Contacts of the helix formed by residues 147 - 161 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146H GLU* 1.3 85.2 - - + +
148H ALA* 1.3 64.6 + - - +
149H GLU* 3.4 9.1 + - - +
150H GLU* 2.9 39.2 + - - +
151H LEU* 3.0 28.8 + - - +
176H LEU* 5.4 2.5 - - - -
180H ILE* 4.4 1.6 - - - -
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Residues in contact with ALA 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147H THR* 1.3 74.4 - - - +
149H GLU* 1.3 57.6 + - - +
151H LEU* 3.4 2.2 + - - +
152H ALA* 2.9 34.5 + - - +
176H LEU* 5.0 3.5 - - + +
179H GLU* 4.2 11.0 - - + +
180H ILE* 3.8 27.1 - - + +
183H ALA* 3.9 22.4 - - + +
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Residues in contact with GLU 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147H THR* 3.2 8.8 - - - +
148H ALA* 1.3 80.1 - - - +
150H GLU* 1.3 65.4 + - + +
152H ALA* 3.4 4.4 + - - +
153H ARG* 3.1 25.0 + - + +
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Residues in contact with GLU 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144H GLN 4.0 3.2 - - - +
145H GLY* 3.7 11.3 - - - -
146H GLU* 2.8 35.6 + - - +
147H THR* 2.9 25.8 + - - +
149H GLU* 1.3 77.5 - - + +
151H LEU* 1.3 63.7 + - - +
153H ARG* 3.3 7.2 + - - +
154H ASP* 3.0 23.9 + - - +
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Residues in contact with LEU 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H LEU* 4.1 10.6 - - + +
144H GLN* 3.3 38.8 - - - +
145H GLY 3.5 13.5 - - - +
147H THR 3.0 20.8 + - - +
148H ALA* 3.9 3.8 - - - +
150H GLU* 1.3 74.8 - - - +
152H ALA* 1.3 57.2 + - - +
154H ASP* 3.4 2.6 + - - +
155H ALA* 2.9 29.1 + - - +
168H LEU* 3.8 21.5 - - + -
172H ARG* 3.5 27.4 - - - +
180H ILE* 3.9 22.0 - - + -
184H VAL* 4.1 16.1 - - + +
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Residues in contact with ALA 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H ALA 2.9 19.0 + - - +
149H GLU* 3.8 5.8 - - - +
151H LEU* 1.3 74.4 - - - +
153H ARG* 1.3 60.8 + - - +
155H ALA* 3.3 4.2 + - - -
156H ALA* 2.9 28.9 + - - +
183H ALA* 3.9 21.1 - - + +
184H VAL* 4.6 0.8 - - - +
187H GLU* 3.4 28.7 - - + +
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Residues in contact with ARG 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149H GLU* 3.1 18.0 + - + +
150H GLU* 3.6 7.2 - - - +
152H ALA* 1.3 75.6 - - - +
154H ASP* 1.3 64.5 + - - +
156H ALA* 3.3 10.3 + - - +
157H VAL* 3.1 36.9 + - + +
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Residues in contact with ASP 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H TYR* 2.6 33.0 + - - -
142H PHE 4.2 1.6 - - - +
143H LEU* 3.3 12.8 - - + +
144H GLN* 2.9 39.4 + - - +
150H GLU 3.0 16.6 + - - +
151H LEU 3.6 4.7 - - - +
152H ALA 3.3 0.2 - - - -
153H ARG* 1.3 78.3 - - - +
155H ALA* 1.3 56.8 + - - +
157H VAL* 3.4 7.4 + - - +
158H GLY 3.0 23.6 + - - -
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Residues in contact with ALA 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H LEU* 3.6 17.5 - - + +
151H LEU 2.9 18.5 + - - +
152H ALA* 3.7 6.5 - - - +
153H ARG 3.3 0.2 - - - -
154H ASP* 1.3 73.8 - - - +
156H ALA* 1.3 60.4 + - - +
159H HIS* 2.8 32.1 + - - +
166H PHE* 3.5 7.3 - - + -
184H VAL* 3.9 18.2 - - + +
187H GLU* 4.4 1.3 - - + -
188H ILE* 3.7 23.0 - - + +
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Residues in contact with ALA 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152H ALA 2.9 13.5 + - - +
153H ARG* 3.4 16.2 - - - +
155H ALA* 1.3 77.2 - - - +
157H VAL* 1.3 64.0 + - + +
159H HIS* 3.4 2.4 + - - +
160H ALA* 3.0 23.7 + - - +
187H GLU* 4.1 29.1 - - + +
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Residues in contact with VAL 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H TYR* 5.1 4.0 - - - +
153H ARG* 3.1 29.9 + - + +
154H ASP* 3.8 8.5 - - - +
156H ALA* 1.3 74.0 - - + +
158H GLY* 1.3 67.3 + - - +
160H ALA* 3.1 7.8 + - + +
161H GLN* 2.9 49.1 + - + +
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Residues in contact with GLY 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H TYR* 4.0 12.3 + - - -
154H ASP 3.0 16.3 + - - -
155H ALA 3.9 0.9 - - - -
157H VAL* 1.3 77.4 - - - +
159H HIS* 1.3 62.7 + - - +
161H GLN* 3.1 19.1 + - - +
162H GLY 3.3 0.2 + - - -
163H GLU* 3.1 40.0 + - - +
166H PHE* 4.0 1.3 - - - -
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Residues in contact with HIS 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155H ALA 2.8 19.2 + - - +
156H ALA 3.7 4.0 - - - +
158H GLY* 1.3 76.3 - - - +
160H ALA* 1.3 64.9 + - - +
162H GLY* 3.1 14.2 + - - -
163H GLU 4.2 5.5 + - - +
166H PHE* 3.5 15.3 - + + -
187H GLU 4.0 9.9 + - - +
188H ILE* 3.3 40.6 + - + -
189H GLY* 4.9 2.9 - - - -
190H ASP* 5.5 1.6 + - - -
191H ALA* 4.1 13.2 + - + +
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Residues in contact with ALA 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156H ALA 3.0 18.5 + - - +
157H VAL* 3.1 7.8 + - - +
159H HIS* 1.3 79.4 + - - +
161H GLN* 1.3 59.7 + - + +
162H GLY* 3.1 1.7 + - - -
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Residues in contact with GLN 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H TYR* 4.5 11.3 + - - -
157H VAL* 2.9 38.9 + - + +
158H GLY* 3.1 13.5 + - - +
160H ALA* 1.3 77.5 - - + +
162H GLY* 1.3 59.3 + - - +
163H GLU* 3.6 8.3 - - + +
345H ASN* 3.5 15.1 + - - +
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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