Contacts of the helix formed by residues 147 - 161 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146D GLU* 1.3 88.8 - - + +
148D ALA* 1.3 65.4 + - - +
149D GLU* 3.6 8.7 + - - +
150D GLU* 2.9 37.7 + - - +
151D LEU* 2.9 29.3 + - - +
176D LEU* 5.4 2.5 - - - -
180D ILE* 4.3 1.1 - - - -
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Residues in contact with ALA 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D THR* 1.3 72.8 - - - +
149D GLU* 1.3 56.9 + - - +
151D LEU* 3.4 1.3 + - - +
152D ALA* 2.8 33.2 + - - +
176D LEU* 5.0 4.1 - - + +
179D GLU* 4.2 15.0 - - + +
180D ILE* 3.7 26.6 - - + +
183D ALA* 3.9 18.0 - - + +
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Residues in contact with GLU 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D THR* 3.2 8.1 + - - +
148D ALA* 1.3 80.5 - - - +
150D GLU* 1.3 62.5 + - - +
152D ALA* 3.4 5.7 + - - +
153D ARG* 3.0 60.8 + - + +
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Residues in contact with GLU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D GLN 4.2 2.8 - - - +
145D GLY* 3.6 10.9 - - - -
146D GLU* 2.7 37.6 + - - +
147D THR* 2.9 31.4 + - - +
149D GLU* 1.3 76.5 - - + +
151D LEU* 1.3 62.5 + - - +
153D ARG* 3.2 31.3 + - - +
154D ASP* 3.0 22.7 + - - +
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Residues in contact with LEU 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D LEU* 4.2 8.4 - - + +
144D GLN* 3.4 36.1 - - - +
145D GLY 3.6 19.1 - - - +
146D GLU 4.8 0.2 - - - -
147D THR 2.9 22.3 + - - +
148D ALA* 3.9 3.8 - - - +
150D GLU* 1.3 75.5 - - - +
152D ALA* 1.3 57.0 + - - +
154D ASP* 3.3 3.1 + - - +
155D ALA* 2.8 30.0 + - - +
168D LEU* 3.9 18.4 - - + -
172D ARG* 3.8 18.4 - - - +
180D ILE* 3.8 28.5 - - + -
184D VAL* 4.1 16.1 - - + +
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Residues in contact with ALA 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D ALA 2.8 19.0 + - - +
149D GLU* 3.7 5.6 - - - +
151D LEU* 1.3 76.6 - - - +
153D ARG* 1.3 58.6 + - + +
155D ALA* 3.3 3.9 + - - -
156D ALA* 2.9 26.0 + - - +
183D ALA* 4.1 20.9 - - + +
184D VAL* 4.7 0.8 - - - +
187D GLU* 3.3 33.9 - - + +
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Residues in contact with ARG 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D GLU* 3.0 63.7 + - + +
150D GLU* 3.4 34.5 + - - +
152D ALA* 1.3 77.6 - - + +
154D ASP* 1.3 62.1 + - - +
156D ALA* 3.3 8.9 + - - +
157D VAL* 3.1 25.5 + - - +
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Residues in contact with ASP 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D TYR* 2.6 34.1 + - - -
142D PHE 4.2 1.9 - - - +
143D LEU* 3.3 12.4 - - + -
144D GLN* 2.8 40.2 + - - +
150D GLU 3.0 13.2 + - - +
151D LEU* 3.7 7.2 - - - +
153D ARG* 1.3 73.1 - - - +
155D ALA* 1.3 67.6 + - - +
157D VAL* 2.9 9.5 + - - +
158D GLY 2.9 19.1 + - - -
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Residues in contact with ALA 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D LEU* 3.7 14.5 - - + +
151D LEU 2.8 18.1 + - - +
152D ALA* 3.5 7.2 - - - +
154D ASP* 1.3 76.5 - - - +
156D ALA* 1.3 58.8 + - - +
158D GLY 3.2 1.0 + - - -
159D HIS* 2.8 31.6 + - - +
166D PHE* 3.7 6.2 - - - -
184D VAL* 4.0 16.8 - - + -
187D GLU* 3.9 15.7 - - + -
188D ILE* 3.9 13.9 - - + -
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Residues in contact with ALA 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ALA 2.9 13.6 + - - +
153D ARG* 3.4 13.0 - - - +
154D ASP 3.2 0.2 - - - -
155D ALA* 1.3 78.0 - - - +
157D VAL* 1.3 56.9 + - + +
159D HIS* 3.8 4.8 - - - +
160D ALA* 2.9 30.7 + - - +
187D GLU* 3.5 25.7 - - - +
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Residues in contact with VAL 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D TYR* 3.7 13.5 - - - +
153D ARG 3.1 15.3 + - - +
154D ASP* 2.9 13.3 + - - +
156D ALA* 1.3 73.9 - - + +
158D GLY* 1.3 67.4 + - - +
160D ALA* 3.1 8.5 + - - +
161D GLN* 3.1 34.6 + - - +
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Residues in contact with GLY 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D TYR* 3.6 28.9 - - - -
154D ASP 2.9 10.9 + - - -
155D ALA 3.2 1.5 + - - -
157D VAL* 1.3 77.0 - - - +
159D HIS* 1.3 58.8 + - - +
161D GLN* 3.1 12.7 - - - +
163D GLU* 2.9 38.4 + - - -
166D PHE* 4.0 0.7 - - - -
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Residues in contact with HIS 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D ALA 2.8 17.5 + - - +
156D ALA* 3.8 4.0 - - - +
158D GLY* 1.3 72.6 - - - +
160D ALA* 1.3 68.5 + - - +
162D GLY* 3.0 14.4 + - - +
163D GLU 4.5 5.0 + - - +
166D PHE* 3.7 15.5 - - + -
187D GLU 3.7 20.6 - - - +
188D ILE* 3.5 32.8 + - - +
189D GLY* 4.4 3.0 + - - -
191D ALA* 4.7 4.4 - - + +
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Residues in contact with ALA 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D ALA 2.9 19.0 + - - +
157D VAL* 3.1 7.6 + - - +
159D HIS* 1.3 79.9 - - - +
161D GLN* 1.3 56.8 + - - +
162D GLY 3.2 3.0 + - - -
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Residues in contact with GLN 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D TYR* 3.8 14.6 - - - -
157D VAL* 3.1 24.2 + - - +
158D GLY* 3.1 16.6 - - - +
160D ALA* 1.3 74.7 - - - +
162D GLY* 1.3 58.2 + - - +
163D GLU* 2.9 27.3 + - + +
343D PRO 5.8 1.4 + - - -
345D ASN* 3.2 19.6 + - - -
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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