Contacts of the helix formed by residues 173 - 188 (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 GLY 173 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171D GLY* 3.3 6.1 + - - -
172D ARG* 1.3 77.4 - - - +
174D GLU* 1.3 66.5 + - - -
175D LYS* 3.4 2.9 - - - -
176D LEU 3.6 1.2 + - - -
177D ASP* 2.9 28.8 + - - +
201D TRP* 5.5 1.7 - - - +
209D MSE 5.1 0.2 - - - -
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Residues in contact with GLU 174 (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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173D GLY* 1.3 71.5 - - - +
175D LYS* 1.3 66.8 + - - +
177D ASP* 3.8 0.3 - - - +
178D LEU* 3.1 44.5 + - + +
209D MSE 3.5 21.4 - - - -
212D LYS* 2.8 41.1 + - - +
2400D GOL 2.7 39.6 + - - +
190G ASP* 5.4 3.8 - - - +
192G ARG* 5.9 0.5 - - - +
217G ASP* 4.8 1.4 - - - +
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Residues in contact with LYS 175 (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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173D GLY 3.4 0.8 - - - -
174D GLU* 1.3 81.8 - - - +
176D LEU* 1.3 62.9 + - + +
178D LEU* 3.6 5.1 + - - +
179D GLU* 2.8 57.4 + - + +
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Residues in contact with LEU 176 (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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146D GLU 4.6 15.5 - - - +
147D THR* 5.4 0.7 - - - -
148D ALA* 5.0 6.1 - - + +
172D ARG* 3.8 43.5 - - + +
173D GLY 3.6 1.4 + - - -
174D GLU 3.4 0.2 - - - -
175D LYS* 1.3 77.6 - - + +
177D ASP* 1.3 67.6 + - - +
179D GLU* 3.1 17.1 + - + +
180D ILE* 2.8 47.6 + - + +
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Residues in contact with ASP 177 (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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170D VAL* 3.4 15.0 - - + +
171D GLY* 2.7 30.9 + - - -
172D ARG* 2.8 29.7 + - - +
173D GLY 2.9 27.1 + - - +
174D GLU 3.8 0.2 - - - +
176D LEU* 1.3 72.7 - - - +
178D LEU* 1.3 58.5 + - - +
180D ILE* 3.3 7.1 - - - +
181D THR* 2.7 34.8 + - - -
201D TRP* 3.7 12.1 + - - -
209D MSE 3.7 19.3 - - + +
213D LEU* 4.7 1.6 - - + -
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Residues in contact with LEU 178 (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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174D GLU* 3.1 43.2 + - + +
175D LYS* 3.9 4.5 - - - +
177D ASP* 1.3 76.3 - - - +
179D GLU* 1.3 58.6 + - + +
181D THR* 3.9 2.8 - - - -
182D ALA* 2.9 31.7 + - - +
209D MSE 4.3 4.0 - - + -
212D LYS* 3.8 37.9 - - + +
213D LEU* 3.8 20.0 - - + -
216D TYR* 4.1 15.2 + - + +
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Residues in contact with GLU 179 (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* 4.2 10.7 - - + +
175D LYS* 2.8 57.7 + - + +
176D LEU* 3.1 26.6 + - + +
178D LEU* 1.3 78.5 - - + +
180D ILE* 1.3 57.5 + - - +
182D ALA* 3.7 4.5 - - - +
183D ALA* 3.0 28.4 + - - +
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Residues in contact with ILE 180 (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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146D GLU 5.3 0.9 - - - +
147D THR 4.3 0.7 - - - -
148D ALA* 3.7 26.7 - - + +
151D LEU* 3.8 19.5 - - + -
168D LEU* 4.2 8.3 - - + -
169D LYS 3.7 11.4 - - - +
170D VAL* 4.6 2.2 - - + -
172D ARG* 3.5 38.1 - - - +
176D LEU* 2.8 44.9 + - + +
177D ASP* 3.3 15.0 - - - +
179D GLU* 1.3 69.7 - - - +
181D THR* 1.3 65.7 + - - +
183D ALA* 3.6 1.4 - - - +
184D VAL* 3.0 33.4 + - - +
