Contacts of the helix formed by residues 147 - 161 (chain A) in PDB entry 2PGW
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 THR 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A GLU* 1.3 85.5 - - + +
148A ALA* 1.3 65.9 + - - +
149A GLU* 3.7 8.6 + - - +
150A GLU* 2.9 37.6 + - - +
151A LEU* 3.1 28.0 + - - +
176A LEU* 5.3 3.1 - - - -
180A ILE* 4.4 2.2 - - - -
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Residues in contact with ALA 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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147A THR* 1.3 75.3 - - - +
149A GLU* 1.3 59.3 + - - +
151A LEU* 3.5 1.4 + - - +
152A ALA* 2.9 28.9 + - - +
176A LEU* 4.9 4.4 - - + +
179A GLU* 4.3 14.1 - - + +
180A ILE* 3.9 22.5 - - + +
183A ALA* 3.7 21.0 - - + +
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Residues in contact with GLU 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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147A THR* 3.7 9.3 + - - +
148A ALA* 1.3 76.4 - - - +
150A GLU* 1.3 64.5 + - + +
152A ALA* 3.6 8.3 - - + +
153A ARG* 2.9 60.1 + - - +
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Residues in contact with GLU 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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144A GLN 4.1 2.9 - - - +
145A GLY* 3.9 10.7 - - - -
146A GLU* 2.7 35.9 + - - +
147A THR* 2.9 34.1 + - - +
149A GLU* 1.3 78.5 - - + +
151A LEU* 1.3 58.3 + - - +
153A ARG* 3.3 20.9 + - - +
154A ASP* 2.9 28.4 + - - +
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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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143A LEU* 4.2 9.3 - - + +
144A GLN* 3.3 35.9 - - - +
145A GLY 3.6 17.5 - - - +
147A THR 3.1 17.0 + - - +
148A ALA* 3.9 3.4 - - - +
150A GLU* 1.3 72.9 - - - +
152A ALA* 1.3 61.2 + - - +
154A ASP* 3.2 1.4 + - - +
155A ALA* 2.8 32.3 + - - +
168A LEU* 3.9 18.6 - - + -
172A ARG* 3.9 20.6 - - - +
180A ILE* 3.7 30.5 - - + -
184A VAL* 4.1 13.9 - - + +
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Residues in contact with ALA 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 ALA 2.9 19.0 + - - +
149A GLU* 3.6 10.3 - - + +
151A LEU* 1.3 76.8 - - - +
153A ARG* 1.3 57.3 + - - +
155A ALA* 3.4 2.8 + - - +
156A ALA* 2.9 24.3 + - - +
183A ALA* 4.0 24.2 - - + +
184A VAL* 4.7 0.8 - - - +
187A GLU* 3.2 28.2 - - + +
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Residues in contact with ARG 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 GLU* 2.9 50.6 + - - +
150A GLU* 3.4 29.9 - - - +
152A ALA* 1.3 76.3 - - - +
154A ASP* 1.3 63.1 + - - +
156A ALA* 3.2 9.5 + - + +
157A VAL* 3.1 29.7 + - + +
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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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141A TYR* 2.7 31.9 + - - -
142A PHE 4.2 1.6 - - - +
143A LEU* 3.2 13.3 - - + +
144A GLN* 2.9 43.0 + - - +
150A GLU 2.9 16.5 + - - +
151A LEU 3.8 3.1 - - - +
153A ARG* 1.3 76.7 - - - +
155A ALA* 1.3 62.5 + - - +
157A VAL* 3.3 9.3 + - - +
158A GLY 3.1 17.0 + - - -
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Residues in contact with ALA 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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143A LEU* 3.6 14.1 - - + +
151A LEU 2.8 18.3 + - - +
152A ALA 3.6 5.4 - - - +
154A ASP* 1.3 73.6 - - - +
156A ALA* 1.3 60.3 + - - +
158A GLY* 3.1 2.1 + - - -
159A HIS* 2.9 30.1 + - - +
166A PHE* 3.7 7.2 - - + -
184A VAL* 3.8 28.7 - - + +
187A GLU* 4.1 8.1 - - + -
188A ILE* 4.0 10.4 - - + +
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Residues in contact with ALA 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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152A ALA 2.9 13.2 + - - +
153A ARG* 3.3 14.6 - - + +
155A ALA* 1.3 77.4 - - - +
157A VAL* 1.3 62.0 + - + +
159A HIS* 3.4 2.6 + - - +
160A ALA* 3.0 24.3 + - - +
187A GLU* 3.8 27.8 - - - +
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Residues in contact with VAL 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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141A TYR* 4.1 11.2 - - - +
153A ARG* 3.1 20.1 + - + +
154A ASP* 3.5 12.3 - - - +
155A ALA 3.2 0.2 - - - -
156A ALA* 1.3 79.3 - - + +
158A GLY* 1.3 63.1 + - - +
160A ALA* 3.3 9.2 + - + +
161A GLN* 3.2 34.4 + - - +
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Residues in contact with GLY 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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141A TYR* 3.7 24.6 - - - -
154A ASP 3.1 11.1 + - - -
155A ALA 3.1 3.5 + - - -
157A VAL* 1.3 76.9 - - - +
159A HIS* 1.3 61.9 + - - +
161A GLN* 3.1 12.7 + - - +
163A GLU* 3.1 34.9 + - - -
166A PHE* 3.8 4.3 - - - -
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Residues in contact with HIS 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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155A ALA 2.9 13.5 + - - +
156A ALA 3.7 4.3 - - - +
158A GLY* 1.3 74.3 - - - +
160A ALA* 1.3 65.9 + - - +
162A GLY* 3.0 15.4 + - - -
163A GLU 4.7 5.2 + - - +
166A PHE* 3.5 15.0 - - + -
187A GLU 3.6 25.5 + - - +
188A ILE* 3.9 26.0 + - - +
189A GLY* 4.7 3.0 + - - -
191A ALA* 5.0 4.4 - - + +
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Residues in contact with ALA 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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156A ALA 3.0 18.1 + - - +
157A VAL* 3.5 9.6 - - + +
159A HIS* 1.3 79.0 - - - +
161A GLN* 1.3 57.9 + - + +
162A GLY 3.4 0.7 + - - -
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Residues in contact with GLN 161 (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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141A TYR* 3.6 18.8 - - - -
157A VAL* 3.2 24.0 + - - +
158A GLY* 3.2 14.4 - - - +
159A HIS 3.0 1.2 + - - -
160A ALA* 1.3 76.5 - - - +
162A GLY* 1.3 59.5 + - - +
163A GLU* 3.3 22.2 - - - +
345A ASN* 3.5 18.0 + - - +
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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