Contacts of the helix formed by residues 143 - 154 (chain A) in PDB entry 2G73
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 ASP 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A GLY 5.5 0.9 - - - -
45A GLN* 4.2 18.7 + - - +
142A CYS* 1.3 74.8 - - - +
144A LEU* 1.3 66.2 + - - +
145A ALA* 4.3 7.2 - - + +
146A ASP* 2.9 37.2 + - - +
147A VAL* 3.2 13.5 + - - +
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A TRP* 4.5 11.0 - - + -
40A PHE* 4.3 12.8 - - + -
44A GLY 5.1 2.4 + - - -
46A LEU* 4.0 26.6 - - + +
142A CYS 3.6 4.2 + - - -
143A ASP* 1.3 69.8 - - - +
145A ALA* 1.3 54.6 + - - +
147A VAL* 2.9 10.1 + - + +
148A LEU* 2.8 54.4 + - + +
175A LEU* 3.5 20.6 - - + +
176A SER* 3.5 42.2 - - - +
179A THR* 4.0 20.1 - - + +
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Residues in contact with ALA 145 (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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143A ASP* 3.1 7.0 - - + +
144A LEU* 1.3 81.2 - - - +
146A ASP* 1.3 62.8 + - - +
148A LEU* 3.4 9.2 + - - +
149A HIS* 3.0 39.6 + - + -
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Residues in contact with ASP 146 (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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142A CYS* 5.4 3.4 - - + +
143A ASP* 2.9 34.4 + - - +
145A ALA* 1.3 75.9 - - - +
147A VAL* 1.3 62.2 + - + +
149A HIS* 3.0 17.8 + - - +
150A GLY 2.8 24.6 + - - -
153B ALA* 3.4 28.2 - - + +
154B THR* 3.7 3.6 - - + +
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Residues in contact with VAL 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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38A TRP* 4.9 1.8 - - + -
46A LEU* 3.9 18.8 - - + -
48A VAL* 3.9 9.2 - - + -
142A CYS* 3.5 33.4 - - + -
143A ASP 3.5 11.0 - - - +
144A LEU* 2.9 9.1 + - + +
146A ASP* 1.3 75.5 - - + +
148A LEU* 1.3 58.8 + - + +
150A GLY* 3.2 1.9 + - - -
151A ILE* 2.8 34.0 + - + +
158A PHE* 4.9 3.0 - - + -
162A MET* 3.7 30.1 - - + -
154B THR* 4.0 8.1 - - + +
156B TRP* 4.3 10.3 - - + -
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Residues in contact with LEU 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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38A TRP* 5.5 1.3 - - + -
144A LEU* 2.8 46.5 + - + +
145A ALA* 3.7 8.5 - - - +
147A VAL* 1.3 78.5 - - + +
149A HIS* 1.3 58.6 + - + +
151A ILE* 3.2 5.5 + - + +
152A ASP* 2.7 36.9 + - - +
166A ALA* 3.7 31.4 - - + +
172A ARG* 3.8 51.6 - - + +
175A LEU* 5.7 2.7 - - + -
176A SER* 4.2 8.7 - - - +
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Residues in contact with HIS 149 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A ALA* 3.0 34.4 + - + +
146A ASP* 3.0 17.8 + - - +
148A LEU* 1.3 78.4 - - + +
150A GLY* 1.3 63.6 + - - +
152A ASP* 3.1 11.4 + - + +
153A ALA* 2.8 27.1 + - - +
149B HIS 5.5 0.7 - - - +
153B ALA* 3.7 14.4 - - + +
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Residues in contact with GLY 150 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A ASP 2.8 13.4 + - - -
147A VAL 3.2 3.6 + - - -
149A HIS* 1.3 76.1 - - - +
151A ILE* 1.3 55.7 - - - +
153A ALA 3.2 0.5 + - - -
154A THR* 2.8 38.5 + - - -
158A PHE* 3.7 7.9 - - - -
150B GLY* 4.5 8.5 - - - -
153B ALA* 3.6 11.6 - - - +
154B THR* 4.1 17.0 - - - -
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Residues in contact with ILE 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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38A TRP* 4.3 2.0 - - + -
147A VAL* 2.8 24.8 + - + +
148A LEU* 3.2 7.6 + - + +
150A GLY* 1.3 75.5 - - - +
152A ASP* 1.3 62.6 + - - +
155A PRO* 3.4 23.5 - - - +
158A PHE* 3.9 27.8 - - + -
162A MET* 3.9 33.4 - - + +
163A VAL* 4.0 26.0 - - + +
166A ALA* 3.5 26.7 - - + -
167A THR* 4.1 19.5 - - + +
172A ARG* 5.1 0.2 - - - +
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Residues in contact with ASP 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 LEU 2.7 22.7 + - - +
149A HIS* 3.1 12.1 + - + +
151A ILE* 1.3 76.3 - - - +
153A ALA* 1.3 60.4 + - - +
155A PRO* 4.3 4.6 - - - +
167A THR* 4.2 8.5 - - - +
172A ARG* 2.9 41.5 + - - -
146B ASP* 6.0 0.2 - - - -
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Residues in contact with ALA 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 HIS 2.8 15.6 + - - +
150A GLY 3.9 1.6 - - - +
152A ASP* 1.3 80.0 - - + +
154A THR* 1.3 59.0 - - - +
155A PRO* 3.6 6.5 - - - +
156A TRP* 4.8 1.7 + - - -
146B ASP* 3.4 48.2 - - - +
149B HIS* 3.8 13.9 - - + +
150B GLY* 3.7 13.7 - - - +
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Residues in contact with THR 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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150A GLY* 2.8 20.5 + - - -
153A ALA* 1.3 80.0 - - - +
155A PRO* 1.3 68.4 - - - +
156A TRP* 3.1 41.7 - - + +
157A ALA* 3.0 16.7 + - - +
158A PHE* 3.7 6.9 - - - -
146B ASP* 3.6 18.2 - - + +
147B VAL* 3.8 12.1 - - + +
150B GLY* 3.9 10.8 - - - -
158B PHE* 3.7 17.6 - - + -
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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