Contacts of the helix formed by residues 432 - 447 (chain C) in PDB entry 2BT4
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 THR 432 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C LEU* 3.3 18.4 - - - +
421C GLY* 4.8 4.3 - - - +
422C GLN* 6.1 2.5 - - + -
430C SER 4.5 5.4 - - - +
431C ASP* 1.3 76.4 - - - +
433C LEU* 1.3 66.5 + - - +
434C ALA* 3.4 11.5 + - - +
435C ASP* 2.8 32.1 + - - +
436C VAL* 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 433 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C ASN* 4.2 11.0 - - + +
417C LEU* 3.6 33.2 - - + +
418C ASN* 4.3 10.9 + - - +
420C LEU* 3.9 23.1 + - + +
432C THR* 1.3 74.7 - - - +
434C ALA* 1.3 58.2 + - - +
436C VAL* 3.1 7.3 + - + +
437C GLU* 2.8 27.9 + - - +
453C PHE* 3.8 28.1 - - + -
455C GLN* 3.7 37.7 - - + -
538C TYR* 4.7 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 434 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C THR* 3.1 10.9 + - - +
433C LEU* 1.3 78.9 - - - +
435C ASP* 1.3 62.7 + - - +
437C GLU* 3.3 13.5 + - - +
438C ALA* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 435 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C SER 4.4 1.4 - - - +
431C ASP* 3.4 27.1 - - + +
432C THR* 2.8 38.5 + - - +
434C ALA* 1.3 82.9 - - - +
436C VAL* 1.3 61.3 + - - +
438C ALA* 3.3 7.7 + - - +
439C LEU* 3.0 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 436 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C LEU* 3.6 16.4 - - + -
431C ASP* 4.8 2.9 - - + -
432C THR 3.0 18.0 + - - +
433C LEU* 3.1 10.3 + - + +
435C ASP* 1.3 73.4 - - - +
437C GLU* 1.3 65.2 + - - +
439C LEU* 3.1 11.5 + - + +
440C CYS* 3.0 21.3 + - - -
453C PHE* 3.9 12.8 - - + -
535C VAL* 3.5 32.5 - - + +
538C TYR* 3.7 42.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 437 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433C LEU 2.8 13.7 + - - +
434C ALA* 3.5 13.8 - - - +
436C VAL* 1.3 77.0 - - - +
438C ALA* 1.3 57.9 + - - +
440C CYS* 3.0 3.6 + - - +
441C VAL* 2.8 40.9 + - + +
451C VAL* 5.7 0.5 - - - +
453C PHE* 3.6 50.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 438 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C ALA 3.1 10.2 + - - +
435C ASP* 3.6 10.5 - - - +
437C GLU* 1.3 78.7 - - - +
439C LEU* 1.3 63.9 + - - +
441C VAL* 3.2 9.1 + - - +
442C LYS* 3.0 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 439 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C ASP* 5.3 3.8 - - - +
435C ASP 3.0 17.6 + - - +
436C VAL* 3.1 13.4 + - + +
438C ALA* 1.3 77.2 - - - +
440C CYS* 1.3 58.9 + - - +
442C LYS* 3.5 16.1 + - + +
443C ALA* 3.0 29.6 + - - +
535C VAL* 3.7 42.4 - - + +
536C GLN* 4.9 1.6 - - - +
538C TYR* 6.0 0.7 - - + -
539C VAL* 4.2 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 440 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C ILE* 4.2 15.0 - - + -
436C VAL 3.0 16.4 + - - +
437C GLU 3.0 8.3 + - - +
439C LEU* 1.3 75.4 - - - +
441C VAL* 1.3 65.8 + - - +
443C ALA* 4.1 5.3 - - - +
444C ALA* 2.9 28.1 + - - +
451C VAL* 3.6 19.7 - - + +
453C PHE* 4.2 14.8 - - + -
538C TYR* 3.8 37.9 - - - -
539C VAL* 5.6 0.7 - - - -
542C VAL* 4.6 8.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 441 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C GLU* 2.8 30.3 + - + +
438C ALA* 3.2 10.7 + - - +
440C CYS* 1.3 76.3 - - - +
442C LYS* 1.3 64.3 + - - +
444C ALA* 4.0 1.4 - - - +
445C ALA* 3.0 26.1 + - + +
449C GLY 5.0 0.5 - - - +
450C THR* 5.8 1.1 - - - +
451C VAL* 3.7 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 442 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C ALA 3.0 16.6 + - - +
439C LEU* 3.6 16.8 - - + +
441C VAL* 1.3 79.5 - - - +
443C ALA* 1.3 62.9 + - - +
445C ALA* 3.2 6.9 + - - +
446C ALA* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 443 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C LEU 3.0 18.2 + - - +
440C CYS* 3.4 2.9 + - - +
442C LYS* 1.3 78.0 - - - +
444C ALA* 1.3 61.8 + - - +
446C ALA* 3.3 8.4 + - - +
447C HIS* 3.1 28.2 - - + -
539C VAL* 4.2 27.1 - - + +
542C VAL* 3.8 20.6 - - + -
543C GLU* 5.5 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 444 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C LEU* 5.2 0.9 - - - -
409C ILE* 4.4 5.4 - - + -
440C CYS 2.9 17.3 + - - +
441C VAL 4.0 2.0 - - - +
443C ALA* 1.3 76.4 - - - +
445C ALA* 1.3 61.8 + - - +
447C HIS* 3.0 13.6 + - - +
448C GLY 3.1 0.3 + - - -
449C GLY* 2.8 39.3 + - - +
450C THR* 4.0 3.4 - - - +
451C VAL* 3.5 23.3 - - + -
542C VAL* 3.5 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 445 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C VAL* 3.0 21.9 + - + +
442C LYS* 3.2 7.8 + - - +
444C ALA* 1.3 76.9 - - - +
446C ALA* 1.3 61.6 + - - +
448C GLY* 3.1 13.1 + - - +
449C GLY 3.4 12.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 446 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C LYS* 3.0 22.5 + - - +
443C ALA* 3.6 9.4 - - - +
444C ALA 3.2 0.4 - - - -
445C ALA* 1.3 76.3 - - - +
447C HIS* 1.3 67.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 447 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C LEU* 4.0 13.1 - - + +
443C ALA* 3.1 25.3 - - + +
444C ALA* 3.0 7.9 + - - +
446C ALA* 1.3 86.7 + - + +
448C GLY* 1.3 60.7 + - - +
449C GLY 3.3 2.4 + - - -
542C VAL* 5.2 1.8 - - + -
543C GLU* 3.9 33.6 + - + +
546C ALA* 3.9 27.9 - - + +
----------------------------------------------------------
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