Contacts of the strand formed by residues 216 - 219 (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 VAL 216 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212F TRP* 3.5 35.7 - - + -
213F GLY 4.7 4.3 - - - +
215F SER* 1.3 81.9 - - - +
217F LEU* 1.3 61.6 + - - +
218F LEU* 3.6 10.1 + - + +
239F THR 3.7 6.4 + - - +
240F PHE* 3.4 41.5 - - + -
241F ASN 3.3 22.7 + - - +
256F HIS* 4.5 2.2 - - - -
258F THR* 3.4 26.7 - - + +
260F VAL* 3.6 11.4 - - + -
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Residues in contact with LEU 217 (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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216F VAL* 1.3 72.3 - - - +
218F LEU* 1.3 55.8 + - - +
219F VAL* 4.2 9.9 - - + -
241F ASN* 3.9 11.7 - - + +
243F ILE* 3.3 32.8 - - + -
248F LEU* 4.9 3.4 - - + -
252F SER* 3.9 18.6 - - - +
253F MET* 4.4 14.4 - - + +
256F HIS* 3.3 41.7 - - + +
258F THR 3.1 18.9 + - - +
259F LEU* 4.0 18.6 - - + -
260F VAL* 2.8 36.6 + - - +
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Residues in contact with LEU 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F LEU* 4.4 11.7 - - + -
193F LEU* 4.2 15.7 - - + -
203F LEU* 4.2 12.6 - - + -
212F TRP* 4.5 3.6 - - + -
216F VAL* 4.1 8.7 - - + +
217F LEU* 1.3 72.1 - - - +
219F VAL* 1.3 63.8 + - - +
230F ILE* 4.2 11.2 - - + -
234F THR* 3.6 31.0 - - + -
240F PHE* 4.5 12.1 - - + -
241F ASN 2.8 16.5 + - - +
242F LEU* 3.4 16.0 - - + +
243F ILE* 2.9 27.4 + - - +
260F VAL* 3.6 31.6 - - + -
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Residues in contact with VAL 219 (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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193F LEU* 4.2 3.6 - - - +
217F LEU* 4.2 9.9 - - + -
218F LEU* 1.3 80.3 - - - +
220F ASP* 1.3 64.0 + - - +
243F ILE* 3.4 10.8 - - + +
244F PRO 4.6 0.7 - - - -
245F ALA* 4.0 21.8 - - + -
248F LEU* 3.9 16.4 - - + -
259F LEU* 3.7 28.7 - - + -
260F VAL 2.8 13.6 + - - +
261F LEU* 3.6 14.8 - - + -
262F THR* 3.3 25.6 + - - +
265F THR* 3.9 16.8 - - + -
269F LEU* 5.8 0.9 - - + -
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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