Contacts of the helix formed by residues 457 - 486 (chain B) in PDB entry 4R0C
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 457 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B LEU* 3.9 10.2 - - - +
450B ARG* 4.1 9.2 - - - -
455B GLU 3.3 4.7 + - - -
456B THR* 1.3 78.9 + - - +
458B ILE* 1.3 68.2 + - - +
459B GLY 3.3 2.7 - - - -
460B THR* 3.1 17.5 + - - -
461B LEU* 3.4 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B PRO* 4.4 15.7 - - + -
442B PHE* 3.6 28.8 - - + -
446B LEU* 4.6 13.0 - - + +
457B GLY* 1.3 69.6 - - - -
459B GLY* 1.3 53.8 - - - +
461B LEU* 3.0 5.7 + - - +
462B ILE* 2.8 50.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 459 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B GLY 3.3 0.8 - - - -
458B ILE* 1.3 79.7 - - - +
460B THR* 1.3 55.8 + - - +
462B ILE* 3.6 13.7 - - - +
463B ALA* 2.8 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 460 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B THR* 3.1 30.2 - - - +
457B GLY* 3.1 17.3 + - - -
458B ILE 3.2 0.8 - - - -
459B GLY* 1.3 77.4 - - - +
461B LEU* 1.3 50.8 + - - +
463B ALA* 3.7 3.6 - - - +
464B LEU* 2.7 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ILE* 5.4 1.3 - - + -
163B PHE* 4.5 5.4 - - + -
434B ILE 4.8 0.3 - - - +
442B PHE* 3.7 30.3 - - + +
445B VAL* 4.0 12.8 - - + +
446B LEU* 3.5 41.5 - - + +
449B ALA* 5.1 11.4 - - + -
456B THR* 4.2 4.4 + - - +
457B GLY 3.4 7.4 + - - +
458B ILE* 3.0 7.7 + - - +
460B THR* 1.3 77.0 - - - +
462B ILE* 1.3 65.1 + - - +
463B ALA 3.2 0.2 - - - -
464B LEU* 4.0 11.2 - - + -
465B MET* 3.1 60.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 462 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B ILE* 4.3 30.1 - - + +
437B PRO* 5.2 9.2 - - + -
442B PHE* 4.2 10.5 - - + -
458B ILE* 2.8 40.9 + - + +
459B GLY* 3.6 11.2 - - - +
461B LEU* 1.3 71.7 - - - +
463B ALA* 1.3 62.0 + - + +
465B MET* 3.4 3.0 + - - +
466B LEU* 2.9 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 463 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B GLY 2.8 19.4 + - - +
460B THR* 3.9 4.0 - - - +
462B ILE* 1.3 79.8 - - + +
464B LEU* 1.3 65.8 + - - +
466B LEU* 3.9 7.6 - - + +
467B PRO* 3.2 22.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 464 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ILE* 3.6 31.2 - - + +
159B ILE* 5.1 2.7 - - + -
160B ALA* 3.8 21.5 - - + +
228B THR* 3.9 18.2 - - + -
232B LEU* 5.9 3.1 - - + -
449B ALA* 6.2 0.7 - - + -
460B THR* 2.7 24.5 + - + +
461B LEU* 3.7 16.6 - - + +
462B ILE 3.4 0.2 - - - -
463B ALA* 1.3 73.7 - - - +
465B MET* 1.3 83.1 + - + +
467B PRO* 4.0 7.7 - - - +
468B TYR* 3.5 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 465 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ILE* 4.5 1.8 - - + +
160B ALA* 3.4 32.1 - - - +
163B PHE* 3.5 46.9 - - + -
164B ALA 4.4 4.0 - - - -
434B ILE* 3.7 28.5 - - + +
435B ILE* 4.6 0.7 - - + -
461B LEU* 3.1 24.9 + - + +
462B ILE 4.0 1.8 - - - +
464B LEU* 1.3 99.5 - - + +
466B LEU* 1.3 54.2 + - - +
467B PRO 3.3 1.3 - - - -
468B TYR* 2.5 48.8 + - - +
469B SER 3.0 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 466 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B ILE* 4.2 25.1 - - + +
462B ILE* 2.9 31.3 + - + +
463B ALA* 3.4 6.7 + - - +
465B MET* 1.3 73.9 - - - +
467B PRO* 1.3 70.8 - - + +
469B SER* 4.2 3.1 - - - -
470B LEU* 3.2 55.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 467 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ILE* 3.9 21.8 - - + -
227B LEU* 4.7 17.3 - - + -
463B ALA 3.2 20.4 - - - +
464B LEU 4.0 8.7 - - - +
466B LEU* 1.3 88.1 - - + +
