Contacts of the strand formed by residues 247 - 253 (chain B) in PDB entry 4BJ3
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 LYS 247 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B ASP* 3.5 4.0 - - + +
231B ARG 5.6 2.2 + - - -
235B TYR* 4.1 41.8 - - + +
242B ARG 5.9 2.7 - - - +
243B ARG* 6.2 3.4 - - - +
245B ALA 4.8 3.6 - - - +
246B THR* 1.3 82.8 - - - +
248B VAL* 1.3 63.3 + - - +
273B ASP* 3.9 29.8 + - - +
274B ASN 3.6 13.6 + - - +
275B ILE* 3.8 13.8 - - + -
276B LEU* 3.2 30.5 + - - +
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Residues in contact with VAL 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ILE* 4.5 13.7 - - + -
145B ASP 2.7 19.3 + - - +
146B VAL* 3.7 26.2 - - + -
147B VAL* 3.2 17.6 + - - +
235B TYR* 2.6 21.0 + - - -
246B THR* 4.2 11.9 - - - +
247B LYS* 1.3 79.4 - - - +
249B MET* 1.3 61.3 + - - +
250B VAL* 5.0 0.4 - - + -
275B ILE* 4.2 1.1 - - - -
276B LEU* 3.4 19.5 - - + +
278B PHE* 3.9 26.7 - - + -
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Residues in contact with MET 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B VAL* 3.4 9.9 - - + +
149B VAL* 4.0 12.6 - - + -
227B ILE* 3.6 33.2 - - + +
230B ALA* 3.8 29.4 - - - -
231B ARG* 5.1 1.8 - - + +
235B TYR* 3.6 8.3 - - - +
248B VAL* 1.3 78.0 - - - +
250B VAL* 1.3 63.6 + - - +
251B VAL* 3.7 14.9 + - + +
270B CYS* 4.1 14.1 - - - -
275B ILE* 3.8 24.9 - - + +
276B LEU 3.1 8.3 + - - +
277B ARG* 3.6 11.2 - - + -
278B PHE* 2.8 28.4 + - - +
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Residues in contact with VAL 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B VAL* 3.7 26.7 - - + -
147B VAL 2.7 9.1 + - - -
148B VAL* 3.3 20.2 - - + +
149B VAL 2.7 30.6 + - - +
165B PHE* 4.5 8.5 - - + -
169B PHE* 4.1 18.2 - - + -
248B VAL* 5.0 0.4 - - + -
249B MET* 1.3 72.8 - - - +
251B VAL* 1.3 55.8 + - - +
252B VAL* 3.7 9.1 + - + -
278B PHE* 4.1 19.5 - - + -
280B ILE* 3.7 31.0 - - + -
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Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B VAL* 3.4 13.2 - - + +
187B TYR* 4.5 9.2 - - - +
223B THR* 4.6 2.7 - - + -
227B ILE* 3.9 36.8 - - + -
249B MET* 4.0 21.3 - - + +
250B VAL* 1.3 74.3 - - - +
252B VAL* 1.3 61.9 + - - +
253B THR* 3.8 21.4 + - + +
277B ARG* 5.6 1.6 - - + -
278B PHE 3.4 18.6 + - - +
279B GLY* 3.9 2.0 - - - -
280B ILE* 3.0 26.5 + - - +
303B ILE* 4.0 12.8 - - + -
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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
----------------------------------------------------------
148B VAL* 4.1 16.2 - - + -
149B VAL 2.9 11.5 + - - +
150B CYS* 4.3 7.6 - - - -
151B ASP* 2.8 32.4 + - - +
156B ILE* 5.0 0.2 - - - +
162B VAL* 4.4 19.7 - - + -
165B PHE* 3.8 27.1 - - + -
166B LEU* 4.8 1.8 - - + -
250B VAL* 4.1 8.7 - - + -
251B VAL* 1.3 74.7 - - - +
253B THR* 1.3 57.2 + - - +
280B ILE* 3.6 23.1 - - + +
282B VAL* 3.8 22.4 - - + +
315B VAL* 4.6 3.4 - - + -
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Residues in contact with THR 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ASP* 2.8 20.9 + - - -
156B ILE* 4.4 0.2 - - - -
187B TYR* 3.3 23.0 + - - +
221B THR* 4.8 0.7 - - - +
223B THR* 4.0 8.3 + - + +
251B VAL* 3.8 17.0 - - + +
252B VAL* 1.3 71.9 - - - +
254B ASP* 1.3 69.6 + - - +
255B GLY* 3.3 10.1 + - - +
256B GLU 5.2 0.2 + - - -
280B ILE 3.2 7.7 + - - +
281B ALA* 3.7 2.9 - - - -
282B VAL* 3.1 27.6 + - - -
300B ILE* 3.7 23.4 - - + +
303B ILE* 4.8 9.9 - - + -
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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
------------------------------------------------------------
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