Contacts of the helix formed by residues 445 - 453 (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 LYS 445 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C LEU* 5.0 0.4 - - - -
443C GLY 4.0 2.2 + - - -
444C ARG* 1.3 72.7 - - - +
446C GLN* 1.3 70.7 + - + +
447C LEU 3.1 2.9 + - - -
448C LEU* 3.4 18.2 - - + -
449C GLU* 2.8 59.4 + - - +
470C VAL* 4.9 14.8 - - + +
471C ASP* 3.8 35.8 + - - +
474C LEU* 4.9 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 446 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C ARG* 3.5 10.6 - - + +
445C LYS* 1.3 85.0 - - + +
447C LEU* 1.3 81.2 + - - +
449C GLU* 3.9 10.3 - - - +
450C LYS* 3.6 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 447 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C VAL* 4.6 9.4 - - + -
444C ARG* 4.7 4.6 + - + +
445C LYS 3.2 0.6 - - - +
446C GLN* 1.3 103.5 - - + +
448C LEU* 1.3 70.9 + - - +
449C GLU 3.1 0.9 - - - -
450C LYS* 3.0 20.0 + - + +
451C TRP* 3.0 55.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 448 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C CYS* 4.9 8.7 - - - -
439C VAL* 4.5 1.7 - - + +
440C LEU* 4.2 12.8 - - + -
444C ARG 3.9 11.8 + - - +
445C LYS* 3.2 33.8 + - + +
447C LEU* 1.3 78.0 - - - +
449C GLU* 1.3 68.0 + - + +
451C TRP* 3.3 23.6 + - + +
452C LEU* 2.9 48.0 + - + +
463C LEU* 5.8 0.4 - - + -
467C VAL* 3.5 28.0 - - + -
470C VAL* 6.4 0.7 - - + -
474C LEU* 3.4 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 449 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C LYS* 2.8 64.4 + - + +
446C GLN* 3.9 8.5 - - - +
448C LEU* 1.3 77.6 - - + +
450C LYS* 1.3 65.4 + - - +
452C LEU* 2.7 20.4 + - - +
453C LYS* 2.7 25.5 + - + +
474C LEU* 3.5 29.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 450 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C GLN 3.6 11.4 + - - +
447C LEU* 3.0 19.1 + - + +
449C GLU* 1.3 79.5 - - - +
451C TRP* 1.3 62.9 + - + +
453C LYS* 3.0 17.3 + - + +
454C GLU* 2.6 62.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 451 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C LEU* 3.5 34.3 - - + +
435C LEU* 3.6 23.6 - - + -
436C CYS* 4.3 13.5 - - - -
439C VAL* 3.2 41.5 - - + -
447C LEU* 3.0 40.0 + - + +
448C LEU* 3.5 28.3 - - + +
450C LYS* 1.3 84.1 - - + +
452C LEU* 1.3 61.7 + - - +
454C GLU* 3.1 19.7 + - - -
456C LYS* 3.0 35.7 + - + +
457C LEU* 3.9 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 452 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C LEU* 2.9 52.8 + - + +
449C GLU* 2.7 17.8 + - - +
451C TRP* 1.3 67.6 - - - +
453C LYS* 1.3 61.4 + - - +
454C GLU 2.8 4.5 - - - -
455C ASP* 2.7 17.9 + - - +
457C LEU* 3.5 27.6 - - + +
459C CYS* 4.5 9.2 - - - -
463C LEU* 5.6 0.4 - - + -
474C LEU* 4.1 9.0 - - + -
477C SER* 4.9 5.6 - - - -
478C VAL* 3.4 35.0 - - + +
481C ARG* 3.7 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 453 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C GLU* 2.7 21.2 + - + +
450C LYS* 3.4 19.1 - - + +
452C LEU* 1.3 72.3 - - - +
454C GLU* 1.3 61.1 + - + +
455C ASP* 3.7 4.7 + - - +
481C ARG* 4.6 8.7 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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