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Residues in contact with THR 181 (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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168D LEU* 3.9 17.6 - - - +
170D VAL* 4.0 8.1 - - - +
177D ASP 2.7 23.7 + - - -
178D LEU 3.9 2.5 - - - -
180D ILE* 1.3 74.1 - - - +
182D ALA* 1.3 65.7 + - - +
184D VAL* 3.9 1.2 - - - +
185D ARG* 3.0 23.7 + - - +
193D LEU* 4.3 7.6 - - + +
195D LEU* 4.3 3.5 - - + +
213D LEU* 3.5 21.0 - - + +
216D TYR* 3.6 33.9 - - + -
218D ILE* 4.2 13.2 - - + -
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Residues in contact with ALA 182 (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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178D LEU 2.9 19.5 + - - +
179D GLU* 3.7 5.6 - - - +
181D THR* 1.3 79.3 - - - +
183D ALA* 1.3 61.6 + - - +
185D ARG* 3.4 2.4 + - - +
186D GLY* 3.0 19.9 + - - -
216D TYR* 3.5 33.6 - - + +
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Residues in contact with ALA 183 (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* 3.9 30.3 - - + +
152D ALA* 4.1 10.8 - - + +
179D GLU 3.0 18.7 + - - +
180D ILE 3.6 4.7 - - - +
182D ALA* 1.3 76.9 - - - +
184D VAL* 1.3 61.8 + - - +
186D GLY* 3.2 11.0 + - - -
187D GLU* 3.4 17.7 + - - +
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Residues in contact with VAL 184 (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* 3.8 29.8 - - + -
151D LEU* 4.1 27.4 - - + +
152D ALA* 4.8 1.1 - - - +
155D ALA* 4.0 14.8 - - + -
166D PHE* 4.9 0.4 - - + -
168D LEU* 3.9 16.6 - - + -
180D ILE 3.0 21.2 + - - +
181D THR 3.9 3.1 - - - +
183D ALA* 1.3 71.9 - - - +
185D ARG* 1.3 67.8 + - - +
187D GLU* 2.9 12.3 + - - +
188D ILE* 3.2 22.1 + - + +
193D LEU* 4.0 19.7 - - + -
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Residues in contact with ARG 185 (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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181D THR 3.0 18.7 + - - +
182D ALA* 3.5 8.1 - - - +
184D VAL* 1.3 78.0 - - - +
186D GLY* 1.3 62.5 + - - +
187D GLU 3.2 1.0 + - - -
188D ILE* 3.3 32.6 + - - +
189D GLY* 2.9 36.3 + - - +
190D ASP* 3.3 6.0 + - - -
191D ALA 2.6 32.5 + - - +
193D LEU* 4.1 10.1 - - + +
216D TYR* 3.0 47.6 + - + +
217D ASP* 3.1 27.0 + - - +
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Residues in contact with GLY 186 (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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182D ALA 3.0 14.0 + - - -
183D ALA* 3.2 6.0 + - - -
184D VAL 3.1 0.6 - - - -
185D ARG* 1.3 77.9 - - - +
187D GLU* 1.3 63.5 + - - +
188D ILE 3.6 0.2 - - - -
189D GLY 4.8 2.7 + - - -
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Residues in contact with GLU 187 (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* 3.3 37.7 - - + +
155D ALA* 3.9 9.4 - - + -
156D ALA* 3.5 20.7 - - - +
159D HIS* 3.7 22.5 - - - +
183D ALA 3.4 12.5 + - - +
184D VAL 2.9 8.2 + - - +
186D GLY* 1.3 81.1 - - - +
188D ILE* 1.3 60.6 + - - +
189D GLY 3.6 1.3 - - - -
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Residues in contact with ILE 188 (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* 3.9 13.2 - - + +
159D HIS* 3.5 19.1 - - - -
166D PHE* 3.7 58.3 - - + -
184D VAL* 3.4 23.3 - - + +
185D ARG* 3.3 35.6 + - - +
187D GLU* 1.3 81.5 - - - +
189D GLY* 1.3 62.2 + - - +
190D ASP 3.1 0.2 + - - -
191D ALA* 3.0 23.8 + - + +
193D LEU* 4.1 16.2 - - + -
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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