Contacts of the strand formed by residues 365 - 368 (chain O) in PDB entry 5C7O
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 SER 365 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227O ASN 4.4 2.2 - - - -
228O CYS* 2.8 28.6 + - - -
231O PRO* 4.6 4.9 - - - -
232O LEU* 4.3 2.4 - - - +
345O ILE 3.2 5.0 + - - +
346O LEU* 3.3 21.3 - - - +
347O ALA* 2.8 24.9 + - - +
363O HIS* 3.3 2.0 - - - +
364O SER* 1.3 80.3 - - - +
366O ILE* 1.3 61.9 - - - +
367O PHE 4.0 0.7 - - - -
384O SER* 2.6 22.5 + - - -
385O TRP 3.4 6.7 + - - -
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Residues in contact with ILE 366 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347O ALA* 3.5 20.9 - - + +
348O TYR 4.7 0.2 - - - -
349O THR* 4.1 19.5 - - + -
358O PHE* 3.5 43.5 - - + -
361O ASP* 3.7 24.0 - - + +
363O HIS* 3.9 21.5 - - + +
365O SER* 1.3 76.2 - - - +
367O PHE* 1.3 64.8 + - - +
368O ASP 3.4 1.0 + - - -
384O SER* 3.1 4.5 + - - -
385O TRP* 2.8 52.6 + - + +
386O TYR* 4.4 4.3 - - - -
387O ASP 5.2 0.2 - - - +
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Residues in contact with PHE 367 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232O LEU* 3.8 25.6 - - + -
327O TYR* 3.7 19.5 - + - -
330O ILE* 4.1 18.6 - - + -
331O LYS* 4.4 6.7 - - + -
334O VAL* 3.6 28.7 - - + -
346O LEU* 4.6 4.7 - - + +
347O ALA 2.8 11.9 + - - +
348O TYR* 3.6 29.4 - + - -
349O THR* 3.0 33.0 + - - +
365O SER 4.0 0.8 - - - -
366O ILE* 1.3 70.4 - - - +
368O ASP* 1.3 57.9 + - - +
369O ALA* 3.6 21.1 - - + -
382O LEU* 4.1 26.0 - - + -
383O ILE 3.7 15.3 - - - -
384O SER* 3.5 6.0 + - - +
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Residues in contact with ASP 368 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327O TYR* 3.9 3.1 + - - -
349O THR* 4.1 5.4 - - + +
351O ASP 4.4 3.5 - - - +
353O VAL* 3.5 7.7 - - - +
366O ILE 3.4 0.6 + - - -
367O PHE* 1.3 73.2 - - - +
369O ALA* 1.3 65.8 + - - +
370O LYS* 3.5 2.1 + - - +
371O ALA* 3.1 35.8 + - + +
372O GLY* 3.6 8.0 + - - -
383O ILE* 2.8 22.6 + - + +
385O TRP* 2.9 32.9 + - + +
269P ARG* 2.8 33.6 + - - -
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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