Contacts of the strand formed by residues 342 - 346 (chain C) in PDB entry 6BW4
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 LEU 342 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334C ALA* 3.8 26.5 - - + -
335C SER 3.3 10.1 - - - +
336C SER* 4.1 6.5 - - - -
341C ARG* 1.3 72.8 - - - +
343C ASN* 1.3 64.8 + - - +
344C VAL* 4.1 3.7 + - + +
368C PHE 4.0 0.3 - - - +
369C ILE* 3.7 1.2 - - - -
370C HIS* 2.8 46.2 + - + +
377C ILE* 3.8 9.6 - - + +
380C PHE* 3.6 37.5 - - + -
390C ILE* 4.1 4.3 - - + -
392C SER* 3.9 17.9 - - - -
402C TRP* 3.9 25.8 - - + -
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Residues in contact with ASN 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C SER* 3.8 18.2 + - - -
316C HIS* 3.2 41.3 + - - +
334C ALA* 3.1 6.8 - - - +
335C SER 2.8 31.1 + - - -
339C ASP* 5.3 0.2 + - - -
341C ARG* 4.0 5.1 - - - +
342C LEU* 1.3 73.2 - - - +
344C VAL* 1.3 63.0 + - - +
345C TRP* 3.6 25.4 - - + +
366C LEU* 3.9 10.3 - - + -
368C PHE 3.6 2.7 - - - -
369C ILE* 3.5 30.1 - - - +
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Residues in contact with VAL 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C ILE* 3.8 25.6 - - + -
333C LEU 3.6 4.9 - - - +
334C ALA* 4.5 3.6 - - + -
342C LEU* 4.2 16.4 - - + +
343C ASN* 1.3 77.0 - - - +
345C TRP* 1.3 57.3 + - - +
366C LEU* 3.7 3.6 - - - +
367C LEU* 2.8 40.8 + - + +
368C PHE* 2.9 24.6 + - + +
382C TRP* 4.1 7.4 - - + -
388C TRP* 4.3 0.4 - - + -
390C ILE* 4.7 4.7 - - + -
402C TRP* 4.4 11.0 - - + -
404C MET* 3.8 33.0 - - + -
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Residues in contact with TRP 345 (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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298C VAL* 4.5 4.0 - - + +
313C PHE* 3.4 47.1 - + + -
314C GLU 3.7 37.0 - - - -
315C SER* 3.7 9.0 - - - -
316C HIS* 4.2 10.1 - + - -
331C THR 3.6 0.5 - - - +
332C ILE* 3.3 10.9 - - - +
333C LEU* 2.7 68.8 + - + +
334C ALA* 4.4 0.2 - - - -
335C SER* 2.9 21.9 + - - -
343C ASN* 3.6 33.3 - - + +
344C VAL* 1.3 75.4 - - - +
346C ASP* 1.3 60.1 + - - +
347C LEU* 4.1 1.3 - - + -
363C PRO* 4.4 6.7 - - + -
365C GLU* 3.2 20.4 - - + +
366C LEU* 3.9 21.5 - - + -
367C LEU* 4.7 1.8 - - - -
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Residues in contact with ASP 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C THR* 2.8 24.9 + - - -
332C ILE* 3.6 17.4 - - + +
344C VAL 4.4 0.2 + - - -
345C TRP* 1.3 72.6 - - - +
347C LEU* 1.3 57.0 + - - +
348C SER* 2.9 22.8 + - - -
349C LYS* 3.0 32.8 + - + +
365C GLU* 2.8 28.0 + - - +
367C LEU* 4.4 20.8 - - + +
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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