Contacts of the strand formed by residues 342 - 349 (chain C) in PDB entry 5BZZ
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 342 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C MET 3.6 0.3 - - - +
200C PHE* 3.3 4.7 - - - -
201C GLU* 2.8 64.3 + - + +
319C THR* 3.9 22.6 - - + +
320C LEU 3.3 8.3 - - - +
321C THR* 4.2 21.8 - - + -
340C ASN* 3.6 18.5 + - - +
341C PHE* 1.3 88.6 - - - +
343C VAL* 1.3 65.6 + - - +
344C LYS* 4.1 1.3 - - - +
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Residues in contact with VAL 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C MET* 4.4 12.8 - - + -
199C MET 3.2 8.7 - - - +
200C PHE* 4.1 13.7 - - + -
257C PHE* 4.9 0.2 - - + -
271C PHE* 3.5 34.3 - - + -
273C PHE* 4.7 6.3 - - + -
318C LEU 3.8 0.9 - - - +
319C THR* 3.6 1.2 - - - +
320C LEU* 2.8 39.0 + - + +
325C LEU* 3.9 8.3 - - + -
341C PHE* 3.8 15.3 - - + -
342C LYS* 1.3 76.5 - - - +
344C LYS* 1.3 66.7 + - - +
345C LEU* 3.8 22.5 - - + +
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Residues in contact with LYS 344 (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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198C MET* 3.1 8.5 - - - +
199C MET* 2.8 50.4 + - + +
201C GLU* 3.1 29.2 + - + +
310C ASP* 6.1 2.7 - - - -
317C VAL* 4.3 10.3 - - + -
318C LEU 3.3 4.0 - - - +
319C THR* 3.8 31.0 - - + +
342C LYS* 5.4 1.3 - - + +
343C VAL* 1.3 75.1 - - - +
345C LEU* 1.3 61.7 + - - +
346C TYR* 3.6 32.5 + - + +
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Residues in contact with LEU 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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195C PHE* 4.0 5.2 - - + -
197C LYS 3.9 3.8 - - - -
198C MET* 3.6 24.0 - - + -
255C VAL* 5.6 0.4 - - + -
273C PHE* 3.6 39.5 - - + -
275C VAL* 4.6 4.9 - - + -
316C LEU 3.5 0.9 - - - +
317C VAL* 3.1 9.2 - - - +
318C LEU* 2.7 59.9 + - + +
320C LEU* 4.4 6.7 - - + -
343C VAL* 3.8 12.1 - - + +
344C LYS* 1.3 77.6 - - - +
346C TYR* 1.3 60.7 + - - +
347C PHE* 3.5 30.0 - - + -
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Residues in contact with TYR 346 (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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195C PHE* 3.4 6.5 - - - -
196C HIS* 3.0 24.9 + - - +
197C LYS* 3.0 58.0 + - + +
199C MET* 4.1 24.6 - - + +
240C TYR* 5.7 0.6 - + - -
312C ASP* 4.6 9.2 - - - -
315C TYR* 3.9 29.2 - + + -
316C LEU 3.5 1.6 - - - -
317C VAL* 3.8 26.9 - - + -
344C LYS* 3.6 46.3 + - + +
345C LEU* 1.3 73.8 - - - +
347C PHE* 1.3 62.1 + - - +
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Residues in contact with PHE 347 (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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193C LEU* 4.1 22.4 - - + -
194C LEU 3.1 16.8 - - - +
195C PHE* 3.4 40.4 - + + -
196C HIS* 4.0 2.2 - - - -
249C VAL* 4.1 11.9 - - + -
253C ILE* 6.2 3.6 - - + -
275C VAL* 5.2 1.6 - - + -
277C THR* 5.4 0.9 - - + -
280C ILE* 3.5 40.2 - - + -
315C TYR* 3.4 3.7 - - - -
316C LEU* 2.7 56.5 + - + +
318C LEU* 4.7 1.3 - - + -
345C LEU* 3.5 35.4 - - + -
346C TYR* 1.3 73.9 - - - +
348C THR* 1.3 69.4 + - - +
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Residues in contact with THR 348 (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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193C LEU* 3.4 10.9 - - - +
194C LEU* 2.8 45.9 + - - +
196C HIS* 2.6 35.5 + - + +
314C GLU 3.9 19.1 - - - +
315C TYR* 4.0 7.4 - - + -
316C LEU* 4.3 7.0 - - + -
347C PHE* 1.3 78.6 - - - +
349C LYS* 1.3 65.8 + - - +
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Residues in contact with LYS 349 (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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189C ARG* 4.5 15.8 - - - +
191C VAL* 4.5 18.6 - - + -
192C ALA 4.7 3.8 - - - -
193C LEU* 3.5 19.3 - - + -
194C LEU* 5.1 0.7 - - - +
316C LEU* 3.8 22.3 - - + +
348C THR* 1.3 82.0 + - - +
350C THR* 1.3 66.3 + - - +
351C VAL* 3.1 32.4 + - - +
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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