Contacts of the helix formed by residues 444 - 458 (chain F) in PDB entry 4R8A
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 GLY 444 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443F ASP* 1.3 76.7 - - - +
445F SER* 1.3 62.9 + - - +
446F TYR* 3.1 8.4 + - - -
447F ARG* 3.5 20.6 + - - +
448F ASP* 4.4 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 445 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440F ARG* 3.2 50.5 + - - +
443F ASP* 3.1 19.7 + - - -
444F GLY* 1.3 75.5 - - - +
446F TYR* 1.3 50.2 + - - +
447F ARG 3.3 0.2 - - - -
448F ASP* 3.2 8.6 + - - +
449F ALA* 2.7 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 446 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397F LEU* 4.4 10.5 - - + -
440F ARG* 3.0 24.9 + - - +
441F LEU* 3.5 26.5 - - + -
443F ASP 3.8 15.3 - - - -
444F GLY* 3.1 5.7 + - - -
445F SER* 1.3 76.9 + - - +
447F ARG* 1.3 116.9 + - + +
449F ALA* 3.7 7.0 - - - +
450F ILE* 3.1 33.9 + - + +
479F LEU* 3.9 17.4 + - + -
482F LEU 4.0 10.3 + - - -
484F ALA* 3.8 24.8 + - + +
487F LEU* 3.7 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 447 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444F GLY* 4.1 10.1 - - - +
445F SER 3.3 1.0 - - - -
446F TYR* 1.3 135.9 + - + +
448F ASP* 1.3 62.9 - - - +
450F ILE 3.8 0.2 + - - -
451F ARG* 3.4 38.5 + - - +
479F LEU* 3.5 41.7 + - + +
480F ASP* 3.7 14.6 + - - +
482F LEU 5.5 0.6 + - - -
484F ALA* 5.6 0.8 - - - +
516F ARG* 3.5 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 448 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444F GLY 4.4 1.3 + - - +
445F SER* 3.2 9.4 + - - +
447F ARG* 1.3 78.1 - - - +
449F ALA* 1.3 65.2 + - - +
450F ILE 3.3 0.4 - - - -
451F ARG* 3.3 20.7 + - - +
452F CYS* 3.2 36.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 449 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397F LEU* 4.4 10.1 - - + -
440F ARG* 3.4 33.3 - - - +
445F SER 2.7 22.4 + - - +
446F TYR* 3.7 7.2 - - - +
448F ASP* 1.3 73.5 - - - +
450F ILE* 1.3 61.9 + - - +
452F CYS* 3.4 5.5 + - - +
453F ARG* 3.2 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 450 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393F LEU* 3.9 15.0 - - + +
396F LEU* 3.6 26.9 - - + +
397F LEU* 3.4 48.0 - - + +
446F TYR* 3.1 21.9 + - + +
447F ARG 4.0 5.4 - - - +
449F ALA* 1.3 74.8 - - - +
451F ARG* 1.3 65.3 + - - +
452F CYS 3.1 0.2 + - - -
453F ARG* 3.1 6.3 + - - +
454F TYR* 2.9 21.8 + - - +
475F LEU* 3.8 22.9 - - + -
479F LEU* 4.4 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 451 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447F ARG* 3.4 38.8 + - - +
448F ASP* 3.3 24.7 + - - +
450F ILE* 1.3 79.4 - - - +
452F CYS* 1.3 60.6 + - - +
454F TYR* 3.8 6.3 - - - +
455F ARG* 3.5 41.9 + - - +
475F LEU* 4.9 5.2 - - + -
476F GLU* 3.4 42.0 + - - +
479F LEU* 3.9 19.0 - - + +
480F ASP* 4.2 15.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 452 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448F ASP* 3.2 29.9 + - - -
449F ALA* 3.7 9.4 - - - +
450F ILE 3.1 0.8 - - - -
451F ARG* 1.3 78.3 - - - +
453F ARG* 1.3 69.7 + - - +
454F TYR 3.2 0.2 - - - -
455F ARG* 3.3 5.1 + - - +
456F ASP* 2.9 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 453 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396F LEU* 3.2 43.8 + - + +
397F LEU 5.5 0.4 + - - -
399F TRP* 4.0 14.5 - - - +
400F GLU* 2.6 42.6 + - - -
440F ARG* 5.5 5.7 - - - +
449F ALA* 3.2 30.0 + - - +
450F ILE 3.1 6.5 + - - +
452F CYS* 1.3 84.2 - - - +
454F TYR* 1.3 58.7 + - - +
456F ASP* 4.5 7.8 + - - -
457F LYS* 2.6 51.5 + - + +
458F PHE 4.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 454 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396F LEU* 4.1 6.0 - - + +
450F ILE 2.9 16.2 + - - +
451F ARG 3.8 5.6 - - - +
453F ARG* 1.3 78.5 - - - +
455F ARG* 1.3 74.3 + - + +
458F PHE* 3.1 57.1 + + - +
467F TRP* 3.9 19.5 - + - -
470F LEU* 2.8 46.8 + - + -
471F GLY* 3.8 1.4 - - - -
472F GLU* 3.7 32.8 + - + +
475F LEU* 3.7 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 455 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451F ARG* 3.5 34.5 + - - +
452F CYS* 3.3 6.3 + - - +
453F ARG 3.2 0.4 - - - -
454F TYR* 1.3 94.7 - - + +
456F ASP* 1.3 72.0 + - - +
458F PHE* 4.2 8.1 + - - +
472F GLU* 3.3 24.0 + - - +
475F LEU* 5.3 1.0 - - - +
476F GLU* 4.5 14.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 456 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F ARG* 5.4 4.9 + - - -
452F CYS* 2.9 30.0 + - - +
453F ARG* 3.9 6.7 + - - +
455F ARG* 1.3 84.4 - - - +
457F LYS* 1.3 74.6 + - + +
458F PHE 3.3 3.0 + - - +
460F LEU* 5.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 457 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201F GLU* 2.5 40.3 + - - +
399F TRP* 3.3 45.6 - - + +
453F ARG* 2.6 33.8 + - + +
456F ASP* 1.3 82.8 - - + +
458F PHE* 1.3 64.0 + - - +
460F LEU* 3.1 26.4 + - + +
467F TRP* 3.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 458 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F ARG* 3.0 21.1 + - - -
454F TYR* 3.1 55.0 + + - +
455F ARG* 4.2 7.9 - - - +
456F ASP 3.3 4.6 - - - +
457F LYS* 1.3 77.0 - - - +
459F GLY* 1.3 65.0 + - - +
460F LEU 3.4 0.2 + - - -
467F TRP* 3.4 45.5 - + + -
----------------------------------------------------------
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