Contacts of the helix formed by residues 209 - 219 (chain E) in PDB entry 3PUY
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 ASP 209 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150E ASN* 3.1 13.1 - - - +
152E GLN* 3.6 19.5 + - + +
207E ASP 3.7 1.8 + - - -
208E THR* 1.3 78.7 - - - +
210E TYR* 1.3 65.6 + - - +
211E SER* 3.5 8.3 + - - -
212E ILE* 3.1 36.9 + - - +
213E ALA* 3.3 16.6 + - - +
337F LYS* 5.0 22.0 + - - +
338F GLY* 5.5 3.6 - - - -
341F ASN* 4.0 15.4 + - - +
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Residues in contact with TYR 210 (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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150E ASN* 3.1 26.1 - - - +
156E PHE* 3.4 30.1 - + - -
209E ASP* 1.3 74.9 - - - +
211E SER* 1.3 69.4 + - - +
212E ILE 3.2 0.3 + - - -
213E ALA* 3.2 3.7 + - - +
214E GLU* 3.0 57.3 + - + +
227E ASN* 3.4 34.1 + - - -
230E TRP* 3.1 30.4 + + - -
231E ALA* 4.0 0.7 - - - +
256G GLN* 4.7 13.2 - - - -
257G ASN* 4.6 6.9 - - + +
260G TRP* 6.1 4.3 - - - -
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Residues in contact with SER 211 (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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209E ASP* 3.4 10.8 + - - -
210E TYR* 1.3 85.6 - - - +
212E ILE* 1.3 63.4 + - - +
214E GLU* 3.8 5.7 + - - +
215E ALA* 3.4 17.2 + - - +
44G PHE* 5.6 1.9 - - - +
45G ALA* 3.1 33.9 + - - +
46G THR* 3.4 27.1 + - - +
260G TRP* 5.9 1.8 - - - -
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Residues in contact with ILE 212 (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 MET* 4.3 6.5 - - + -
208E THR* 3.7 20.9 - - + -
209E ASP* 3.1 33.4 + - - +
211E SER* 1.3 77.4 - - - +
213E ALA* 1.3 65.9 + - - +
215E ALA* 3.4 3.5 + - - +
216E ALA* 3.1 22.5 + - + +
338F GLY* 5.4 8.5 - - - +
341F ASN* 4.8 9.0 - - + +
344F PHE* 4.1 48.7 - - + -
345F GLY* 5.5 1.6 - - - +
46G THR* 3.9 25.8 - - + +
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Residues in contact with ALA 213 (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 MET* 3.6 30.9 - - + +
149E PHE* 3.6 19.3 - - - +
150E ASN 4.2 1.3 - - - +
208E THR* 4.3 1.6 - - + -
209E ASP 3.3 13.2 + - - +
210E TYR* 3.2 4.1 + - - +
212E ILE* 1.3 79.2 - - - +
214E GLU* 1.3 65.6 + - - +
216E ALA* 3.2 8.1 + - - +
217E PHE* 3.1 23.0 + - - +
222E THR* 4.6 2.6 - - - +
225E THR* 4.4 4.8 + - - +
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Residues in contact with GLU 214 (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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210E TYR* 3.0 52.7 + - + +
211E SER* 4.0 6.2 - - - +
213E ALA* 1.3 76.0 - - - +
215E ALA* 1.3 62.9 + - - +
217E PHE* 3.3 5.6 + - - +
218E ASN* 2.9 35.2 + - - +
225E THR* 5.4 2.4 + - - -
227E ASN* 4.9 10.2 - - - +
231E ALA* 4.3 9.8 - - + +
234E ASN* 2.9 31.7 + - - +
43G ASN 3.8 9.5 - - - +
44G PHE* 3.6 18.1 - - + -
45G ALA 5.5 0.7 + - - -
260G TRP* 5.6 2.6 + - - -
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Residues in contact with ALA 215 (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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211E SER 3.4 16.0 + - - +
212E ILE 3.8 4.0 - - - +
213E ALA 3.3 0.4 - - - -
214E GLU* 1.3 79.6 - - - +
216E ALA* 1.3 61.6 + - - +
218E ASN* 3.5 1.5 + - - +
219E LYS* 3.2 43.5 + - + +
221E GLU* 5.6 0.2 - - - -
44G PHE* 4.4 14.5 - - + -
46G THR* 3.7 26.2 - - + +
47G GLY* 5.7 0.2 - - - -
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Residues in contact with ALA 216 (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 MET* 3.8 27.4 - - - -
212E ILE* 3.1 14.2 + - + +
213E ALA 3.2 9.1 + - - +
215E ALA* 1.3 78.2 - - - +
217E PHE* 1.3 58.8 + - - +
219E LYS 3.7 0.2 + - - -
220E GLY 3.4 1.9 + - - -
221E GLU* 2.8 50.6 + - + +
222E THR* 3.3 9.2 + - + -
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Residues in contact with PHE 217 (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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116E ILE* 3.9 14.6 - - + -
117E TYR* 3.4 31.4 - - - -
118E ASN* 3.4 9.2 + - + -
213E ALA 3.1 14.6 + - - +
214E GLU* 3.8 5.4 - - - +
216E ALA* 1.3 73.6 - - - +
218E ASN* 1.3 60.8 + - - +
219E LYS 3.1 4.7 - - - -
220E GLY* 3.1 18.0 + - - -
222E THR* 3.7 21.5 - - + +
223E ALA 3.6 8.1 - - - -
224E MET* 3.5 25.6 - - - -
225E THR* 3.6 29.8 - - + -
235E ILE* 4.1 31.9 - - + -
240E VAL* 4.4 11.3 - - + +
242E TYR* 4.3 5.6 - - + -
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Residues in contact with ASN 218 (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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214E GLU* 2.9 36.3 + - - +
215E ALA* 4.1 3.6 - - - +
217E PHE* 1.3 79.5 - - - +
219E LYS* 1.3 62.3 + - + +
220E GLY 3.4 0.4 - - - -
234E ASN* 3.2 17.3 - - - +
235E ILE* 3.4 27.1 - - - +
238E SER* 2.8 37.3 + - - +
240E VAL* 3.9 12.5 - - - +
44G PHE* 3.3 26.3 - - + -
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Residues in contact with LYS 219 (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 LYS* 5.2 2.6 + - - -
215E ALA* 3.2 26.8 + - + +
216E ALA 4.3 1.3 - - - +
217E PHE 3.1 0.8 - - - -
218E ASN* 1.3 80.7 - - + +
220E GLY* 1.3 61.6 + - - +
221E GLU* 3.2 27.4 + - - +
240E VAL* 6.0 0.2 - - - -
40G ARG* 5.9 2.5 - - - +
46G THR 4.7 2.6 + - - -
47G GLY* 3.7 27.7 - - - -
48G SER* 4.2 7.5 + - - +
52G GLU* 3.3 34.7 + - - +
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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