Contacts of the helix formed by residues 147 - 161 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146G GLU* 1.3 83.8 - - + +
148G ALA* 1.3 64.8 + - - +
149G GLU* 3.5 8.8 + - - +
150G GLU* 3.1 35.6 + - - +
151G LEU* 3.1 24.8 + - - +
176G LEU* 5.2 3.8 - - - -
180G ILE* 4.4 4.3 - - - -
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Residues in contact with ALA 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147G THR* 1.3 73.4 - - - +
149G GLU* 1.3 58.1 + - - +
151G LEU* 3.5 1.1 + - - +
152G ALA* 2.8 31.9 + - - +
176G LEU* 4.8 4.2 - - + +
179G GLU* 4.1 16.2 - - + +
180G ILE* 3.8 25.8 - - + +
183G ALA* 3.7 21.3 - - + +
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Residues in contact with GLU 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147G THR* 3.2 8.9 + - - +
148G ALA* 1.3 80.1 - - - +
150G GLU* 1.3 62.8 + - - +
152G ALA* 3.2 6.9 + - - +
153G ARG* 3.0 58.4 + - - +
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Residues in contact with GLU 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G GLN 4.2 2.9 - - - +
145G GLY* 4.1 10.3 - - - -
146G GLU* 2.8 36.2 + - - +
147G THR* 3.1 26.0 + - - +
149G GLU* 1.3 76.6 - - + +
151G LEU* 1.3 63.0 + - - +
153G ARG* 3.3 29.1 + - - +
154G ASP* 3.1 22.7 + - - +
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Residues in contact with LEU 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143G LEU* 4.1 9.9 - - + +
144G GLN* 3.3 36.6 - - - +
145G GLY 3.7 13.0 - - - +
147G THR 3.1 19.6 + - - +
148G ALA* 3.9 3.6 - - - +
150G GLU* 1.3 75.0 - - - +
152G ALA* 1.3 61.6 + - - +
154G ASP* 3.4 2.5 + - - +
155G ALA* 2.9 30.5 + - - +
168G LEU* 3.8 20.6 - - + -
172G ARG* 3.8 22.9 - - - +
180G ILE* 3.8 29.8 - - + +
184G VAL* 4.1 14.4 - - + +
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Residues in contact with ALA 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148G ALA 2.8 19.0 + - - +
149G GLU* 3.4 9.2 - - - +
151G LEU* 1.3 77.6 - - - +
153G ARG* 1.3 56.7 + - + +
155G ALA* 3.4 2.4 + - - -
156G ALA* 3.0 24.6 + - - +
183G ALA* 4.1 24.9 - - + +
184G VAL* 4.9 0.4 - - - +
187G GLU* 3.3 25.7 - - + +
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Residues in contact with ARG 153 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149G GLU* 3.0 56.2 + - - +
150G GLU* 3.6 28.4 + - - +
152G ALA* 1.3 76.3 - - + +
154G ASP* 1.3 62.8 + - - +
156G ALA* 3.5 7.2 + - - +
157G VAL* 3.2 27.8 + - - +
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Residues in contact with ASP 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G TYR* 2.7 30.1 + - - -
142G PHE 4.2 1.9 - - - +
143G LEU* 3.4 14.6 - - + +
144G GLN* 3.0 38.2 + - - +
150G GLU 3.1 16.6 + - - +
151G LEU 3.9 3.4 - - - +
153G ARG* 1.3 73.2 - - - +
155G ALA* 1.3 66.9 + - - +
157G VAL* 3.1 9.5 + - - +
158G GLY 2.9 19.4 + - - -
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Residues in contact with ALA 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143G LEU* 3.6 13.6 - - + +
151G LEU 2.9 17.1 + - - +
152G ALA 3.6 6.1 - - - +
154G ASP* 1.3 78.3 - - - +
156G ALA* 1.3 57.0 + - - +
158G GLY 3.3 0.9 + - - -
159G HIS* 2.9 30.1 + - - +
166G PHE* 3.6 8.0 - - - -
184G VAL* 4.0 19.5 - - + +
187G GLU* 4.0 9.4 - - + -
188G ILE* 4.0 19.4 - - + +
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Residues in contact with ALA 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152G ALA 3.0 16.5 + - - +
153G ARG* 3.7 8.5 - - - +
154G ASP 3.2 0.2 - - - -
155G ALA* 1.3 76.3 - - - +
157G VAL* 1.3 57.8 + - - +
159G HIS* 3.6 5.6 - - - +
160G ALA* 2.8 31.4 + - - +
187G GLU* 3.7 25.7 - - - +
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Residues in contact with VAL 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G TYR* 3.8 13.9 - - - +
153G ARG 3.2 15.5 + - - +
154G ASP* 3.1 12.5 + - - +
156G ALA* 1.3 76.1 - - + +
158G GLY* 1.3 66.3 + - - +
160G ALA* 3.2 8.1 + - - +
161G GLN* 3.1 35.3 + - - +
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Residues in contact with GLY 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G TYR* 3.6 26.0 - - - -
154G ASP 2.9 11.1 + - - -
155G ALA 3.7 2.0 - - - -
157G VAL* 1.3 76.8 - - - +
159G HIS* 1.3 63.4 + - - +
161G GLN* 3.2 13.0 + - - +
163G GLU* 3.0 35.5 + - - -
166G PHE* 3.9 3.1 - - - -
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Residues in contact with HIS 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G ALA 2.9 17.9 + - - +
156G ALA* 3.6 4.5 - - - +
158G GLY* 1.3 76.3 - - - +
160G ALA* 1.3 64.4 + - - +
162G GLY* 3.1 14.0 + - - -
163G GLU 4.6 5.0 + - - +
166G PHE* 3.6 15.2 - - + -
187G GLU 3.6 19.5 - - - +
188G ILE* 3.4 32.9 + - - +
189G GLY* 4.3 3.8 + - - -
191G ALA* 4.7 4.9 - - + +
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Residues in contact with ALA 160 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156G ALA 2.8 17.5 + - - +
157G VAL* 3.4 9.4 - - - +
159G HIS* 1.3 80.0 - - - +
161G GLN* 1.3 57.9 + - + +
162G GLY 3.3 0.9 + - - -
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Residues in contact with GLN 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G TYR* 3.8 13.7 - - - -
157G VAL* 3.1 28.8 + - - +
158G GLY* 3.2 11.4 - - - +
159G HIS 3.2 0.2 - - - -
160G ALA* 1.3 75.0 - - - +
162G GLY* 1.3 60.6 + - - +
163G GLU* 2.8 27.0 + - - +
343G PRO 6.0 0.4 + - - -
345G ASN* 3.5 16.9 + - - +
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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