Contacts of the strand formed by residues 292 - 296 (chain C) in PDB entry 2BZN
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 THR 292 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265C LEU* 3.7 28.7 - - + -
266C PHE 3.5 6.3 - - - +
267C TYR* 3.5 12.5 - - - +
271C SER* 4.3 2.1 + - - -
273C MET* 3.5 30.9 + - + +
291C LYS* 1.3 78.1 - - - +
293C VAL* 1.3 76.4 + - - +
256F ILE* 4.4 7.9 - - + -
257F GLU* 3.4 31.6 + - - +
258F ARG* 4.2 6.7 - - + -
259F ASP 5.3 0.3 + - - -
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Residues in contact with VAL 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C SER 5.7 0.2 - - - +
185C VAL* 3.9 22.0 - - + -
265C LEU* 3.5 4.0 - - - -
266C PHE* 2.8 44.1 + - + +
291C LYS* 4.4 19.7 - - + +
292C THR* 1.3 83.9 - - - +
294C GLU* 1.3 67.1 + - - +
295C VAL* 3.9 22.4 - - + -
258F ARG* 4.8 5.2 - - - -
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Residues in contact with GLU 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C ILE* 3.8 11.6 - - + +
258C ARG* 2.8 42.6 + - - +
263C TYR* 3.7 23.0 - - + +
264C LYS 3.5 4.3 - - - +
265C LEU* 3.7 19.1 - - + -
293C VAL* 1.3 74.7 - - - +
295C VAL* 1.3 64.0 + - - +
296C PRO* 3.9 6.2 - - - +
256F ILE* 3.5 11.8 - - + +
258F ARG* 3.2 19.4 + - - +
294F GLU* 2.4 32.7 - - - +
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Residues in contact with VAL 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C GLY 5.7 0.9 - - - +
246C ALA* 4.2 4.9 - - + +
247C GLY* 3.9 14.8 - - - -
263C TYR* 3.2 2.5 - - - -
264C LYS* 2.8 39.0 + - - +
266C PHE* 3.8 32.1 - - + -
293C VAL* 3.9 11.4 - - + -
294C GLU* 1.3 74.9 - - - +
296C PRO* 1.4 85.5 - - + +
297C PHE* 3.2 0.5 + - - -
298C LYS* 3.8 27.4 - - - +
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Residues in contact with PRO 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C LYS 3.5 10.1 - - - +
263C TYR* 3.9 15.2 - - + -
294C GLU 3.9 6.7 - - - +
295C VAL* 1.4 97.4 - - + +
297C PHE* 1.3 68.0 + - - +
298C LYS* 3.4 9.7 + - - +
260H GLY 6.0 2.0 - - - +
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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