468B TYR* 1.3 59.3 + - + +
470B LEU* 3.3 2.8 + - + +
471B THR* 2.9 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 468 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ALA* 3.7 24.9 - - + +
161B THR 4.0 0.2 + - - -
164B ALA* 3.8 10.3 - - + -
220B VAL* 3.4 48.5 - - + -
223B ILE* 3.6 19.3 - - + -
224B THR* 2.9 15.9 + - - -
228B THR* 2.3 37.5 + - + +
434B ILE* 3.5 15.7 - - + -
464B LEU 3.5 26.0 - - - -
465B MET* 2.5 25.1 + - - +
467B PRO* 1.3 74.2 - - + +
469B SER* 1.3 63.0 + - - +
471B THR* 4.0 5.3 - - - -
472B LEU* 3.1 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 469 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B SER* 3.1 25.2 + - - +
432B THR* 3.8 5.9 - - - +
434B ILE* 3.5 3.3 - - - +
435B ILE* 3.2 44.3 - - - +
465B MET 3.0 5.0 + - - -
466B LEU* 3.5 8.3 - - - -
468B TYR* 1.3 76.6 - - - +
470B LEU* 1.3 60.9 + - - +
472B LEU* 2.9 8.6 + - - +
473B LEU* 2.6 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 470 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B THR* 6.4 0.2 - - + -
435B ILE* 5.2 3.4 - - + -
466B LEU* 3.2 40.1 + - + +
467B PRO* 4.2 2.5 - - + +
469B SER* 1.3 83.0 - - - +
471B THR* 1.3 65.8 + - - +
472B LEU 3.0 1.6 - - - -
473B LEU* 4.0 21.3 - - + +
474B LEU* 3.1 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 471 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU* 3.5 45.5 - - + +
223B ILE* 3.6 26.0 - - + +
467B PRO* 2.9 20.7 + - - +
468B TYR 4.0 3.8 - - - -
470B LEU* 1.3 76.7 - - - +
472B LEU* 1.3 58.2 + - + +
474B LEU* 5.3 1.1 - - - -
475B GLY* 3.0 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 472 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ALA* 4.7 5.2 - - + +
168B GLY* 3.9 30.3 - - - +
169B GLY 4.8 0.2 - - - +
215B LEU* 6.0 0.9 - - + -
216B VAL* 4.1 34.8 - - + -
219B LEU* 4.8 12.8 - - + -
220B VAL* 4.5 18.4 - - + -
431B SER* 3.5 18.8 + - - +
434B ILE* 4.7 4.7 - - + -
468B TYR 3.1 24.5 + - - +
469B SER 2.9 11.4 + - - +
471B THR* 1.3 78.6 - - + +
473B LEU* 1.3 66.7 + - - +
476B TRP* 2.8 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 473 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B VAL* 4.1 24.7 - - + +
384B VAL* 5.5 10.1 - - + +
387B ALA* 4.2 21.3 - - + -
427B VAL* 4.6 1.5 - - + +
428B GLY* 5.1 0.2 - - - -
431B SER* 3.7 18.3 + - - +
432B THR* 4.5 11.4 - - + -
469B SER 2.6 17.4 + - - +
470B LEU* 3.3 22.4 + - + +
472B LEU* 1.3 77.1 - - - +
474B LEU* 1.3 57.6 + - - +
476B TRP* 4.0 0.5 - - - +
477B SER* 2.3 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 474 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B LEU* 3.1 12.5 + - + +
471B THR* 4.9 1.1 - - - +
473B LEU* 1.3 78.3 - - - +
475B GLY* 1.3 66.2 + - - +
477B SER* 3.0 10.0 + - - -
478B VAL* 2.9 43.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 475 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 3.7 16.7 - - - +
219B LEU* 4.1 8.3 - - - -
471B THR 3.0 21.3 + - - -
474B LEU* 1.3 80.8 - - - +
476B TRP* 1.3 59.7 + - - +
478B VAL* 3.7 7.1 + - - +
479B LEU* 3.3 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 476 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B GLY 3.2 24.0 - - - -
169B GLY* 4.4 10.1 - - - -
171B SER* 4.3 12.1 - - - -
172B ALA* 4.4 11.2 - - + -
208B PHE* 3.7 13.2 - + - -
209B ILE* 6.3 0.7 - - + -
212B SER* 2.9 37.8 + - - -
215B LEU* 3.9 17.4 - - + +
216B VAL* 4.5 12.3 - - + -
426B ARG* 4.7 1.3 - - + -
427B VAL* 3.4 36.8 - - + +
430B SER* 3.5 25.8 - - - -
431B SER* 3.2 21.5 - - - -
471B THR 4.2 0.2 + - - -
472B LEU* 2.8 38.4 + - + +
475B GLY* 1.3 68.8 - - - -
477B SER* 1.3 65.2 + - - +
