Contacts of the strand formed by residues 472 - 474 (chain C) in PDB entry 3HB0
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 ILE 472 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C ILE 3.9 6.9 - - - +
332C HIS* 3.9 14.0 - - - -
333C VAL 5.0 0.5 + - - -
391C TYR* 3.5 27.1 - - + +
445C LEU* 3.6 23.3 - - + -
447C THR* 5.2 1.3 - - + -
451C LEU* 4.0 21.5 - - + +
454C ALA* 4.9 11.0 - - + -
455C LEU* 3.4 27.1 - - + -
458C VAL* 4.4 13.7 - - + -
467C PHE* 4.4 11.9 - - + -
468C PRO 4.2 4.5 - - - +
469C ILE* 3.6 15.2 + - - +
470C GLU 3.5 0.8 - - - -
471C ASN* 1.3 83.1 - - - +
473C TYR* 1.3 69.1 + - - +
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Residues in contact with TYR 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C ILE* 3.5 14.4 - - + +
332C HIS* 3.7 20.6 + + - -
444C VAL* 3.9 16.8 - - + -
445C LEU 2.7 16.2 + - - +
446C VAL* 3.3 12.9 - - + +
447C THR* 3.0 28.3 + - - +
471C ASN* 3.5 26.7 - - - -
472C ILE* 1.3 80.1 - - - +
474C SER* 1.3 60.7 + - - +
475C ALA 3.8 0.3 + - - -
483C CYS* 4.4 14.4 - - + -
486C ARG* 3.6 38.7 + - + +
487C ILE* 4.0 19.4 - - + +
490C ARG* 3.2 34.5 + - - +
491C PHE* 5.0 0.6 - + - -
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Residues in contact with SER 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C ASP* 5.7 0.7 - - - +
330C GLN 3.9 8.3 + - - +
331C ILE* 2.9 36.7 + - - +
447C THR* 3.4 7.4 - - - -
449C THR 2.8 18.9 + - - -
450C GLN* 3.6 0.5 - - - -
451C LEU* 3.1 38.0 + - - +
473C TYR* 1.3 71.9 - - - +
475C ALA* 1.3 58.2 + - - +
476C THR* 3.0 15.6 + - - -
477C LYS 5.1 0.7 + - - -
478C THR* 4.5 0.3 + - - -
483C CYS* 4.0 1.4 - - - -
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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
------------------------------------------------------------
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