Contacts of the helix formed by residues 147 - 161 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146B GLU* 1.3 85.9 - - + +
148B ALA* 1.3 65.9 + - - +
149B GLU* 3.7 7.1 + - - +
150B GLU* 3.0 33.3 + - - +
151B LEU* 3.0 24.5 + - - +
176B LEU* 5.2 3.8 - - - -
180B ILE* 4.3 6.7 - - - -
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Residues in contact with ALA 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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147B THR* 1.3 73.6 - - - +
149B GLU* 1.3 57.5 + - - +
151B LEU* 3.7 2.1 - - - +
152B ALA* 2.8 32.2 + - - +
176B LEU* 4.9 4.1 - - + +
179B GLU* 4.4 12.1 - - + +
180B ILE* 3.8 25.7 - - + +
183B ALA* 3.9 20.6 - - + +
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Residues in contact with GLU 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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147B THR* 3.2 7.6 + - - +
148B ALA* 1.3 78.3 - - - +
150B GLU* 1.3 62.8 + - + +
152B ALA* 3.3 7.2 + - + +
153B ARG* 3.0 55.8 + - + +
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Residues in contact with GLU 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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144B GLN 4.0 3.1 - - - +
145B GLY* 3.6 11.0 - - - -
146B GLU* 2.7 35.1 + - - +
147B THR* 3.0 25.9 + - - +
149B GLU* 1.3 76.3 - - + +
151B LEU* 1.3 63.8 + - - +
153B ARG* 3.3 28.0 + - - +
154B ASP* 3.1 23.0 + - - +
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Residues in contact with LEU 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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143B LEU* 4.4 8.5 - - + +
144B GLN* 3.4 36.3 - - - +
145B GLY 3.6 12.8 - - - +
147B THR 3.0 16.4 + - - +
148B ALA* 3.8 3.8 - - - +
150B GLU* 1.3 75.5 - - - +
152B ALA* 1.3 58.6 + - - +
154B ASP* 3.4 2.5 + - - +
155B ALA* 2.9 29.8 + - - +
168B LEU* 3.8 18.4 - - + -
172B ARG* 3.8 23.6 - - - +
180B ILE* 3.6 36.1 - - + +
184B VAL* 4.1 16.4 - - + +
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Residues in contact with ALA 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 ALA 2.8 19.2 + - - +
149B GLU* 3.6 8.1 - - - +
150B GLU 3.2 0.2 - - - -
151B LEU* 1.3 77.2 - - - +
153B ARG* 1.3 56.3 + - + +
155B ALA* 3.3 3.5 + - - +
156B ALA* 2.9 24.6 + - - +
183B ALA* 4.1 19.1 - - + +
184B VAL* 4.8 0.4 - - - +
187B GLU* 3.4 33.2 - - + +
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Residues in contact with ARG 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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149B GLU* 3.0 45.5 + - + +
150B GLU* 3.6 34.2 + - - +
152B ALA* 1.3 78.5 - - + +
154B ASP* 1.3 62.9 + - - +
156B ALA* 3.3 8.1 + - - +
157B VAL* 3.0 29.1 + - + +
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Residues in contact with ASP 154 (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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141B TYR* 2.8 31.0 + - - -
142B PHE 4.1 2.3 - - - +
143B LEU* 3.3 14.4 - - + +
144B GLN* 2.9 39.5 + - - +
150B GLU 3.1 16.1 + - - +
151B LEU 3.8 3.6 - - - +
152B ALA 3.3 0.2 - - - -
153B ARG* 1.3 75.5 - - - +
155B ALA* 1.3 58.7 + - - +
157B VAL* 3.3 9.5 + - - +
158B GLY 2.9 23.0 + - - -
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Residues in contact with ALA 155 (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 13.8 - - + +
151B LEU 2.9 18.0 + - - +
152B ALA 3.5 5.4 - - - +
154B ASP* 1.3 78.0 - - - +
156B ALA* 1.3 56.4 + - - +
158B GLY* 3.1 2.0 + - - +
159B HIS* 2.8 31.2 + - - +
166B PHE* 3.7 5.7 - - - -
184B VAL* 4.0 19.5 - - + +
187B GLU* 4.0 9.6 - - + -
188B ILE* 4.0 19.0 - - + +
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Residues in contact with ALA 156 (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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152B ALA 2.9 14.4 + - - +
153B ARG* 3.3 11.9 + - - +
155B ALA* 1.3 75.3 - - - +
157B VAL* 1.3 62.4 + - + +
159B HIS* 3.4 2.0 + - - +
160B ALA* 3.0 25.3 + - - +
187B GLU* 3.7 30.2 - - - +
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Residues in contact with VAL 157 (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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141B TYR* 3.9 12.1 - - - +
153B ARG* 3.0 19.1 + - + +
154B ASP* 3.4 11.9 - - - +
155B ALA 3.2 0.2 - - - -
156B ALA* 1.3 77.8 - - + +
158B GLY* 1.3 62.7 + - - +
160B ALA* 3.2 8.8 + - - +
161B GLN* 3.2 33.9 + - - +
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Residues in contact with GLY 158 (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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141B TYR* 3.7 19.0 + - - -
154B ASP 2.9 11.1 + - - -
155B ALA 3.1 3.3 + - - -
157B VAL* 1.3 75.6 - - - +
159B HIS* 1.3 60.4 + - - +
161B GLN* 3.2 12.9 - - - +
163B GLU* 3.0 41.9 + - - -
166B PHE* 3.9 2.0 - - - -
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Residues in contact with HIS 159 (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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155B ALA 2.8 19.7 + - - +
156B ALA* 3.7 4.3 - - - +
158B GLY* 1.3 71.0 - - - +
160B ALA* 1.3 66.0 + - - +
162B GLY* 3.1 14.2 + - - -
163B GLU 4.6 5.1 + - - +
166B PHE* 3.5 16.2 - - + -
187B GLU 3.6 21.8 - - - +
188B ILE* 3.5 29.5 + - - +
189B GLY* 4.5 4.2 + - - -
190B ASP 5.6 0.2 - - - -
191B ALA* 4.7 4.1 - - + +
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Residues in contact with ALA 160 (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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156B ALA 3.0 18.4 + - - +
157B VAL* 3.2 8.3 + - - +
159B HIS* 1.3 80.5 - - - +
161B GLN* 1.3 56.4 + - + +
162B GLY 3.3 3.1 + - - -
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Residues in contact with GLN 161 (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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141B TYR* 3.9 12.7 - - - -
157B VAL* 3.2 22.6 + - - +
158B GLY* 3.2 16.4 - - - +
160B ALA* 1.3 77.1 - - + +
162B GLY* 1.3 57.9 + - - +
163B GLU* 2.8 29.7 + - + +
343B PRO 5.7 1.8 + - - -
345B ASN* 3.3 17.8 + - - +
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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