Contacts of the helix formed by residues 464 - 478 (chain D) in PDB entry 4BGG
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 ASP 464 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418D MET* 3.7 18.6 - - - +
419D VAL 5.0 0.2 - - - +
420D SER* 3.2 30.6 + - - +
421D ASN* 4.7 1.6 - - - +
460D ARG 5.0 0.4 - - - +
461D TRP 3.0 9.5 + - - +
462D PHE 3.3 0.2 - - - -
463D SER* 1.3 80.5 - - - +
465D PRO* 1.4 60.0 - - - +
466D THR* 2.8 22.4 + - - -
467D LEU* 3.0 16.6 + - + -
468D THR* 2.8 41.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 465 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463D SER 4.1 5.4 - - - +
464D ASP* 1.4 91.6 - - - +
466D THR* 1.3 59.4 + - - +
468D THR* 3.5 8.2 - - + +
469D SER* 3.1 29.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 466 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D THR* 4.5 12.4 - - - +
305D CYS* 5.5 0.2 - - - -
306D LEU* 3.9 39.2 - - + +
418D MET* 4.3 21.8 - - - -
464D ASP* 2.8 9.4 + - - -
465D PRO* 1.3 76.7 - - - +
467D LEU* 1.3 58.8 + - - +
468D THR 3.1 1.3 - - - -
469D SER* 3.0 8.7 + - - -
470D LEU* 2.8 38.1 + - + +
498D ILE* 4.6 12.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 467 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415D ALA* 3.6 40.2 - - + +
418D MET* 4.1 28.9 - - + +
420D SER* 3.9 31.0 - - - +
461D TRP* 3.6 51.1 - - + +
464D ASP* 3.0 14.3 + - + +
466D THR* 1.3 75.1 - - - +
468D THR* 1.3 56.7 + - - +
470D LEU* 3.6 7.5 - - + +
471D ALA* 2.8 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 468 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461D TRP 3.1 10.6 + - - -
462D PHE* 3.2 37.8 + - + +
464D ASP 2.8 23.8 + - - -
465D PRO* 3.5 9.8 - - + +
467D LEU* 1.3 78.3 - - - +
469D SER* 1.3 62.6 + - - +
471D ALA* 3.3 2.4 + - - +
472D LYS* 3.2 45.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 469 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465D PRO 3.1 14.7 + - - -
466D THR* 3.0 10.5 + - - -
468D THR* 1.3 76.9 - - - +
470D LEU* 1.3 62.5 + - - +
472D LYS* 3.4 10.8 + - - +
473D LEU* 3.2 26.0 + - - +
494D THR* 5.7 4.8 - - - +
498D ILE* 3.6 33.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 470 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D CYS* 3.8 29.4 - - - -
306D LEU* 4.5 6.5 - - + -
309D VAL* 4.4 5.6 - - + -
411D LEU* 4.2 23.6 - - + +
415D ALA* 4.4 20.4 - - + -
461D TRP* 5.9 0.2 - - + -
466D THR* 2.8 32.4 + - + +
467D LEU* 3.8 10.5 - - + +
469D SER* 1.3 71.5 - - - +
471D ALA* 1.3 64.7 + - - +
473D LEU* 3.7 8.5 - - + +
474D MET* 2.9 31.1 + - - +
495D LEU* 3.5 31.6 - - + -
498D ILE* 5.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 471 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457D ILE* 4.1 18.1 - - + +
461D TRP* 4.3 5.3 - - + -
462D PHE* 3.8 29.4 - - + -
467D LEU 2.8 20.4 + - - +
468D THR 3.3 5.1 + - - +
470D LEU* 1.3 72.2 - - - +
472D LYS* 1.3 62.9 + - - +
474D MET* 3.3 14.0 + - - +
475D LYS* 3.1 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 472 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462D PHE* 5.5 4.5 - - + -
468D THR* 3.2 33.8 + - + +
469D SER* 3.7 10.5 - - - +
470D LEU 3.3 0.2 - - - -
471D ALA* 1.3 76.9 - - + +
473D LEU* 1.3 63.8 + - + +
475D LYS* 3.4 16.0 + - - +
476D GLU* 3.1 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 473 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411D LEU* 4.2 12.1 - - + -
469D SER* 3.2 15.8 + - - +
470D LEU* 3.7 13.0 - - + +
471D ALA 3.3 0.2 - - - -
472D LYS* 1.3 76.6 - - + +
474D MET* 1.3 67.3 + - - +
476D GLU* 3.0 18.0 + - - +
477D CYS* 3.1 18.9 + - - -
486D LEU* 3.6 25.8 - - + +
491D ILE* 4.2 18.2 - - + -
494D THR* 4.2 31.9 - - + +
495D LEU* 3.6 36.8 - - + -
498D ILE* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 474 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408D GLY* 3.8 16.4 - - - +
411D LEU* 3.9 15.9 - - + +
412D TRP* 3.3 34.8 - - + -
415D ALA* 5.1 2.2 - - - -
457D ILE* 3.8 15.5 - - + -
461D TRP* 3.7 20.4 - - + -
470D LEU* 2.9 23.6 + - - +
471D ALA* 3.5 7.4 - - - +
473D LEU* 1.3 75.8 - - - +
475D LYS* 1.3 58.0 + - - +
477D CYS* 2.9 29.5 + - - +
478D TRP* 3.1 48.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 475 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457D ILE* 3.8 29.4 - - + -
462D PHE* 4.5 19.6 - - - -
471D ALA 3.1 15.2 + - - +
472D LYS* 3.7 17.4 - - - +
474D MET* 1.3 79.1 - - - +
476D GLU* 1.3 59.6 - - + +
478D TRP* 3.1 28.2 + - + +
479D TYR* 3.7 18.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 476 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472D LYS* 3.1 26.1 + - - +
473D LEU* 3.0 8.1 + - - +
475D LYS* 1.3 76.8 - - + +
477D CYS* 1.3 58.9 + - - +
478D TRP 3.4 0.2 - - - -
479D TYR* 3.4 33.9 + - + +
485D ARG* 3.3 10.2 - - - -
486D LEU* 3.2 58.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 477 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404D ILE* 3.5 36.8 - - - +
405D TRP* 3.6 12.0 - - - -
407D PHE* 4.2 4.9 - - - -
408D GLY* 3.9 21.5 - - - -
411D LEU* 4.9 1.3 - - - -
473D LEU* 3.1 18.8 + - - -
474D MET* 2.9 10.5 + - - +
476D GLU* 1.3 78.8 - - - +
478D TRP* 1.3 58.1 + - + +
479D TYR 3.6 1.1 - - - -
485D ARG* 3.1 24.2 + - - -
486D LEU* 5.1 1.3 - - - -
491D ILE* 3.8 21.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 478 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405D TRP* 3.4 28.8 - + - -
408D GLY* 3.6 35.5 - - - -
409D LEU* 3.6 10.4 - - + +
412D TRP* 4.2 3.4 - - + -
454D ARG* 2.6 63.7 + - + -
455D PRO* 3.7 46.7 - - + -
457D ILE* 4.4 10.1 - - + -
474D MET* 3.1 51.6 - - + -
475D LYS* 3.1 15.4 + - + +
477D CYS* 1.3 85.5 - - + +
479D TYR* 1.3 60.8 + - - +
----------------------------------------------------------
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