Contacts of the strand formed by residues 244 - 248 (chain E) in PDB entry 4DHJ
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 TRP 244 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E LYS* 4.0 2.2 - - - +
232E GLU* 3.7 4.2 - - - +
233E TYR* 2.8 45.8 + - + +
235E ASP* 3.3 24.0 - - - -
237E THR* 3.0 19.6 + - - -
238E ALA 3.5 21.7 + - - -
239E ALA* 3.6 15.9 - - + +
240E PRO* 3.3 31.6 - - + -
243E GLY* 1.3 73.6 - - - -
245E HIS* 1.3 61.4 + - - +
246E TYR* 4.1 13.9 - + + -
531F GLN* 5.6 1.6 - - - -
535F GLY 3.6 21.5 - - - -
536F ILE* 5.0 0.2 - - - -
537F PRO* 3.5 32.8 - - + -
540F GLN* 3.4 21.1 - - - +
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Residues in contact with HIS 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E ARG* 3.2 48.6 + - - -
231E ILE 3.1 13.7 - - - +
232E GLU* 3.5 20.3 + - - +
233E TYR* 4.1 1.1 - - - +
240E PRO* 5.6 0.6 - - + +
241E ASN 5.9 2.0 - - - -
242E GLY* 5.3 3.7 + - - -
243E GLY 3.5 13.9 + - - -
244E TRP* 1.3 77.0 - - - +
246E TYR* 1.3 81.5 + - - +
247E ASP* 4.3 7.0 + - - -
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Residues in contact with TYR 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229E VAL 3.7 1.2 - - - +
230E ARG* 3.4 1.6 - - - -
231E ILE* 2.7 50.4 + - + +
233E TYR* 4.3 24.9 - + + -
244E TRP* 4.1 15.3 - + + -
245E HIS* 1.3 87.6 - - - +
247E ASP* 1.3 64.4 + - - +
248E ILE* 4.0 12.2 + - + -
536F ILE* 4.0 26.6 - - + +
537F PRO* 4.2 1.0 - - - +
540F GLN* 2.7 30.2 + - - -
571F LEU* 3.5 37.9 - - + -
573F LEU* 4.8 7.0 - - + -
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Residues in contact with ASP 247 (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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229E VAL 3.3 4.2 - - - +
230E ARG* 2.8 59.6 + - - +
245E HIS* 4.3 4.9 + - - -
246E TYR* 1.3 73.9 - - - +
248E ILE* 1.3 64.3 + - - +
249E PRO 4.0 0.7 - - - -
250E SER* 3.5 38.6 + - - +
251E ASP 5.2 1.2 - - - +
252E ASP* 5.8 2.8 - - - +
253E GLN 5.6 1.7 - - - +
257E PRO* 4.6 7.6 - - - +
509F THR* 4.9 4.7 - - - +
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Residues in contact with ILE 248 (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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215E HIS* 4.1 24.5 - - + +
218E ILE* 3.8 24.7 - - + -
219E ASN* 3.6 25.6 - - - +
222E ILE* 3.6 28.4 - - + +
228E ARG* 3.5 1.2 - - - -
229E VAL* 2.8 35.3 + - + +
231E ILE* 3.8 18.2 - - + -
246E TYR* 4.7 8.7 - - + +
247E ASP* 1.3 82.1 - - - +
249E PRO* 1.4 72.4 - - + +
250E SER* 3.1 4.4 + - - -
509F THR* 6.2 2.5 - - + -
571F LEU* 6.0 0.4 - - + -
573F LEU* 4.5 4.0 - - + -
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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