Contacts of the helix formed by residues 244 - 248 (chain F) in PDB entry 3J7Y
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 244 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F VAL* 4.6 0.2 - - - -
220F ASP 3.5 10.1 - - - +
222F THR 4.1 28.0 - - - +
223F HIS* 4.1 19.5 - - + +
226F MET* 6.2 2.5 - - - -
242F LEU 4.9 0.2 - - - -
243F ILE* 1.3 98.3 - - + +
245F ALA* 1.3 61.4 + - - +
246F VAL* 4.4 9.0 - - + +
247F GLY 2.8 21.0 + - - +
248F LEU* 3.3 2.4 + - - -
57i TYR* 3.6 36.6 - - + +
26q ARG* 6.1 0.2 - - - +
27q ALA* 4.2 6.3 - - + -
30q PRO* 5.0 2.5 - - + -
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Residues in contact with ALA 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F VAL* 4.0 14.7 - - + +
221F LEU* 4.2 12.1 - - + +
222F THR 5.0 0.2 - - - +
243F ILE 3.9 1.2 + - - -
244F PRO* 1.3 72.3 - - - +
246F VAL* 1.3 62.7 + - - +
248F LEU* 3.1 19.3 + - + +
265F THR* 3.8 25.8 - - + +
268F PHE* 3.4 30.3 - - + -
269F LEU* 4.9 5.8 - - + -
63i LEU* 3.7 13.3 - - - +
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Residues in contact with VAL 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222F THR* 5.9 6.7 - - - +
244F PRO* 3.2 9.4 - - + -
245F ALA* 1.3 77.2 - - - +
247F GLY* 1.3 57.3 + - - +
268F PHE* 4.1 10.1 - - + -
57i TYR* 4.5 7.6 - - + +
59i ASN 3.3 9.4 - - - +
60i ILE* 3.6 31.7 - - + +
63i LEU* 3.2 43.1 - - - +
64i GLY* 4.5 8.3 - - - -
30q PRO* 5.2 7.0 - - + -
32q ARG* 6.2 2.0 - - - +
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Residues in contact with GLY 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243F ILE* 3.8 13.3 - - - +
244F PRO* 2.8 13.5 + - - +
246F VAL* 1.3 78.4 - - - +
248F LEU* 1.3 65.1 + - - +
249F ASN* 3.2 16.1 - - - +
56i VAL* 3.9 1.7 - - - -
57i TYR* 3.4 37.9 + - - -
58i ASP 4.4 0.6 - - - +
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Residues in contact with LEU 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174F LEU* 3.5 28.5 - - + +
178F LEU* 5.1 4.7 - - + -
217F LEU* 4.9 1.8 - - + -
219F VAL* 3.9 30.1 - - + -
243F ILE* 4.1 9.4 - - - +
244F PRO 3.3 5.9 + - - +
245F ALA* 3.1 20.4 + - + +
246F VAL 4.4 0.2 - - - +
247F GLY* 1.3 77.9 - - - +
249F ASN* 1.3 63.3 + - - +
252F SER* 4.9 0.4 - - - +
253F MET* 4.3 12.1 - - + -
259F LEU* 3.9 22.9 - - + -
261F LEU* 4.0 9.9 - - + -
269F LEU* 4.1 27.8 - - + -
59i ASN* 4.5 2.4 - - - +
63i LEU* 4.1 17.5 - - + +
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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