Contacts of the helix formed by residues 147 - 162 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146E GLU* 1.3 85.5 - - + +
148E ALA* 1.3 65.1 + - - +
149E GLU* 3.6 9.1 + - - +
150E GLU* 3.0 36.6 + - - +
151E LEU* 3.0 27.3 + - - +
176E LEU* 5.3 2.7 - - - -
180E ILE* 4.5 0.7 - - - -
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Residues in contact with ALA 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E THR* 1.3 73.1 - - - +
149E GLU* 1.3 58.1 + - - +
151E LEU* 3.2 3.4 + - - +
152E ALA* 2.8 33.7 + - - +
176E LEU* 4.9 3.7 - - + +
179E GLU* 4.3 11.4 - - + +
180E ILE* 3.9 28.2 - - + +
183E ALA* 4.0 18.4 - - + +
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Residues in contact with GLU 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E THR* 3.2 8.6 - - - +
148E ALA* 1.3 79.3 - - - +
150E GLU* 1.3 62.6 + - + +
152E ALA* 3.4 5.3 + - - +
153E ARG* 2.7 64.4 + - + +
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Residues in contact with GLU 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E GLN 4.0 2.1 - - - +
145E GLY* 3.6 10.7 - - - -
146E GLU* 2.8 35.8 + - - +
147E THR* 3.0 31.1 + - + +
149E GLU* 1.3 77.9 - - + +
151E LEU* 1.3 58.7 + - - +
153E ARG* 3.3 13.6 + - - +
154E ASP* 2.9 28.8 + - - +
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Residues in contact with LEU 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E LEU* 4.3 6.6 - - + +
144E GLN* 3.2 36.8 - - - +
145E GLY 3.4 13.7 - - - +
146E GLU 5.0 0.2 - - - -
147E THR 3.0 17.3 + - - +
148E ALA* 3.7 4.3 - - - +
150E GLU* 1.3 77.0 - - - +
152E ALA* 1.3 55.6 + - - +
154E ASP* 3.3 2.5 + - - +
155E ALA* 2.9 30.1 + - - +
168E LEU* 3.8 23.6 - - + -
172E ARG* 3.9 15.0 - - - +
180E ILE* 3.6 35.9 - - + -
184E VAL* 4.1 15.3 - - + +
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Residues in contact with ALA 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E ALA 2.8 21.4 + - - +
149E GLU* 3.8 5.4 - - - +
151E LEU* 1.3 73.5 - - - +
153E ARG* 1.3 57.9 + - + +
155E ALA* 3.5 3.7 + - - +
156E ALA* 3.0 23.2 + - - +
183E ALA* 3.9 22.0 - - + +
184E VAL* 4.6 0.8 - - - +
187E GLU* 3.2 34.0 - - + +
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Residues in contact with ARG 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E GLU* 2.7 59.6 + - - +
150E GLU* 3.6 12.1 - - - +
151E LEU 3.2 0.2 - - - -
152E ALA* 1.3 75.0 - - + +
154E ASP* 1.3 65.8 + - - +
156E ALA* 3.2 7.7 + - + +
157E VAL* 3.0 27.8 + - + +
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Residues in contact with ASP 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E TYR* 2.7 30.3 + - - -
142E PHE 4.1 1.7 - - - +
143E LEU* 3.2 15.4 - - + +
144E GLN* 2.9 41.2 + - - +
150E GLU 2.9 15.6 + - - +
151E LEU 3.3 3.3 + - - +
153E ARG* 1.3 76.0 - - - +
155E ALA* 1.3 58.6 + - - +
157E VAL* 3.3 8.2 + - - +
158E GLY 2.9 23.7 + - - -
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Residues in contact with ALA 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E LEU* 3.6 13.8 - - + +
151E LEU 2.9 16.9 + - - +
152E ALA* 3.6 7.4 - - - +
153E ARG 3.2 0.2 - - - -
154E ASP* 1.3 74.7 - - - +
156E ALA* 1.3 54.8 + - - +
158E GLY* 3.1 1.8 + - - +
159E HIS* 2.8 35.3 + - - +
166E PHE* 3.7 6.2 - - - -
184E VAL* 3.9 26.9 - - + -
187E GLU* 4.1 5.8 - - + -
188E ILE* 3.9 13.0 - - + +
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Residues in contact with ALA 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E ALA 3.0 14.7 + - - +
153E ARG* 3.2 11.4 + - - +
155E ALA* 1.3 74.8 - - - +
157E VAL* 1.3 62.9 + - + +
159E HIS* 3.3 2.3 + - - +
160E ALA* 2.9 25.5 + - - +
187E GLU* 3.6 28.4 - - - +
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Residues in contact with VAL 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E TYR* 4.0 10.5 - - - +
153E ARG* 3.0 19.1 + - + +
154E ASP* 3.3 11.9 - - - +
156E ALA* 1.3 76.8 - - + +
158E GLY* 1.3 64.2 + - - +
160E ALA* 3.2 8.0 + - - +
161E GLN* 3.1 41.4 + - + +
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Residues in contact with GLY 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E TYR* 3.7 24.7 + - - -
154E ASP 2.9 10.9 + - - -
155E ALA 3.1 3.1 + - - -
157E VAL* 1.3 77.1 - - - +
159E HIS* 1.3 61.4 + - - +
161E GLN* 3.1 12.3 + - - -
163E GLU* 3.1 36.9 + - - +
166E PHE* 3.9 2.5 - - - -
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Residues in contact with HIS 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E ALA 2.8 19.6 + - - +
156E ALA* 3.7 4.5 - - - +
157E VAL 3.3 0.2 - - - -
158E GLY* 1.3 72.3 - - - +
160E ALA* 1.3 62.4 + - - +
162E GLY* 3.3 12.4 + - - +
163E GLU 4.7 4.6 + - - +
166E PHE* 3.5 15.7 - - + -
187E GLU 3.6 22.2 - - - +
188E ILE* 3.3 32.6 + - - +
189E GLY* 4.4 4.4 + - - -
190E ASP 5.6 0.4 - - - -
191E ALA* 4.4 7.4 - - + +
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Residues in contact with ALA 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E ALA 2.9 17.0 + - - +
157E VAL* 3.2 7.8 + - - +
159E HIS* 1.3 77.6 - - - +
161E GLN* 1.3 62.3 + - + +
162E GLY* 3.5 0.7 + - - -
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Residues in contact with GLN 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E TYR* 4.2 11.2 + - - -
157E VAL* 3.1 30.6 + - + +
158E GLY 3.1 6.5 + - - +
160E ALA* 1.3 77.4 - - + +
162E GLY* 1.3 58.0 + - - +
163E GLU* 3.5 26.6 + - + +
344E LYS* 5.1 5.5 - - - +
345E ASN* 3.3 17.7 + - - +
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Residues in contact with GLY 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E GLY 3.3 1.4 + - - -
159E HIS 3.3 8.5 + - - -
160E ALA 3.2 4.9 + - - -
161E GLN* 1.3 79.6 - - - +
163E GLU* 1.3 68.0 + - - +
164E ARG* 3.5 6.4 + - - +
345E ASN* 3.3 33.9 - - - +
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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