Contacts of the helix formed by residues 246 - 253 (chain B) in PDB entry 4JF7
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 PRO 246 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188B HIS* 3.9 28.2 - - + +
245B GLN* 1.3 95.2 - - + +
247B GLU* 1.3 64.8 + - - +
248B ARG* 3.3 4.0 - - + +
249B ASP* 3.2 36.9 + - - +
250B ASP* 3.4 7.8 + - - +
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Residues in contact with GLU 247 (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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245B GLN 3.7 0.6 + - - -
246B PRO* 1.3 72.1 - - - +
248B ARG* 1.3 64.5 + - - +
250B ASP* 2.9 30.6 + - + +
251B TYR* 3.2 35.5 + - + -
288B ASN* 4.3 10.8 + - - +
306B TYR* 4.2 14.9 + - - -
353B PHE* 3.9 22.5 - - + -
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Residues in contact with ARG 248 (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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246B PRO* 3.3 4.5 - - + +
247B GLU* 1.3 78.1 - - - +
249B ASP* 1.3 71.1 + - - +
251B TYR* 3.0 13.0 + - - +
252B PHE* 3.3 40.0 + - + -
351B SER 5.2 1.2 + - - -
352B TRP* 3.0 80.0 + - - +
353B PHE* 4.0 20.7 - - + -
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Residues in contact with ASP 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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245B GLN* 3.7 22.5 - - + +
246B PRO* 3.2 34.8 + - - +
248B ARG* 1.3 85.0 - - - +
250B ASP* 1.3 56.8 + - - +
252B PHE* 3.2 8.8 + - - +
253B SER* 2.7 33.6 + - - -
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Residues in contact with ASP 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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241B PHE* 4.1 18.2 - - - -
243B SER* 5.0 2.3 + - - -
244B THR* 5.6 1.0 + - - -
245B GLN* 3.1 29.2 + - - +
246B PRO 3.4 11.7 + - - +
247B GLU* 2.9 20.7 + - + +
249B ASP* 1.3 79.3 - - - +
251B TYR* 1.3 61.0 + - + +
252B PHE 3.4 0.3 + - - -
253B SER* 3.5 7.6 + - - +
255B ALA 5.0 0.5 - - - +
257B PRO* 3.7 18.4 - - + +
285B ALA 3.2 22.5 - - - +
286B THR* 3.4 26.8 + - + +
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Residues in contact with TYR 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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247B GLU* 3.2 42.8 + - + -
248B ARG 3.0 7.5 + - - +
250B ASP* 1.3 79.5 - - + +
252B PHE* 1.3 59.9 + - - +
285B ALA* 3.7 4.0 - - - +
286B THR* 3.5 29.5 - - + +
288B ASN* 5.3 3.1 + - - -
306B TYR* 4.2 18.0 - - - -
307B GLY* 4.0 6.3 + - - -
308B GLY* 3.7 24.7 - - - -
353B PHE* 3.2 63.8 - + + +
354B GLY* 4.1 0.9 - - - -
356B ARG* 2.8 34.8 + - + +
358B ILE* 3.9 13.4 - - + +
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Residues in contact with PHE 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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248B ARG* 3.3 46.7 + - + +
249B ASP* 3.2 11.8 + - - +
251B TYR* 1.3 77.2 - - - +
253B SER* 1.3 60.1 + - - +
254B ALA* 3.8 0.5 + - - +
351B SER 4.6 4.9 - - - -
352B TRP 3.5 15.5 - - - -
354B GLY* 3.3 36.3 - - - -
355B ASN* 5.7 2.5 - - - -
356B ARG* 3.2 15.6 + - - +
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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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245B GLN* 3.5 16.5 + - - -
249B ASP* 2.7 18.9 + - - +
250B ASP* 3.5 8.7 + - - +
252B PHE* 1.3 78.5 - - - +
254B ALA* 1.3 64.2 + - - +
255B ALA* 3.6 10.9 + - - -
285B ALA* 3.3 20.3 - - - +
356B ARG* 4.1 0.4 - - - -
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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