Contacts of the strand formed by residues 242 - 245 (chain D) in PDB entry 1JLH
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 242 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204D LEU* 4.1 0.6 - - - +
205D PHE* 3.5 39.0 - + + -
207D ILE* 4.2 11.0 - - + -
221D ALA 4.1 9.6 - - - -
224D ALA* 3.8 7.9 - - + -
225D LYS* 3.5 33.9 - - + -
228D PHE* 4.0 26.2 - + + -
238D VAL* 2.9 29.2 + - + +
239D ALA 4.0 11.1 - - - +
240D LYS 3.8 0.6 - - - -
241D HIS* 1.3 86.9 - - + +
243D VAL* 1.3 66.6 + - - +
255D PHE* 3.7 17.3 - + - -
257D ILE* 3.6 32.9 - - + +
258D ASP 4.9 0.2 + - - -
261D ASN* 5.0 0.9 - - - +
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Residues in contact with VAL 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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131D PHE* 3.6 33.9 - - + -
140D TRP* 4.9 4.3 - - + -
204D LEU* 4.3 10.1 - - + -
205D PHE 2.9 17.3 + - - +
206D ILE* 3.8 25.4 - - + -
207D ILE* 2.9 29.6 + - - +
242D PHE* 1.3 78.8 - - - +
244D ALA* 1.3 60.6 + - - +
257D ILE* 3.8 4.7 - - - -
261D ASN* 3.8 24.9 - - + +
263D PHE* 4.3 5.4 - - + -
281D LEU* 4.5 11.9 - - + -
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Residues in contact with ALA 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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207D ILE 3.4 3.1 - - - -
212D PHE* 3.6 25.8 - - + -
243D VAL* 1.3 74.1 - - - +
245D LEU* 1.3 60.0 + - - +
246D SER* 3.6 2.7 - - - +
252D VAL* 3.8 32.1 - - + -
257D ILE* 3.8 4.4 - - + +
261D ASN 3.1 8.6 + - - +
262D MET* 3.2 4.5 - - + -
263D PHE* 2.7 34.3 + - - -
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Residues in contact with LEU 245 (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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153D ASN* 4.5 2.2 - - - +
206D ILE* 3.5 27.6 - - + -
207D ILE 2.8 12.2 + - - +
208D ALA* 3.8 16.6 - - + -
209D SER 3.0 25.5 + - - +
243D VAL* 5.3 0.4 - - + -
244D ALA* 1.3 78.4 - - - +
246D SER* 1.3 57.9 + - - +
263D PHE* 3.3 22.4 - - + +
265D PHE* 3.6 14.0 - - + -
278D ALA 3.4 24.2 - - - +
279D ILE* 3.6 21.1 - - + +
281D LEU* 3.7 31.0 - - + -
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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