Contacts of the helix formed by residues 173 - 186 (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 GLY 173 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171E GLY 3.3 4.9 + - - -
172E ARG* 1.3 78.9 - - - +
174E GLU* 1.3 56.9 + - - -
175E LYS* 3.4 2.7 - - - -
176E LEU 3.4 2.4 + - - -
177E ASP* 2.8 37.7 + - - +
201E TRP* 5.7 1.0 - - - +
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Residues in contact with GLU 174 (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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173E GLY* 1.3 69.1 - - - +
175E LYS* 1.3 66.1 + - - +
177E ASP* 3.6 0.5 - - - +
178E LEU* 2.9 45.2 + - + +
209E MSE 3.6 24.0 - - - -
212E LYS* 2.8 39.1 + - + +
2500E GOL 2.6 36.3 + - - +
190H ASP* 5.5 3.5 - - - +
192H ARG* 5.7 1.7 - - - +
217H ASP* 4.9 0.7 - - - +
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Residues in contact with LYS 175 (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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173E GLY 3.4 1.0 - - - -
174E GLU* 1.3 79.6 - - - +
176E LEU* 1.3 62.8 + - - +
178E LEU* 3.8 5.6 - - - +
179E GLU* 3.0 56.0 + - + +
190H ASP* 5.9 0.8 + - - -
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Residues in contact with LEU 176 (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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146E GLU 4.5 14.6 - - - +
147E THR* 5.3 1.1 - - - -
148E ALA* 4.9 6.3 - - + +
172E ARG* 3.7 45.3 - - + +
173E GLY* 3.4 2.2 + - - -
174E GLU 3.4 0.2 - - - -
175E LYS* 1.3 76.3 - - - +
177E ASP* 1.3 60.8 + - - +
179E GLU* 3.2 16.6 + - + +
180E ILE* 2.8 56.5 + - + +
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Residues in contact with ASP 177 (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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170E VAL* 3.4 15.0 - - + +
171E GLY* 2.7 31.4 + - - -
172E ARG* 2.8 27.8 + - - +
173E GLY 2.8 26.9 + - - +
174E GLU 3.6 3.6 - - - +
176E LEU* 1.3 71.7 - - - +
178E LEU* 1.3 58.1 + - - +
180E ILE* 3.2 6.7 - - - +
181E THR* 2.9 35.0 + - - -
201E TRP* 3.6 14.4 + - - -
209E MSE 3.6 16.7 - - + +
213E LEU* 4.8 1.6 - - + -
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Residues in contact with LEU 178 (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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174E GLU* 2.9 44.2 + - + +
175E LYS* 3.8 5.6 - - - +
177E ASP* 1.3 77.9 - - - +
179E GLU* 1.3 60.0 + - + +
181E THR* 4.0 2.8 - - - -
182E ALA* 3.1 30.1 + - - +
209E MSE 4.4 3.8 - - + -
212E LYS* 3.6 39.7 - - + +
213E LEU* 3.8 19.5 - - + -
215E LYS* 5.7 0.2 - - + -
216E TYR* 3.9 15.7 + - + +
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Residues in contact with GLU 179 (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* 4.3 11.5 - - + +
175E LYS* 3.0 54.1 + - + +
176E LEU* 3.7 19.6 - - + +
178E LEU* 1.3 76.9 - - + +
180E ILE* 1.3 59.4 + - + +
182E ALA* 3.5 5.4 + - - +
183E ALA* 3.0 28.2 + - - +
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Residues in contact with ILE 180 (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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146E GLU 5.3 0.7 - - - +
147E THR* 4.5 0.7 - - - -
148E ALA* 3.9 16.8 - - + +
151E LEU* 3.6 24.2 - - + -
168E LEU* 4.2 10.8 - - + -
169E LYS 3.6 12.6 - - - +
170E VAL* 4.4 2.2 - - + -
172E ARG* 3.5 38.6 - - - +
176E LEU* 2.8 43.2 + - + +
177E ASP* 3.2 17.7 - - - +
179E GLU* 1.3 71.0 - - - +
181E THR* 1.3 68.4 + - - +
183E ALA* 3.4 6.0 + - - +
184E VAL* 3.0 30.5 + - - +
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Residues in contact with THR 181 (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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168E LEU* 3.9 16.4 - - - +
170E VAL* 4.1 9.0 - - - +
177E ASP 2.9 21.3 + - - -
178E LEU 4.0 3.1 - - - -
180E ILE* 1.3 74.4 - - - +
182E ALA* 1.3 65.9 + - - +
184E VAL* 3.3 1.9 + - - +
185E ARG* 2.9 22.9 + - - +
193E LEU* 4.2 8.3 - - + +
195E LEU* 4.1 3.6 - - + +
213E LEU* 3.5 21.9 - - + +
216E TYR* 3.6 33.9 - - + -
218E ILE* 4.1 13.7 - - + -
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Residues in contact with ALA 182 (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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178E LEU 3.1 19.1 + - - +
179E GLU* 3.7 5.2 - - - +
181E THR* 1.3 77.6 - - - +
183E ALA* 1.3 62.8 + - - +
185E ARG* 3.3 2.8 + - - +
186E GLY* 3.0 19.9 + - - -
216E TYR* 3.5 32.3 - - + +
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Residues in contact with ALA 183 (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* 4.0 20.2 - - + +
152E ALA* 3.9 20.0 - - + +
179E GLU 3.0 17.1 + - - +
180E ILE* 3.7 4.9 - - - +
181E THR 3.3 0.2 - - - -
182E ALA* 1.3 76.7 - - - +
184E VAL* 1.3 62.8 + - + +
186E GLY* 3.3 10.1 + - - -
187E GLU* 3.5 18.7 + - - +
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Residues in contact with VAL 184 (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* 3.9 26.5 - - + -
151E LEU* 4.1 29.4 - - + +
152E ALA* 4.7 1.3 - - - +
155E ALA* 3.9 15.3 - - + -
166E PHE* 5.0 0.2 - - + -
168E LEU* 3.8 17.9 - - + -
180E ILE 3.0 18.9 + - - +
181E THR 3.9 3.1 - - - +
183E ALA* 1.3 72.4 - - - +
185E ARG* 1.3 66.5 + - - +
187E GLU* 3.0 12.3 + - - +
188E ILE* 3.3 28.9 + - + +
193E LEU* 4.2 11.4 - - + -
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Residues in contact with ARG 185 (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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181E THR 2.9 18.2 + - - +
182E ALA* 3.4 8.7 - - - +
184E VAL* 1.3 77.6 - - - +
186E GLY* 1.3 61.6 + - - +
187E GLU 3.1 1.3 + - - -
188E ILE* 3.5 22.3 + - - +
189E GLY* 2.8 40.5 + - - +
190E ASP* 3.3 6.7 + - - -
191E ALA 2.6 36.8 + - - +
193E LEU* 4.1 10.9 - - + +
216E TYR* 3.0 47.1 + - + +
217E ASP* 3.1 26.3 + - - +
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Residues in contact with GLY 186 (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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182E ALA 3.0 13.8 + - - -
183E ALA* 3.3 4.2 + - - -
184E VAL 3.1 0.6 - - - -
185E ARG* 1.3 76.3 - - - +
187E GLU* 1.3 70.5 + - - +
189E GLY 4.9 2.5 + - - -
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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