Contacts of the strand formed by residues 249 - 253 (chain E) in PDB entry 1LE9
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 ALA 249 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E LEU 3.2 8.5 - - - +
215E LEU* 3.8 10.5 - - + -
216E CYS* 4.2 3.2 - - - +
243E ASP 3.7 0.4 - - - +
244E VAL* 3.3 5.5 - - - +
245E HIS* 2.8 37.5 + - + +
247E GLN 3.7 1.0 - - - -
248E VAL* 1.3 85.8 - - + +
250E ILE* 1.3 66.9 + - - +
251E VAL* 5.2 0.4 - - - -
269F LEU* 3.6 31.6 - - + -
308F ALA* 5.2 1.3 - - + -
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Residues in contact with ILE 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212E ILE 3.6 0.9 - - - +
213E PHE* 3.6 2.6 - - - -
214E LEU* 2.8 43.9 + - + +
216E CYS* 4.4 13.0 - - - -
219E VAL* 4.9 1.3 - - + -
224E ILE* 4.2 24.9 - - + -
226E VAL* 4.5 3.6 - - + -
239E PHE* 3.8 41.3 - - + -
243E ASP 3.5 6.1 - - - +
244E VAL* 4.0 12.8 - - + -
249E ALA* 1.3 82.1 - - - +
251E VAL* 1.3 69.1 + - - +
252E PHE* 3.8 6.9 + - + +
272E LEU* 4.1 25.8 - - + -
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Residues in contact with VAL 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211E GLU* 3.4 24.9 - - - +
212E ILE 3.2 5.8 - - - +
213E PHE* 3.5 28.7 - - + -
238E SER 4.7 0.2 - - - +
239E PHE* 3.7 4.5 - - - +
243E ASP* 3.2 32.1 + - + +
245E HIS* 5.8 0.7 - - + +
249E ALA 5.2 0.4 - - - +
250E ILE* 1.3 81.7 - - - +
252E PHE* 1.3 59.2 + - - +
253E ARG* 5.8 0.2 - - - +
252F ARG* 3.4 35.3 + - - +
269F LEU* 4.0 24.9 - - + -
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Residues in contact with PHE 252 (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 GLU* 3.5 3.5 - - - +
212E ILE* 2.8 67.6 + - + +
214E LEU* 3.9 26.0 - - + -
226E VAL* 3.5 26.9 - - + -
228E PHE* 3.2 26.7 - + - -
237E GLY* 3.8 17.0 - - - -
238E SER 3.4 8.1 - - - +
239E PHE* 3.6 27.6 - - + -
250E ILE* 4.5 5.2 - - + -
251E VAL* 1.3 75.6 - - - +
253E ARG* 1.3 66.6 + - - +
254E THR* 4.7 0.2 - - - -
270E MET* 3.8 17.9 - - - -
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Residues in contact with ARG 253 (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 GLY* 3.1 32.9 + - - +
210E ASP 4.0 1.6 - - - -
211E GLU* 3.6 38.1 + - - +
237E GLY* 3.3 4.2 - - - -
238E SER* 2.9 44.9 + - - +
251E VAL 5.8 0.4 - - - +
252E PHE* 1.3 76.1 - - - +
254E THR* 1.3 65.4 + - - +
255E PRO* 3.5 0.3 - - - +
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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