Contacts of the helix formed by residues 146 - 153 (chain B) in PDB entry 2DH3
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 ARG 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B PHE* 4.0 28.5 - - + -
133B GLN* 4.7 16.0 + - + +
142B GLY 4.7 8.3 - - - +
143B LEU* 3.3 11.3 + - - +
144B LYS 3.1 1.0 - - - -
145B GLY* 1.3 80.1 + - - +
147B LEU* 1.3 63.8 + - - +
148B ASP 3.3 2.9 - - - -
149B TYR* 3.2 11.2 + - + +
150B LEU* 3.1 25.6 + - + +
390B TRP* 3.3 70.5 - - + +
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Residues in contact with LEU 147 (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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143B LEU* 3.8 11.0 + - + +
144B LYS* 3.2 26.5 + - - +
146B ARG* 1.3 77.4 - - - +
148B ASP* 1.3 59.5 + - - +
150B LEU* 3.4 12.1 + - + +
151B SER* 3.0 26.7 + - - -
158B LEU* 4.0 26.7 - - + -
192B LEU* 4.2 13.7 - - + -
195B SER* 4.1 25.8 - - - -
196B ALA* 4.1 17.5 - - + +
199B LYS* 3.9 20.6 - - + +
201B ILE* 4.7 18.2 - - + +
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Residues in contact with ASP 148 (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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144B LYS 4.8 1.3 + - - -
145B GLY 4.5 8.2 + - - +
146B ARG* 3.3 0.8 - - - +
147B LEU* 1.3 74.7 - - - +
149B TYR* 1.3 63.0 + - - +
151B SER* 3.4 9.5 + - - -
152B SER* 3.1 20.1 + - - -
199B LYS* 2.7 37.7 + - - +
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Residues in contact with TYR 149 (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 TYR* 4.1 7.4 - + - -
132B PHE* 4.9 2.0 - + - -
145B GLY 5.1 0.6 + - - -
146B ARG* 3.2 17.7 + - - +
148B ASP* 1.3 76.3 - - - +
150B LEU* 1.3 67.2 - - + +
152B SER* 2.4 36.3 + - - -
153B LEU* 3.4 21.6 + - + +
370B GLU* 2.6 41.4 + - - +
388B MET* 4.4 1.1 - - + -
390B TRP* 3.7 35.7 - + + -
408B VAL* 3.8 34.4 - - + +
419B LEU* 4.3 2.5 - - + +
423B ARG* 3.9 16.4 - - - -
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Residues in contact with LEU 150 (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 TYR* 3.3 49.8 - - + -
126B ILE* 4.9 7.0 - - + -
132B PHE* 4.8 5.6 - - + -
143B LEU* 5.7 3.1 - - + +
146B ARG* 3.1 18.7 + - + +
147B LEU* 3.7 18.2 - - + +
149B TYR* 1.3 85.8 - - + +
151B SER* 1.3 62.1 + - - +
153B LEU* 3.2 13.8 + - + +
154B LYS 3.4 4.2 + - - -
155B VAL* 3.2 32.2 + - + +
158B LEU* 3.8 29.8 - - + -
201B ILE* 4.8 6.7 - - + -
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Residues in contact with SER 151 (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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147B LEU 3.0 13.7 + - - -
148B ASP* 3.5 13.7 - - - -
149B TYR 3.2 0.2 - - - -
150B LEU* 1.3 76.6 - - - +
152B SER* 1.3 57.2 + - - +
153B LEU 3.2 0.2 - - - -
154B LYS* 3.1 25.3 + - - +
155B VAL 5.2 0.2 - - - -
199B LYS* 4.9 9.9 + - - +
201B ILE* 4.5 15.9 - - - +
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Residues in contact with SER 152 (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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148B ASP 3.1 11.1 + - - -
149B TYR* 2.4 30.1 + - - -
151B SER* 1.3 76.2 - - - +
153B LEU* 1.3 57.8 + - - +
154B LYS* 3.3 6.5 + - - +
423B ARG* 3.4 46.0 + - - +
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Residues in contact with LEU 153 (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 TYR* 3.8 32.5 - - + -
149B TYR* 3.6 34.5 - - + +
150B LEU* 3.2 12.4 + - + +
152B SER* 1.3 79.0 - - - +
154B LYS* 1.3 58.3 + - - +
155B VAL* 3.3 7.5 + - + +
370B GLU* 3.8 6.7 - - + +
419B LEU* 3.7 30.1 - - + -
422B PHE* 4.1 21.9 - - + -
423B ARG* 3.9 20.0 - - + +
426B SER* 2.8 31.0 + - - -
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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