Contacts of the helix formed by residues 454 - 462 (chain C) in PDB entry 3CB4
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 PHE 454 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C CYS* 5.2 1.1 - - - -
408C MET* 4.9 1.3 - - - -
421C LEU* 3.7 31.0 - - + -
422C CYS* 4.6 8.3 - - - -
425C LYS* 4.1 17.7 - - + +
445C ILE* 3.8 30.7 - - + -
449C GLU 3.5 20.4 - - - +
450C VAL* 3.5 31.5 + - + +
452C LEU 2.9 2.7 + - - +
453C ASP* 1.3 72.0 - - - +
455C PHE* 1.3 69.6 + - - +
456C ASP 3.0 2.5 - - - -
457C ARG* 3.0 16.3 + - - +
458C LEU* 3.0 38.9 + - + +
468C LEU* 3.6 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 455 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C HIS* 6.1 7.0 - + - -
345C LEU* 4.7 17.7 - - + -
346C LEU* 6.6 0.2 - - + -
450C VAL* 4.3 4.1 + - + +
453C ASP* 4.6 1.1 + - - +
454C PHE* 1.3 86.8 - - + +
456C ASP* 1.3 69.7 + - - +
458C LEU* 4.1 4.9 - - + +
459C LYS* 3.3 44.4 + - + +
466C ALA 5.3 5.8 - - - -
467C SER* 5.9 0.4 - - - -
468C LEU* 3.7 43.5 - - + -
470C TYR* 6.4 3.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 456 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453C ASP* 2.9 40.5 + - + +
454C PHE 3.0 0.2 - - - -
455C PHE* 1.3 88.4 - - - +
457C ARG* 1.3 61.1 + - + +
459C LYS* 3.0 12.6 + - - +
460C SER* 2.9 29.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 457 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C LEU* 3.5 23.9 - - + +
424C GLU* 2.6 33.5 + - - -
425C LYS* 3.6 19.7 - - - +
453C ASP 3.9 17.0 - - - +
454C PHE* 3.0 12.3 + - - +
456C ASP* 1.3 80.4 - - + +
458C LEU* 1.3 55.4 + - - +
460C SER* 3.3 10.2 + - - +
461C THR* 3.0 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 458 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C MET* 3.5 31.6 - - + -
418C VAL* 4.0 21.8 - - + +
421C LEU* 3.5 14.9 - - + +
422C CYS* 5.1 1.6 - - - -
454C PHE* 3.0 35.2 + - + +
455C PHE* 4.2 7.4 - - + +
457C ARG* 1.3 74.3 - - - +
459C LYS* 1.3 58.6 + - + +
461C THR* 3.3 10.0 - - - +
462C SER* 2.7 27.0 + - - -
466C ALA* 3.5 37.7 - - + +
467C SER 5.2 0.9 - - - +
468C LEU* 4.3 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 459 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455C PHE* 3.3 37.3 + - + +
456C ASP* 3.0 14.0 + - - +
458C LEU* 1.3 83.3 - - + +
460C SER* 1.3 56.6 + - - +
462C SER* 3.4 3.6 + - - -
463C ARG* 2.8 9.4 + - - -
464C GLY* 2.7 50.3 + - - +
466C ALA 5.3 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 460 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456C ASP 2.9 17.0 + - - -
457C ARG* 3.3 16.1 + - - +
459C LYS* 1.3 75.0 - - - +
461C THR* 1.3 59.1 + - - +
462C SER 3.3 0.4 + - - -
463C ARG* 3.9 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 461 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C TYR* 3.7 5.8 - - - -
417C ASN* 3.2 46.8 + - - +
418C VAL* 4.0 21.3 - - + -
421C LEU* 4.0 12.2 - - + +
457C ARG 3.0 16.9 + - - +
458C LEU* 3.3 21.8 - - - +
460C SER* 1.3 77.0 - - - +
462C SER* 1.3 56.8 + - - +
463C ARG* 6.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 462 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C LEU* 6.1 0.2 - - - -
414C TYR* 3.6 34.1 - - - -
418C VAL* 4.5 2.0 - - - -
458C LEU 2.7 21.7 + - - -
459C LYS* 3.5 4.2 + - - -
461C THR* 1.3 81.6 - - - +
463C ARG* 1.3 66.5 + - - +
464C GLY 3.2 0.9 + - - -
465C TYR* 3.2 23.1 + - - +
466C ALA* 3.4 33.4 + - - +
----------------------------------------------------------
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