479B LEU* 3.1 6.5 + - + +
480B LEU* 3.0 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 477 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B LEU* 3.8 25.4 - - - +
383B VAL* 3.9 20.0 - - - +
427B VAL* 4.4 4.4 - - - +
473B LEU* 2.3 30.4 + - - +
474B LEU* 3.3 8.2 - - - -
476B TRP* 1.3 76.1 - - - +
478B VAL* 1.3 53.3 + - - +
480B LEU* 3.0 11.9 + - - +
481B GLY* 2.7 33.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 478 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B LEU* 2.9 41.0 + - + +
475B GLY* 3.8 7.9 - - - +
477B SER* 1.3 77.0 - - - +
479B LEU* 1.3 63.5 + - - +
480B LEU 3.0 0.2 + - - -
481B GLY* 4.4 1.8 - - - +
482B VAL* 2.9 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 479 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B PHE* 3.5 26.2 - - + +
211B ALA* 4.9 7.2 - - + -
212B SER* 4.4 11.0 - - - +
215B LEU* 3.9 24.0 - - + -
475B GLY 3.3 11.5 + - - +
476B TRP* 3.1 10.4 + - + +
478B VAL* 1.3 79.0 - - - +
480B LEU* 1.3 55.6 + - - +
482B VAL* 4.1 7.2 - - + -
483B TRP* 3.2 48.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 480 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B PHE* 4.0 23.8 - - + -
379B LEU* 5.2 7.9 - - + -
380B LEU* 5.3 3.6 - - + -
383B VAL* 4.1 13.0 - - + -
420B ALA 4.9 1.8 - - - +
423B ALA* 4.0 22.0 - - + +
424B ALA* 3.5 36.1 - - + +
427B VAL* 4.7 5.8 - - + -
476B TRP 3.0 11.2 + - - +
477B SER* 3.0 10.2 + - - +
479B LEU* 1.3 77.3 - - - +
481B GLY* 1.3 56.5 + - - +
482B VAL 3.3 0.2 - - - -
483B TRP* 2.8 7.3 + - + +
484B ILE* 2.7 53.8 + - + +
490B LEU* 5.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 481 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B VAL* 3.8 28.1 - - - +
380B LEU* 4.7 6.4 - - - +
477B SER 2.7 17.3 + - - -
478B VAL* 3.7 2.5 - - - -
480B LEU* 1.3 73.1 - - - +
482B VAL* 1.3 57.4 + - - +
484B ILE* 4.8 0.4 - - - -
485B GLY* 2.8 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 482 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B VAL* 2.9 34.2 + - + +
479B LEU* 4.2 9.2 - - + +
481B GLY* 1.3 75.3 - - - +
483B TRP* 1.3 62.0 + - - +
485B GLY* 4.6 0.9 - - - +
486B PHE* 3.1 51.0 + - + +
488B TRP* 5.5 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 483 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B TRP* 3.7 34.1 - + + -
208B PHE* 3.8 12.3 - + - -
211B ALA* 3.7 23.6 - - + -
479B LEU* 3.2 49.0 + - + +
480B LEU* 2.8 12.8 + - + +
482B VAL* 1.3 77.0 - - - +
484B ILE* 1.3 64.1 + - + +
486B PHE* 3.9 0.5 - - - +
487B GLY 3.2 14.6 + - - -
488B TRP* 2.9 51.8 + + + +
489B PRO 2.9 28.5 + - - -
490B LEU* 3.3 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 484 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B LYS* 5.3 8.3 - - + -
376B VAL* 3.5 25.4 - - + +
379B LEU* 3.5 24.5 - - + -
420B ALA* 3.7 28.9 - - + -
480B LEU* 2.7 32.5 + - + +
481B GLY* 5.3 0.2 - - - -
483B TRP* 1.3 72.1 - - + +
485B GLY* 1.3 59.1 + - - +
487B GLY* 2.7 26.5 + - - -
488B TRP 5.7 1.3 - - - +
490B LEU* 4.4 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 485 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B VAL* 3.9 8.9 - - - +
481B GLY 2.8 18.3 + - - -
482B VAL* 4.2 1.3 - - - -
484B ILE* 1.3 79.6 - - - +
486B PHE* 1.3 60.3 + - - +
487B GLY 3.3 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 486 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B VAL* 3.1 51.1 + - + +
483B TRP 4.6 0.7 - - - +
485B GLY* 1.3 75.6 - - - +
487B GLY* 1.3 63.9 + - - +
488B TRP* 3.3 35.4 + + + +
----------------------------------------------------------
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