Contacts of the strand formed by residues 247 - 251 (chain B) in PDB entry 1BZI
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 ALA 247 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190B PHE* 3.8 2.1 - - - -
191B VAL 2.9 30.1 + - - +
225B MET* 3.5 7.5 - - + -
246B GLY* 1.3 74.0 - - - +
248B VAL* 1.3 62.5 + - - +
249B PHE* 3.2 35.7 - - + -
148C HIS* 4.3 1.8 - - + -
192C TYR* 3.9 9.6 - - - +
275C PHE* 3.5 28.5 - - + -
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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
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188B LEU* 5.3 0.7 - - + -
189B TYR 3.2 19.5 - - - +
190B PHE* 3.3 19.7 - - + -
247B ALA* 1.3 69.9 - - - +
249B PHE* 1.3 78.0 + - - +
281B LEU* 3.5 18.6 - - + -
146C VAL* 4.0 19.3 - - + -
147C ALA 5.5 2.2 - - - +
148C HIS* 3.1 22.6 + - + +
192C TYR* 3.0 17.5 + - + +
279C TYR* 3.3 37.5 - - + -
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Residues in contact with PHE 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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188B LEU* 4.1 6.1 - - - +
189B TYR 3.3 27.9 + - - +
191B VAL* 4.4 7.0 - - + -
224B MET* 3.3 64.6 - - + -
225B MET* 3.5 21.1 - - + -
247B ALA* 3.2 32.1 - - + -
248B VAL* 1.3 86.2 - - - +
250B ASN* 1.3 71.6 + - - +
251B LEU* 3.8 11.3 + - + +
148C HIS* 3.5 26.2 - + - -
168C ILE 5.6 2.7 - - - -
169C VAL* 5.6 3.4 - - - -
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Residues in contact with ASN 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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83A SER* 5.8 0.3 + - - -
187B GLY 4.4 4.9 + - - -
188B LEU* 3.7 22.0 - - - +
213B MET* 5.0 2.6 - - - +
249B PHE* 1.3 77.5 - - - +
251B LEU* 1.3 69.9 + - - +
252B THR* 6.2 0.2 - - - +
168C ILE 4.9 0.7 - - - +
169C VAL* 3.3 40.7 - - - +
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Residues in contact with LEU 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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183B ILE* 3.7 27.6 - - + -
186B THR* 3.3 7.1 - - - +
187B GLY 3.2 33.0 + - - +
189B TYR* 3.5 29.6 - - + -
191B VAL* 4.4 8.3 - - + -
213B MET* 3.6 33.4 - - + -
224B MET* 5.1 4.7 - - + -
249B PHE* 4.1 13.7 - - + +
250B ASN* 1.3 84.0 - - - +
252B THR* 1.3 63.3 + - - +
255B ASP* 4.4 2.0 - - + -
257B LEU* 6.2 1.8 - - + -
278B LEU* 3.9 20.0 - - + -
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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