Contacts of the strand formed by residues 246 - 251 (chain B) in PDB entry 5EJK
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 TYR 246 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A PRO* 4.0 32.8 - - + -
242B TRP* 3.9 0.3 - - - -
243B GLY* 3.0 29.5 + - - +
244B ARG 3.2 7.9 + - - +
245B GLY* 1.3 83.9 - - - +
247B ALA* 1.3 61.8 - - - +
259B TRP* 4.1 11.9 - - + -
260B VAL* 3.3 27.1 - - - +
261B PRO* 3.6 23.6 - - + -
262B SER* 4.1 4.4 + - - +
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Residues in contact with ALA 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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239B VAL* 4.3 7.2 - - + -
241B VAL 3.4 11.4 - - - +
242B TRP* 3.9 28.3 - - + +
246B TYR* 1.3 73.5 - - - +
248B ALA* 1.3 60.0 + - - +
249B VAL* 4.8 0.4 - - + -
259B TRP* 3.2 7.9 - - - -
260B VAL* 2.6 42.2 + - + +
262B SER* 4.4 3.8 - - - +
265B VAL* 4.4 15.9 - - + -
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Residues in contact with ALA 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A PRO* 3.5 35.0 - - + -
239B VAL* 3.2 7.1 - - - +
240B LEU* 3.0 25.8 + - + -
241B VAL* 2.7 16.2 + - + +
247B ALA* 1.3 71.0 - - - +
249B VAL* 1.3 60.5 + - - +
257B VAL* 5.8 2.2 - - + -
258B ILE 3.5 6.7 - - - +
259B TRP* 3.6 24.2 - - + +
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Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B VAL* 3.9 12.3 - - + -
226B ILE* 3.8 26.0 - - + -
237B TRP* 3.9 19.2 - - + -
238B ASN 3.3 8.5 - - - +
239B VAL* 3.7 22.7 - - + -
240B LEU 4.5 0.4 - - - +
247B ALA* 4.8 1.3 - - + +
248B ALA* 1.3 78.8 - - - +
250B LYS* 1.3 61.0 + - - +
257B VAL* 3.5 4.1 - - - -
258B ILE* 3.0 43.6 + - + +
260B VAL* 4.3 10.5 - - + -
265B VAL* 4.5 13.2 - - + -
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Residues in contact with LYS 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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219B THR 4.9 3.8 + - - -
220B GLU* 3.5 37.5 + - - +
237B TRP* 3.5 3.3 - - - -
238B ASN* 2.6 40.6 + - - +
240B LEU* 3.7 29.2 - - + +
249B VAL* 1.3 73.2 - - - +
251B ASN* 1.3 74.7 + - - +
252B ARG* 3.6 4.4 + - - +
255B ASP* 4.0 26.6 + - + +
256B LYS 3.6 5.4 - - - +
257B VAL* 3.7 21.5 - - + -
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Residues in contact with ASN 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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234B GLU* 5.8 1.0 + - - -
236B GLY* 3.8 12.0 + - - -
237B TRP* 3.3 43.5 - - + +
250B LYS* 1.3 74.7 - - - +
252B ARG* 1.3 59.7 + - - +
253B ASP* 3.0 28.9 + - - +
254B THR* 3.2 27.5 + - - +
255B ASP* 3.0 29.8 + - - +
256B LYS* 3.0 12.2 + - + +
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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