Contacts of the strand formed by residues 286 - 291 (chain C) in PDB entry 5C51
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 GLY 286 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C LEU* 4.6 0.2 - - - -
277C ASP* 4.6 0.2 - - - +
278C CYS* 2.8 41.8 + - - +
285C LYS* 1.3 76.0 - - - +
287C ASN* 1.3 70.6 + - - -
303C LEU 3.3 11.2 - - - -
304C TRP* 3.9 20.2 - - - -
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Residues in contact with ASN 287 (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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252C LEU* 3.9 18.4 - - - +
253C ASP* 5.7 0.3 - - - -
256C LEU* 3.4 39.4 - - + +
275C SER* 6.2 0.2 - - - -
276C SER 3.3 5.4 - - - +
277C ASP* 3.1 38.4 + - - +
285C LYS* 3.5 18.4 + - - +
286C GLY* 1.3 80.2 + - - -
288C LYS* 1.3 62.3 + - - +
289C LEU* 5.7 0.2 - - - -
303C LEU* 2.7 51.7 + - + +
304C TRP* 5.5 0.4 - - - -
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Residues in contact with LYS 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C SER* 3.8 0.5 - - - -
276C SER* 2.9 36.8 + - - +
277C ASP 5.0 2.0 + - - -
278C CYS* 2.7 44.3 - - - +
287C ASN* 1.3 78.6 - - - +
289C LEU* 1.3 63.7 + - - +
290C TYR* 3.2 40.6 + - + +
299C LEU* 4.1 17.7 - - + -
301C GLU 3.5 3.4 - - - -
302C THR* 4.5 16.4 - - + -
303C LEU 5.2 0.2 - - - +
304C TRP* 5.1 12.1 - - + +
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Residues in contact with LEU 289 (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 LEU* 3.8 28.0 - - + -
259C ARG* 3.8 21.5 - - + -
260C LEU* 4.5 11.7 - - + -
263C TRP* 3.9 13.7 - - + -
273C PHE* 6.4 0.9 - - + -
274C SER 3.5 5.4 - - - +
275C SER* 3.8 16.8 - - - -
288C LYS* 1.3 71.5 - - - +
290C TYR* 1.3 62.6 + - - +
299C LEU* 4.0 2.0 - - - +
300C ILE* 2.9 33.3 + - + +
301C GLU* 2.7 55.2 + - + +
303C LEU* 4.6 9.6 - - + -
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Residues in contact with TYR 290 (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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273C PHE* 3.6 7.6 - - - +
274C SER* 2.9 42.3 + - - +
275C SER 5.5 0.2 - - - -
276C SER* 3.8 26.5 - - - -
288C LYS* 3.2 46.2 - - + +
289C LEU* 1.3 76.6 - - - +
291C TYR* 1.3 60.5 + - - +
297C LYS* 4.6 18.4 - - + -
298C GLU* 3.3 25.8 - - - -
299C LEU* 3.7 20.3 - - + +
300C ILE* 4.8 1.9 - - - +
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Residues in contact with TYR 291 (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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272C ASN* 3.0 37.0 + - + -
273C PHE* 3.5 36.8 - + + -
290C TYR* 1.3 75.3 - - - +
292C ASN* 1.3 73.6 + - - +
293C PHE* 3.6 33.3 + + - -
297C LYS* 3.2 4.6 - - - -
298C GLU 2.9 32.1 + - - +
300C ILE* 3.7 23.8 - - + -
348C ALA* 2.7 44.9 + - + -
351C TYR* 3.9 7.1 - - + +
352C ASP* 3.7 10.9 + - + +
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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