Contacts of the helix formed by residues 146 - 155 (chain A) in PDB entry 2DNH
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 SER 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A GLN 5.2 0.9 - - - -
145A GLN* 1.3 75.2 - - - +
147A GLU* 1.3 67.3 + - - +
148A GLU* 3.7 10.0 + - - +
149A ASP* 2.7 43.3 + - - +
150A VAL* 3.3 9.3 + - - +
165A VAL* 4.8 5.8 - - - -
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Residues in contact with GLU 147 (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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146A SER* 1.3 73.0 - - - +
148A GLU* 1.3 64.4 + - + +
150A VAL* 3.4 3.3 + - - +
151A LEU* 2.9 36.6 + - + +
163A CYS* 2.8 41.0 - - - +
164A THR* 3.5 11.7 + - - +
165A VAL* 3.7 26.9 + - + +
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Residues in contact with GLU 148 (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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146A SER* 3.1 9.9 + - - +
147A GLU* 1.3 79.8 - - + +
149A ASP* 1.3 65.4 + - - +
151A LEU* 3.6 9.2 - - + +
152A ARG* 2.7 43.1 + - + +
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Residues in contact with ASP 149 (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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144A GLN 4.0 4.9 - - - +
145A GLN* 3.4 24.6 - - + +
146A SER* 2.7 40.3 + - - +
148A GLU* 1.3 79.7 - - - +
150A VAL* 1.3 63.6 + - - +
152A ARG* 3.1 7.2 + - - +
153A LEU* 3.0 20.8 + - - +
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Residues in contact with VAL 150 (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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138A VAL* 5.6 2.5 - - + -
141A LEU* 5.0 13.9 - - + -
145A GLN* 3.6 22.9 + - + +
146A SER 3.3 9.4 + - - +
147A GLU* 3.8 7.2 - - - +
149A ASP* 1.3 78.0 - - - +
151A LEU* 1.3 53.7 + - - +
153A LEU* 2.6 28.6 + - + -
154A PHE* 2.6 64.9 + - + -
163A CYS* 4.8 5.8 - - - -
165A VAL* 6.3 1.6 - - + -
177A ALA* 5.7 4.9 - - + -
179A VAL* 3.9 15.0 - - + -
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Residues in contact with LEU 151 (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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147A GLU* 2.9 37.5 + - + +
148A GLU* 3.7 9.0 - - + +
150A VAL* 1.3 75.8 - - - +
152A ARG* 1.3 54.8 + - + +
155A GLN* 2.7 37.4 + - - +
160A ILE* 3.4 42.0 - - + +
161A ASP 6.0 0.4 - - - -
162A GLU* 5.5 0.4 - - - -
163A CYS* 3.0 37.2 - - + +
179A VAL* 4.9 0.2 - - + -
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Residues in contact with ARG 152 (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 GLU* 2.7 42.7 + - + +
149A ASP* 3.2 8.1 - - - +
150A VAL 2.8 0.6 + - - -
151A LEU* 1.3 75.4 - - + +
153A LEU* 1.3 56.1 + - - +
155A GLN* 4.1 3.5 - - - +
156A PRO* 2.8 24.6 - - - +
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Residues in contact with LEU 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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145A GLN* 5.8 2.9 - - - +
149A ASP 3.0 10.1 + - - +
150A VAL* 2.6 14.1 + - + +
152A ARG* 1.3 73.1 - - - +
154A PHE* 1.3 63.0 + - + +
156A PRO* 3.5 10.0 - - + +
157A PHE* 3.3 20.2 - - + -
194A LEU* 3.8 29.2 - - + -
198A GLN* 3.0 36.6 - - - +
200A MET* 5.4 2.0 - - + -
207A LEU* 6.3 0.4 - - + -
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Residues in contact with PHE 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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136A LEU* 5.2 3.1 - - + -
138A VAL* 4.2 18.6 - - + -
150A VAL* 2.6 45.5 + - + +
153A LEU* 1.3 82.8 - - + +
155A GLN* 1.3 53.6 + - - +
156A PRO* 3.1 2.2 - - - -
157A PHE* 2.7 37.3 + - - +
158A GLY 3.2 4.5 + - - +
160A ILE* 3.0 23.8 - - + -
179A VAL* 3.5 33.9 - - + -
181A PHE* 3.9 14.7 - + + -
190A ALA* 4.5 6.1 - - + -
194A LEU* 2.9 36.1 - - + -
207A LEU* 4.9 9.6 - - + -
209A VAL* 5.2 5.2 - - + -
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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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151A LEU 2.7 20.9 + - - +
152A ARG* 4.1 4.7 - - - +
154A PHE* 1.3 71.1 - - - +
156A PRO* 1.3 65.0 - - + +
157A PHE 2.6 12.3 + - - -
158A GLY* 2.7 28.6 + - - +
159A VAL* 3.9 29.6 - - - +
160A ILE* 3.8 5.1 - - + +
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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