Contacts of the helix formed by residues 472 - 482 (chain C) in PDB entry 1BPO
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 PRO 472 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468C LYS* 3.6 28.7 - - + +
470C VAL 4.7 0.4 - - - +
471C ASP* 1.2 100.5 - - - +
473C THR* 1.3 57.3 + - - +
474C LEU 2.5 1.6 + - - -
475C ALA* 2.5 30.3 + - - -
476C LEU* 2.7 11.8 + - - -
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Residues in contact with THR 473 (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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471C ASP* 3.7 10.5 + - - -
472C PRO* 1.3 78.6 - - - +
474C LEU* 1.3 50.4 + - - +
476C LEU* 3.7 26.7 - - + +
477C SER* 2.5 29.8 + - - -
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Residues in contact with LEU 474 (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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445C LYS* 4.9 10.3 - - + +
448C LEU* 3.4 43.7 - - + -
449C GLU* 3.5 39.0 - - + +
452C LEU* 4.1 8.3 - - + -
467C VAL* 3.6 9.2 - - + -
471C ASP* 3.5 18.2 + - + +
472C PRO 2.5 5.7 + - - -
473C THR* 1.3 72.5 - - - +
475C ALA* 1.3 62.5 + - - +
477C SER* 2.7 25.9 + - - +
478C VAL* 3.1 19.4 + - + +
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Residues in contact with ALA 475 (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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464C GLY* 4.0 6.9 - - - +
467C VAL* 3.5 11.3 - - + +
468C LYS* 3.2 57.4 - - + +
471C ASP 3.4 1.0 + - - +
472C PRO 2.5 7.3 + - - +
474C LEU* 1.3 71.0 - - - +
476C LEU* 1.3 54.2 + - - +
478C VAL* 2.9 7.5 + - - +
479C TYR* 2.5 40.8 + - - +
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Residues in contact with LEU 476 (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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468C LYS* 4.3 8.6 - - - +
472C PRO 2.7 14.5 + - - +
473C THR* 3.7 28.3 - - + +
475C ALA* 1.3 71.0 - - - +
477C SER* 1.3 69.7 + - - +
479C TYR* 3.2 7.9 + - - +
480C LEU* 2.7 43.8 + - + +
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Residues in contact with SER 477 (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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452C LEU* 4.9 7.9 - - - -
473C THR 2.5 21.3 + - - -
474C LEU* 2.7 12.8 + - - +
476C LEU* 1.3 86.6 - - - +
478C VAL* 1.3 51.3 + - - +
480C LEU* 3.1 4.3 + - - +
481C ARG* 2.6 54.1 + - - +
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Residues in contact with VAL 478 (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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452C LEU* 3.4 26.9 - - + -
459C CYS* 2.9 52.7 - - + +
460C SER 3.8 0.4 - - - +
463C LEU* 3.6 35.4 - - + -
464C GLY* 4.4 2.5 - - - +
467C VAL* 4.4 6.7 - - + -
474C LEU* 3.2 28.0 - - + +
475C ALA* 2.9 9.8 + - - +
477C SER* 1.3 75.0 - - - +
479C TYR* 1.3 58.3 + - - +
481C ARG* 4.2 0.4 - - - -
482C ALA* 3.1 12.3 + - - +
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Residues in contact with TYR 479 (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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460C SER 4.5 0.4 - - - -
461C GLU* 3.4 37.9 + - + -
464C GLY* 3.4 13.0 - - - -
465C ASP* 2.2 32.1 + - - -
468C LYS* 2.9 40.7 - - + +
475C ALA 2.5 19.0 + - - +
476C LEU* 3.4 7.4 - - - +
478C VAL* 1.3 72.4 - - - +
480C LEU* 1.3 58.3 + - - +
482C ALA* 3.4 4.6 + - - +
483C ASN* 2.9 23.9 + - - -
484C VAL* 3.7 30.5 + - + +
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Residues in contact with LEU 480 (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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476C LEU* 2.7 28.5 + - + +
477C SER* 3.5 5.4 - - - +
479C TYR* 1.3 73.6 - - - +
481C ARG* 1.3 77.1 + - - +
482C ALA 3.0 1.3 - - - -
483C ASN* 3.0 19.2 + - - +
484C VAL* 6.2 0.4 - - - -
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Residues in contact with ARG 481 (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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452C LEU* 3.7 36.5 + - + +
453C LYS* 4.6 6.3 + - - +
455C ASP* 3.2 25.7 + - - +
457C LEU 5.3 3.8 + - - -
459C CYS* 3.6 26.3 + - - +
477C SER* 2.6 44.4 + - - +
478C VAL* 4.2 0.2 - - - -
480C LEU* 1.3 81.3 - - - +
482C ALA* 1.3 59.5 + - - +
483C ASN* 4.9 0.9 - - - +
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Residues in contact with ALA 482 (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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429C LYS* 4.8 10.0 + - - +
459C CYS* 3.8 7.2 - - - -
460C SER* 2.9 46.7 - - - +
461C GLU* 4.3 1.1 - - - +
478C VAL 3.1 13.6 + - - +
479C TYR* 3.6 5.6 - - - +
480C LEU 3.0 0.4 - - - -
481C ARG* 1.3 77.3 - - - +
483C ASN* 1.4 68.9 + - - +
484C VAL* 5.0 1.8 - - + -
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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
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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