Contacts of the helix formed by residues 447 - 457 (chain C) in PDB entry 5JHQ
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 ARG 447 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C CYS 3.5 17.5 - - - +
411C SER 3.0 23.0 + - - +
412C TYR* 3.6 29.3 + - - +
413C GLY* 3.7 10.0 - - - -
442C ALA* 3.0 20.5 + - + +
445C LYS* 3.3 26.6 + - - +
446C ASN* 1.3 71.0 + - - +
448C VAL* 1.3 64.6 + - - +
449C GLU 3.2 3.0 + - - -
450C VAL* 3.3 20.6 + - + -
451C CYS* 3.0 26.3 + - - -
480C LEU* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 448 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C ASN* 3.2 31.6 + - - +
447C ARG* 1.3 71.5 - - - +
449C GLU* 1.3 63.0 + - - +
451C CYS* 3.6 3.1 + - - +
452C SER* 3.1 26.2 + - - -
477C THR* 6.2 0.4 - - - -
480C LEU* 4.1 17.9 - - + +
483C ARG* 3.4 40.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
415C TYR* 3.4 33.4 - - + -
447C ARG 3.2 0.2 - - - -
448C VAL* 1.3 84.0 - - - +
450C VAL* 1.3 61.1 + - + +
452C SER* 3.5 18.6 + - - -
453C LEU 3.1 19.4 + - - -
483C ARG* 3.7 17.8 + - - -
519C PRO* 6.0 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 450 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C CYS* 3.8 37.0 - - + -
413C GLY* 3.9 33.2 - - - +
414C HIS 4.2 2.9 - - - +
415C TYR* 4.3 19.1 - - + +
418C THR* 4.0 12.3 - - + -
442C ALA* 4.3 2.5 - - + -
447C ARG* 3.3 14.4 + - + -
449C GLU* 1.3 74.9 - - + +
451C CYS* 1.3 55.6 + - - +
453C LEU* 3.3 5.8 + - - +
454C LEU* 2.8 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 451 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C LEU* 3.7 25.1 - - + -
442C ALA* 3.7 3.6 - - - -
443C ALA* 3.7 36.6 - - - -
447C ARG 3.0 26.7 + - - +
448C VAL 3.6 4.9 - - - +
450C VAL* 1.3 72.7 - - - +
452C SER* 1.3 66.2 + - - +
454C LEU* 3.2 3.3 + - - +
455C LEU* 2.9 31.4 + - - +
480C LEU* 4.3 10.5 - - + -
483C ARG* 5.9 0.9 - - - -
484C LEU* 3.8 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 452 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C VAL 3.1 15.6 + - - -
449C GLU* 3.5 16.6 + - - -
451C CYS* 1.3 79.4 - - - +
453C LEU* 1.3 61.5 + - - -
455C LEU* 3.6 2.7 + - - +
456C SER* 3.4 19.8 + - - -
483C ARG* 3.7 14.2 + - - +
487C GLU* 3.1 41.2 + - - +
519C PRO* 3.9 16.3 - - - +
520C GLN* 5.2 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 453 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415C TYR* 3.6 28.9 - - + +
418C THR* 3.8 27.8 - - + -
419C GLU* 3.9 31.4 - - + +
422C LEU* 4.1 7.9 - - + -
449C GLU 3.1 11.7 + - - +
450C VAL* 3.5 7.6 - - - +
451C CYS 3.2 0.2 - - - -
452C SER* 1.3 76.4 - - - +
454C LEU* 1.3 64.0 + - - +
456C SER* 2.5 22.5 + - - -
457C HIS* 3.3 29.8 + - + +
520C GLN* 3.8 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 454 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C LEU* 4.5 5.2 - - + -
410C CYS* 3.8 30.7 - - - -
418C THR* 4.5 10.1 - - + -
422C LEU* 4.5 6.7 - - + -
428C VAL* 3.4 24.9 - - + +
438C PRO* 4.0 9.6 - - + +
439C LEU* 3.9 33.0 - - + +
442C ALA* 4.2 5.8 - - + -
450C VAL* 2.8 30.4 + - + +
451C CYS* 3.7 3.4 - - - +
453C LEU* 1.3 73.2 - - - +
455C LEU* 1.3 63.8 + - - +
457C HIS* 3.0 15.3 + - - +
458C GLY 3.3 0.5 + - - -
459C ALA* 3.0 27.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 455 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C LEU* 3.8 20.9 - - + -
451C CYS 2.9 23.4 + - - +
452C SER* 3.8 5.2 - - - +
454C LEU* 1.3 74.7 - - - +
456C SER* 1.3 56.8 + - - +
458C GLY* 3.1 17.2 + - - -
459C ALA* 3.6 25.1 + - - +
461C PRO* 3.9 17.7 - - + -
483C ARG* 4.5 1.3 - - - +
484C LEU* 3.7 28.0 - - + +
487C GLU* 3.7 30.1 - - + +
488C PHE* 4.2 11.4 - - + -
491C HIS* 3.5 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 456 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452C SER 3.4 6.9 + - - -
453C LEU* 2.5 26.0 + - - -
455C LEU* 1.3 80.5 - - - +
457C HIS* 1.3 60.1 + - - -
458C GLY 3.2 2.4 + - - -
491C HIS* 3.3 27.3 + - - +
498C ARG* 5.5 4.3 + - - -
518C GLN* 3.3 31.0 + - - -
519C PRO* 4.6 1.8 - - - -
520C GLN* 3.2 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 457 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C GLU* 5.2 8.2 + - + +
422C LEU* 3.7 41.0 + - + +
423C LYS* 5.1 2.0 - - - -
428C VAL* 3.5 25.4 - - + +
453C LEU* 3.3 33.1 + - + +
454C LEU 3.0 10.9 + - - +
456C SER* 1.3 81.4 - - - +
458C GLY* 1.3 56.8 + - - +
459C ALA 3.6 0.2 - - - -
518C GLN* 5.7 1.3 - - - -
520C GLN* 5.2 3.3 + - - +
----------------------------------------------------------
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