Contacts of the strand formed by residues 241 - 244 (chain E) in PDB entry 2BQZ
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 PHE 241 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206E ILE* 4.3 23.3 - - + -
209E LEU* 3.6 49.1 - - + +
210E ILE* 4.2 15.3 - - + -
214E LYS 4.5 12.3 - - - -
215E GLU* 6.2 0.2 - - + -
236E PHE* 3.8 13.0 - - - -
239E GLY 3.6 2.4 + - - -
240E ASP* 1.3 77.0 - - - +
242E VAL* 1.3 66.5 + - - +
243E VAL* 3.6 29.8 - - - -
244E GLU* 3.7 6.1 - - + -
319E ILE* 3.8 37.5 - - + -
320E LEU 4.5 0.4 - - - -
321E ILE* 3.8 10.3 - - + +
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Residues in contact with VAL 242 (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 LYS 5.3 0.2 - - - +
215E GLU* 5.2 2.3 - - - -
216E GLU 5.0 1.2 + - - +
218E MET* 3.6 19.2 - - - +
236E PHE* 4.0 26.3 - - + -
240E ASP 3.8 1.3 - - - +
241E PHE* 1.3 86.0 - - - +
243E VAL* 1.3 71.2 + - + +
297E ILE* 5.0 0.4 - - + -
305E CYS* 4.0 18.2 - - - -
320E LEU* 2.9 19.5 + - + +
322E ALA* 3.7 28.7 - - + +
326E ILE* 4.7 1.3 - - + -
332E LEU* 3.6 31.9 - - + -
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Residues in contact with VAL 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E GLU* 3.5 37.5 - - + +
218E MET* 4.1 12.3 - - + -
241E PHE* 3.6 14.8 - - - -
242E VAL* 1.3 86.2 - - + +
244E GLU* 1.3 67.3 + - - +
293E LEU* 4.6 0.4 - - + -
294E GLY* 3.9 18.6 - - - +
297E ILE* 3.7 29.6 - - + -
319E ILE* 3.6 1.7 - - - +
320E LEU* 2.8 37.0 + - + +
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Residues in contact with GLU 244 (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 ILE* 3.5 29.0 - - + +
215E GLU* 4.5 2.5 + - - +
241E PHE* 3.7 9.9 - - + -
243E VAL* 1.3 91.0 - - - +
245E TYR* 1.3 72.2 + - - +
246E HIS* 3.2 38.8 + - + +
292E ARG* 4.6 8.5 + - - +
294E GLY* 3.7 8.8 + - - -
317E HIS* 2.8 34.0 + - - +
318E LEU 3.3 14.5 + - - +
319E ILE* 4.2 10.3 - - + +
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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