Contacts of the strand formed by residues 194 - 199 (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 LYS 194 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B SER* 1.3 74.0 + - - +
195B VAL* 1.3 78.1 + - - +
196B TYR* 6.1 0.9 - - + -
242B SER* 5.9 4.7 - - - -
243B SER 3.5 16.8 - - - +
244B TYR* 3.5 17.0 - - + -
245B LEU* 4.7 0.4 - - - -
272B SER* 3.4 17.2 + - - +
273B GLN* 2.9 28.8 - - + +
274B THR* 3.6 0.2 - - - -
275B PHE* 3.2 49.5 + - + +
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Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B LEU* 5.4 3.4 - - + -
162B TRP* 5.0 3.6 - - + -
193B SER* 4.8 0.2 - - - +
194B LYS* 1.3 83.3 - - - +
196B TYR* 1.3 61.1 + - - +
197B PHE* 3.8 24.7 - - + -
209B HIS* 3.4 48.7 - - + +
241B ARG 4.7 0.3 - - - +
242B SER* 3.9 2.0 - - - -
243B SER* 3.3 41.7 + - - +
261B VAL* 4.9 5.2 - - + -
267B VAL* 5.5 4.9 - - + -
273B GLN 3.6 5.4 - - - -
274B THR* 4.3 15.3 - - - +
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Residues in contact with TYR 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LYS* 6.1 1.6 - - + -
195B VAL* 1.3 71.4 - - - +
197B PHE* 1.3 104.7 + - - +
198B ARG* 3.4 18.6 - - + +
240B ALA* 3.1 29.6 - - + +
241B ARG 4.2 2.9 - - - -
242B SER* 3.4 24.9 - - - +
267B VAL* 3.4 16.1 - - - +
268B ASN* 3.1 35.6 + - + +
273B GLN* 2.9 42.2 + - + +
274B THR* 5.5 1.0 - - - +
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Residues in contact with PHE 197 (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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195B VAL* 3.8 30.7 - - + -
196B TYR* 1.3 96.3 - - - +
198B ARG* 1.3 60.4 + - - +
207B LEU* 3.4 43.3 - - + -
208B SER 4.5 7.9 - - - -
209B HIS* 5.2 0.4 - - + -
239B TRP* 3.2 21.5 - - + -
240B ALA* 3.4 1.0 - - - -
241B ARG 3.1 36.1 + - - +
242B SER* 5.9 0.7 - - - -
243B SER* 4.8 2.2 - - - -
261B VAL* 5.5 5.8 - - + -
262B SER 3.8 14.8 - - - -
263B GLU* 3.0 35.2 - - + -
266B LEU 3.3 6.5 - - - -
267B VAL* 3.4 19.1 - - + -
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Residues in contact with ARG 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B TYR* 3.4 24.2 - - + +
197B PHE* 1.3 72.1 - - - +
199B GLY* 1.3 66.2 + - - +
239B TRP* 3.3 22.5 - - - +
265B SER 5.5 1.3 - - - -
266B LEU* 2.9 42.1 + - - +
267B VAL 3.5 19.4 + - - -
268B ASN* 4.0 16.2 - - + +
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Residues in contact with GLY 199 (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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198B ARG* 1.3 86.7 - - - +
239B TRP* 3.1 52.7 + - - +
266B LEU* 4.1 9.2 - - - -
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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