Contacts of the helix formed by residues 248 - 253 (chain B) in PDB entry 2JDQ
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 GLU 248 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205B ASP* 4.4 4.8 + - - -
246B PRO 3.7 1.2 + - - -
247B PRO* 1.3 72.1 - - - +
249B PHE* 1.3 67.6 + - - +
250B ALA* 4.3 17.1 - - + +
251B LYS* 3.1 56.6 + - + +
252B VAL* 3.7 3.3 + - - +
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Residues in contact with PHE 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B PRO* 3.1 6.8 + - + -
248B GLU* 1.3 73.4 - - - +
250B ALA* 1.3 52.4 + - - +
252B VAL* 3.1 6.2 + - + -
253B SER* 2.7 58.9 + - - -
256B LEU* 4.5 5.4 - - + -
281B LEU* 3.5 45.3 - - + -
287B ASP 4.9 1.6 - - - -
288B LYS* 3.6 59.8 - - + +
291B ALA* 3.7 25.1 - - + -
292B VAL* 4.7 1.6 - - + -
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Residues in contact with ALA 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B GLU* 3.2 17.4 + - + +
249B PHE* 1.3 77.1 - - - +
251B LYS* 1.3 60.3 + - - +
253B SER* 3.6 8.1 + - - -
254B PRO* 3.4 16.8 - - - +
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Residues in contact with LYS 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B ASP* 5.2 5.6 - - - +
208B LEU* 4.3 37.0 + - + +
209B ASP* 2.7 33.0 + - - +
213B LEU* 3.0 23.9 - - - +
248B GLU* 3.1 51.5 + - + +
250B ALA* 1.3 78.5 - - - +
252B VAL* 1.3 58.3 + - - +
254B PRO* 3.5 2.4 - - - +
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B LEU* 4.5 8.3 - - + -
213B LEU* 4.1 4.9 - - + +
236B LEU* 5.5 2.5 - - + -
239B LEU* 3.5 34.8 - - + +
240B CYS* 3.7 18.8 - - - -
247B PRO* 4.4 14.4 - - + -
248B GLU 3.7 4.0 + - - +
249B PHE* 3.1 19.1 + - + +
251B LYS* 1.3 80.6 - - + +
253B SER* 1.3 64.2 + - - +
254B PRO* 3.1 7.5 - - - +
255B CYS* 3.3 28.0 + - - +
281B LEU* 3.4 23.7 - - + +
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Residues in contact with SER 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B PHE* 2.7 52.1 + - - -
250B ALA* 3.6 10.0 + - - -
252B VAL* 1.3 72.2 - - - +
254B PRO* 1.4 68.2 - - - +
255B CYS 3.1 1.3 + - - -
256B LEU* 3.2 34.2 + - - +
281B LEU* 4.8 2.7 - - - -
291B ALA* 5.5 1.1 - - - -
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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