Contacts of the strand formed by residues 240 - 244 (chain D) in PDB entry 3ER8
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 TYR 240 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233D LYS* 2.9 37.3 - - - +
234D ILE* 3.3 38.7 + - + +
237D LEU* 3.5 39.9 + - + +
239D ASN* 1.3 77.0 - - - +
241D MET* 1.3 72.6 + - - +
242D VAL* 3.7 13.5 - - + +
250D HIS* 5.0 1.7 - - - -
253D ASP* 3.2 44.0 + - + +
254D SER 3.0 23.6 - - - -
255D PHE* 3.5 25.1 - + + -
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Residues in contact with MET 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 3.8 24.0 - - + -
210D SER* 5.2 3.1 - - - +
211D ARG* 4.1 19.3 - - - -
214D LEU* 2.9 27.2 - - + +
231D LEU* 3.4 40.4 - - + +
232D SER 3.4 4.3 - - - -
233D LYS* 3.8 15.3 - - + -
234D ILE 5.2 0.2 - - - +
240D TYR* 1.3 81.6 - - - +
242D VAL* 1.3 61.5 + - - +
254D SER 3.2 23.2 + - - +
470D ILE* 3.6 12.6 - - + -
479D PHE* 3.5 26.2 - - + -
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Residues in contact with VAL 242 (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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214D LEU* 4.0 0.9 - - - -
230D ILE 3.6 0.7 - - - +
231D LEU* 3.4 2.8 - - - +
232D SER* 2.7 49.2 + - - +
234D ILE* 5.0 9.2 - - + -
240D TYR* 3.7 17.5 - - + +
241D MET* 1.3 74.7 - - - +
243D ILE* 1.3 71.0 + - - +
244D LYS* 4.7 14.3 - - + +
250D HIS* 4.0 14.8 - - + +
252D ILE 3.0 23.6 - - - +
253D ASP* 3.4 21.8 - - + -
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Residues in contact with ILE 243 (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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214D LEU* 3.6 45.3 - - + +
217D LEU* 4.0 15.5 - - + -
218D ALA* 4.0 11.2 - - + +
221D ILE* 5.4 4.3 - - + -
229D ILE* 3.7 31.9 - - + -
230D ILE 3.3 13.7 - - - +
231D LEU* 4.0 8.1 - - + +
242D VAL* 1.3 79.6 - - - +
244D LYS* 1.3 68.0 + - - +
251D ILE* 3.3 25.4 + - + -
252D ILE* 3.0 26.5 + - + +
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Residues in contact with LYS 244 (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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229D ILE* 2.9 9.2 - - - +
230D ILE* 2.8 43.7 + - + +
232D SER* 3.5 30.3 + - - -
242D VAL* 4.7 14.3 - - + +
243D ILE* 1.3 79.4 - - - +
245D ASP* 1.3 63.7 + - - +
248D ASP* 3.1 38.8 - - - +
249D ASN 3.3 13.0 - - - +
250D HIS* 4.0 16.6 - - + +
251D ILE* 3.8 7.0 - - - -
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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