Contacts of the strand formed by residues 211 - 216 (chain E) in PDB entry 1E81
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 211 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E SER* 5.7 0.9 - - - +
191E GLU* 2.5 39.7 - - - +
192E TRP 3.4 8.1 - - - +
193E THR* 3.8 14.9 + - + +
206E SER 4.0 3.0 + - - -
207E ILE* 1.3 71.1 - - - +
212E GLY* 1.3 62.7 + - - +
299E ILE* 4.7 8.8 - - - +
300E ASN* 2.9 28.1 + - - +
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Residues in contact with GLY 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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191E GLU* 3.3 5.1 - - - +
192E TRP* 2.9 34.2 + - - +
207E ILE 3.5 3.4 + - - -
211E ASP* 1.3 76.9 + - - +
213E ILE* 1.3 64.8 + - - -
299E ILE* 5.0 1.1 - - - -
300E ASN* 3.0 20.4 - - - -
302E PHE* 4.2 14.0 - - - -
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Residues in contact with ILE 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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34E GLY* 5.2 1.3 - - - -
189E PHE* 3.6 35.0 - - + -
190E TRP 3.7 4.3 - - - +
191E GLU* 4.1 9.2 - - + -
192E TRP* 4.5 1.1 - - - -
212E GLY* 1.3 78.1 - - - +
214E ALA* 1.3 61.7 + - - +
215E ASP* 3.3 18.5 + - + +
299E ILE* 3.4 29.8 - - + -
300E ASN 2.9 14.3 + - - +
301E ILE* 4.3 12.1 - - + -
302E PHE* 2.9 28.0 + - - -
400E M91 3.9 34.1 - - + -
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Residues in contact with ALA 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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33E THR* 2.7 30.3 + - - +
34E GLY* 5.0 0.2 - - - -
190E TRP* 3.1 16.4 + - + +
192E TRP* 4.2 4.5 - - - +
213E ILE* 1.3 71.3 - - - +
215E ASP* 1.3 52.9 + - - +
302E PHE* 3.8 9.6 - - - -
307E LEU* 4.4 13.7 - - + -
314E PHE* 3.8 27.4 - - + -
321E LEU* 3.8 22.9 - - + -
323E PHE* 5.2 0.9 - - + -
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Residues in contact with ASP 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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32E ASP* 2.7 14.6 - - - +
33E THR* 3.5 1.1 - - - -
34E GLY* 3.3 11.1 + - - +
213E ILE* 3.3 7.8 + - + -
214E ALA* 1.3 73.9 - - - +
216E THR* 1.3 61.5 + - - +
217E GLY 2.9 6.8 + - - -
218E THR* 2.8 22.1 + - - -
301E ILE* 3.6 22.4 - - + +
302E PHE 3.0 9.7 + - - -
303E GLY* 3.2 22.9 - - - -
307E LEU* 3.9 3.8 - - - +
400E M91 2.6 46.5 + - - -
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Residues in contact with THR 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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13E ALA* 6.0 0.2 - - - -
14E TYR* 5.3 2.6 + - - -
30E ASP* 4.5 3.6 - - - +
31E PHE 2.5 25.8 + - - +
33E THR* 3.0 34.7 + - + +
153E ALA* 4.6 9.9 - - + -
155E LEU* 4.8 5.3 - - + +
165E TYR* 3.4 23.7 + - + +
215E ASP* 1.3 71.7 + - - +
217E GLY* 1.3 56.6 + - - +
218E THR 3.2 2.2 - - - -
304E ASP* 2.6 32.0 - - - +
307E LEU* 3.5 19.7 - - + -
314E PHE* 4.5 6.7 - - + -
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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