Contacts of the helix formed by residues 147 - 161 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F GLU* 1.3 87.0 - - + +
148F ALA* 1.3 66.0 + - - +
149F GLU* 3.5 8.7 + - - +
150F GLU* 3.2 35.4 + - - +
151F LEU* 3.0 29.4 + - - +
176F LEU* 5.3 3.6 - - - -
180F ILE* 4.4 2.2 - - - -
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Residues in contact with ALA 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F THR* 1.3 75.3 - - - +
149F GLU* 1.3 56.7 + - - +
151F LEU* 4.0 1.2 - - - +
152F ALA* 2.8 32.8 + - - +
176F LEU* 5.0 3.9 - - + +
179F GLU* 4.0 28.0 - - + +
180F ILE* 4.0 20.2 - - + +
183F ALA* 3.9 10.6 - - + +
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Residues in contact with GLU 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F THR* 3.2 9.0 + - - +
148F ALA* 1.3 78.6 - - - +
150F GLU* 1.3 63.1 + - + +
152F ALA* 3.3 5.4 + - - +
153F ARG* 3.0 53.0 + - - +
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Residues in contact with GLU 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F GLN 4.2 2.6 - - - +
145F GLY* 3.3 13.4 - - - -
146F GLU* 2.8 28.6 + - - +
147F THR* 3.2 29.6 + - - +
149F GLU* 1.3 80.3 - - + +
151F LEU* 1.3 63.1 + - - +
153F ARG* 3.1 18.9 + - - +
154F ASP* 3.0 24.1 + - - +
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Residues in contact with LEU 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F LEU* 4.2 8.1 - - + +
144F GLN* 3.4 37.0 - - - +
145F GLY 3.5 17.5 - - - +
147F THR 3.0 21.4 + - - +
148F ALA* 4.0 3.1 - - - +
150F GLU* 1.3 76.2 - - - +
152F ALA* 1.3 57.8 + - - +
154F ASP* 3.5 1.9 + - - +
155F ALA* 2.9 30.1 + - - +
168F LEU* 3.9 22.4 - - + -
172F ARG* 3.9 14.1 - - - +
180F ILE* 3.7 31.0 - - + -
184F VAL* 4.0 17.0 - - + +
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Residues in contact with ALA 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F ALA 2.8 20.1 + - - +
149F GLU* 3.7 6.5 - - - +
151F LEU* 1.3 76.0 - - - +
153F ARG* 1.3 58.0 + - - +
155F ALA* 3.5 3.5 + - - +
156F ALA* 3.0 23.7 + - - +
183F ALA* 4.0 20.6 - - + +
184F VAL* 4.6 0.4 - - - +
187F GLU* 3.2 33.3 - - + +
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Residues in contact with ARG 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F GLU* 3.0 48.8 + - - +
150F GLU* 3.4 21.4 - - - +
152F ALA* 1.3 75.1 - - - +
154F ASP* 1.3 65.8 + - - +
156F ALA* 3.1 9.8 + - + +
157F VAL* 3.0 32.7 + - + +
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Residues in contact with ASP 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F TYR* 2.7 29.6 + - - -
142F PHE 4.2 1.9 - - - +
143F LEU* 3.2 15.4 - - + -
144F GLN* 2.8 42.3 + - - +
150F GLU 3.0 15.5 + - - +
151F LEU 3.9 2.9 - - - +
153F ARG* 1.3 77.3 - - - +
155F ALA* 1.3 57.7 + - - +
157F VAL* 3.2 10.2 + - - +
158F GLY 3.0 23.2 + - - -
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Residues in contact with ALA 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F LEU* 3.7 15.9 - - + +
151F LEU 2.9 19.5 + - - +
152F ALA* 3.6 8.1 - - - +
154F ASP* 1.3 74.7 - - - +
156F ALA* 1.3 60.3 + - - +
158F GLY* 3.1 1.9 + - - -
159F HIS* 2.8 31.4 + - - +
166F PHE* 3.6 5.9 - - - -
184F VAL* 4.1 20.2 - - + -
187F GLU* 4.0 14.6 - - + -
188F ILE* 4.1 7.2 - - + -
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Residues in contact with ALA 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F ALA 3.0 14.5 + - - +
153F ARG* 3.3 12.1 - - + +
155F ALA* 1.3 76.4 - - - +
157F VAL* 1.3 57.5 + - + +
159F HIS* 3.5 1.4 + - - +
160F ALA* 2.9 30.9 + - - +
187F GLU* 3.6 28.2 - - - +
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Residues in contact with VAL 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F TYR* 3.9 11.2 - - - +
153F ARG* 3.0 28.5 + - + +
154F ASP* 3.3 12.3 - - - +
155F ALA 3.2 0.2 - - - -
156F ALA* 1.3 76.6 - - + +
158F GLY* 1.3 62.5 + - - +
160F ALA* 3.2 8.9 + - - +
161F GLN* 3.1 34.2 + - - +
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Residues in contact with GLY 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F TYR* 3.6 27.1 + - - -
154F ASP 3.0 10.5 + - - -
155F ALA 3.1 2.7 + - - -
157F VAL* 1.3 77.6 - - - +
159F HIS* 1.3 62.3 + - - +
161F GLN* 3.2 16.2 + - - +
163F GLU* 3.0 29.4 + - - -
166F PHE* 3.8 3.4 - - - -
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Residues in contact with HIS 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F ALA 2.8 19.2 + - - +
156F ALA* 3.9 3.6 - - - +
158F GLY* 1.3 71.5 - - - +
160F ALA* 1.3 64.8 + - - +
162F GLY* 3.1 13.0 + - - +
163F GLU 4.6 5.2 - - - +
166F PHE* 3.5 17.3 - + + -
187F GLU 3.6 18.7 + - - +
188F ILE* 3.5 35.3 + - + -
189F GLY* 4.8 3.5 - - - -
191F ALA* 4.5 4.6 - - + +
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Residues in contact with ALA 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156F ALA 2.9 19.5 + - - +
157F VAL* 3.4 9.4 - - - +
158F GLY 3.2 0.2 - - - -
159F HIS* 1.3 79.6 + - - +
161F GLN* 1.3 57.3 + - + +
162F GLY 3.4 2.8 + - - -
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Residues in contact with GLN 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F TYR* 3.8 16.2 - - - -
157F VAL* 3.1 25.2 + - - +
158F GLY* 3.2 15.9 - - - +
160F ALA* 1.3 74.5 - - - +
162F GLY* 1.3 59.9 + - - +
163F GLU* 3.0 25.0 + - + +
343F PRO 5.9 0.6 + - - -
345F ASN* 3.3 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