63.2 + - + +
158A GLU* 3.2 23.2 + - - +
159A TRP* 3.2 48.4 + - + +
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Residues in contact with ILE 156 (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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148A TYR* 4.7 3.4 - - + -
149A VAL* 3.8 42.0 - - + +
152A HIS* 3.4 21.2 + - + +
153A LYS 3.9 8.7 - - - +
154A ASP 3.3 0.4 - - - -
155A GLN* 1.3 78.7 - - + +
157A ALA* 1.3 55.3 + - - +
159A TRP* 3.0 22.9 + - + +
160A THR* 2.7 55.0 + - + +
191A VAL* 4.2 18.8 - - + -
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Residues in contact with ALA 157 (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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153A LYS 3.4 11.7 + - - +
154A ASP* 3.5 13.5 - - - +
155A GLN 3.3 0.2 - - - -
156A ILE* 1.3 76.1 - - - +
158A GLU* 1.3 65.2 + - - +
160A THR* 3.6 7.9 - - - -
161A LYS* 2.9 26.0 + - - +
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Residues in contact with GLU 158 (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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120A GLN* 3.4 9.7 - - - +
122A LYS* 5.6 3.8 - - - +
154A ASP* 3.2 18.0 + - - +
155A GLN* 3.2 24.8 + - - +
157A ALA* 1.3 78.9 - - - +
159A TRP* 1.3 69.9 + - + +
161A LYS* 3.2 17.4 - - - +
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Residues in contact with TRP 159 (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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117A LEU* 3.4 27.7 - - + +
120A GLN* 2.9 48.2 - - - +
121A PHE* 3.5 38.1 - + + -
122A LYS* 2.8 35.7 + - + +
123A TRP* 4.1 8.3 - + + -
148A TYR* 4.5 2.5 - + - -
155A GLN* 3.4 40.8 + - + +
156A ILE* 3.0 24.9 + - + +
158A GLU* 1.3 82.8 + - + +
160A THR* 1.3 58.7 + - + +
161A LYS 3.3 0.2 - - - -
163A VAL* 3.9 0.7 - - - +
187A VAL* 4.0 26.0 - - + -
188A ILE* 4.1 10.1 - - + -
191A VAL* 4.2 14.4 - - + -
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Residues in contact with THR 160 (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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117A LEU* 3.8 15.7 - - + -
156A ILE* 2.7 42.5 + - + +
157A ALA* 3.6 10.2 - - - -
159A TRP* 1.3 73.2 - - + +
161A LYS* 1.3 64.7 + - - +
162A GLY 3.3 0.5 + - - -
163A VAL* 3.0 31.1 + - - +
191A VAL* 3.8 11.4 - - + -
195A LEU* 4.6 17.0 - - + -
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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