Contacts of the helix formed by residues 459 - 473 (chain D) in PDB entry 5DO7
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 ILE 459 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424D ALA* 4.6 2.2 - - + -
427D MET* 4.0 16.2 - - - -
455D ILE 4.2 7.4 - - - +
456D GLY* 3.7 8.0 + - - +
458D LEU* 1.3 75.2 - - - +
460D PRO* 1.3 83.1 - - + +
462D ASN* 2.8 5.7 + - - -
463D VAL* 2.8 24.4 + - + -
507D TYR* 3.4 40.4 - - + +
511D TYR* 3.3 46.4 + - + -
539D VAL* 3.4 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 460 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456D GLY 3.1 20.4 - - - +
457D ALA* 4.2 0.7 - - - -
458D LEU 3.3 0.9 - - - -
459D ILE* 1.3 93.9 - - + +
461D PHE* 1.3 53.9 + - - +
462D ASN 2.7 12.5 + - - -
463D VAL* 2.8 13.4 + - + -
464D ILE* 2.8 33.1 + - + +
538D VAL* 6.3 0.9 - - + -
539D VAL* 5.6 1.3 - - + -
542D CYS* 4.2 18.2 - - + -
567D TYR* 3.2 36.6 - - + -
595D PHE* 4.5 1.3 - - + -
596D LEU* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 461 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C TYR* 3.9 24.0 - + - -
532C SER* 5.0 3.8 - - - -
535C ALA* 3.6 32.8 - - + -
536C LEU* 5.1 11.3 - - + +
539C ILE* 4.9 17.3 - - + -
427D MET* 5.4 2.3 - - - +
458D LEU 2.8 17.1 + - - +
460D PRO* 1.3 71.6 - - - +
462D ASN* 1.3 57.4 + - - +
464D ILE* 4.8 4.5 - - - -
465D LEU* 4.5 24.3 - - + +
564D ASN* 3.2 39.7 - - + -
567D TYR* 4.2 24.4 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 462 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536C LEU* 5.4 4.8 - - + +
423D GLU* 3.0 39.8 + - - +
427D MET* 3.7 30.0 - - + +
458D LEU 4.1 1.0 + - - -
459D ILE 2.8 8.4 + - - +
460D PRO 2.7 5.0 + - - -
461D PHE* 1.3 75.9 - - - +
463D VAL* 1.3 66.9 + - - +
465D LEU* 2.8 21.3 + - - +
466D ASP* 2.9 18.2 + - - +
507D TYR* 2.9 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 463 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459D ILE* 2.8 15.9 + - + +
460D PRO* 2.8 22.9 + - + +
462D ASN* 1.3 73.6 - - - +
464D ILE* 1.3 71.0 + - + +
466D ASP* 2.8 12.3 + - + +
467D VAL* 2.8 23.0 + - + +
507D TYR* 4.3 7.6 + - + +
539D VAL* 4.5 13.5 - - + +
542D CYS* 4.2 21.1 - - + -
543D ARG* 3.0 52.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 464 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460D PRO* 2.8 31.0 + - + +
461D PHE* 5.1 0.9 - - - -
463D VAL* 1.3 76.7 - - + +
465D LEU* 1.3 72.2 - - + +
467D VAL* 3.8 0.9 - - - +
468D ILE* 2.8 40.9 + - + +
542D CYS* 3.2 39.9 - - - +
545D MET* 4.5 16.2 - - + -
546D ALA* 4.5 9.0 - - + -
560D SER* 4.9 1.3 - - - +
563D SER* 3.6 27.4 - - - +
564D ASN* 4.6 14.8 - - - +
567D TYR* 5.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 465 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531C ASN* 6.2 0.4 - - - +
532C SER* 4.6 23.3 - - - +
461D PHE* 4.5 28.7 - - + +
462D ASN* 2.8 10.9 + - - +
464D ILE* 1.3 84.4 - - + +
466D ASP* 1.3 52.1 + - - +
468D ILE* 4.4 4.5 - - - -
469D SER* 2.5 43.1 + - - -
556D PHE* 4.6 11.3 - - + -
560D SER* 3.4 25.1 - - - +
564D ASN* 3.8 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 466 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420D HIS* 2.9 46.9 + - + -
462D ASN* 2.9 13.1 + - - +
463D VAL* 2.8 23.8 + - + +
465D LEU* 1.3 75.7 - - - +
467D VAL* 1.3 55.2 + - - +
469D SER* 2.6 18.4 + - - -
470D LYS* 3.6 22.5 + - - +
507D TYR* 3.4 18.5 - - - -
543D ARG* 3.9 13.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 467 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463D VAL* 2.8 21.1 + - + +
466D ASP* 1.3 73.9 - - + +
468D ILE* 1.3 65.2 + - - +
469D SER 3.3 0.7 - - - -
470D LYS* 3.5 9.8 + - + +
471D CYS* 3.3 21.3 + - - +
496D LYS* 5.3 0.2 - - + -
500D GLU* 3.8 28.5 - - + +
543D ARG* 4.2 28.5 - - + +
546D ALA* 3.3 31.2 - - + -
547D LEU* 3.6 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 468 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D ILE* 2.8 41.9 + - + +
465D LEU* 4.0 4.0 - - - +
467D VAL* 1.3 71.3 - - - +
469D SER* 1.3 67.5 + - - +
470D LYS 3.1 0.3 + - - -
471D CYS* 3.9 0.3 - - - +
472D TYR* 2.8 33.6 + - + +
546D ALA* 3.4 36.1 - - + +
550D ALA* 3.4 20.4 - - + +
556D PHE* 3.6 35.2 - - + +
559D ALA* 4.3 4.3 - - + -
560D SER* 4.4 9.0 - - - +
563D SER* 4.2 10.3 - - - +
----------------------------------------------------------
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 LEU 2.5 25.5 + - - -
466D ASP* 2.6 19.8 + - - -
468D ILE* 1.3 76.0 - - - +
470D LYS* 1.3 54.5 + - - +
472D TYR* 3.9 1.0 - - - +
473D SER* 2.9 30.8 + - - -
556D PHE* 3.7 21.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 470 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D ASP* 4.0 14.1 + - - +
416D THR* 6.5 0.9 - - - -
420D HIS* 4.6 5.8 - - - -
466D ASP* 3.6 27.0 + - - +
467D VAL* 3.5 10.1 + - + +
468D ILE 3.2 0.6 - - - -
469D SER* 1.3 76.5 + - - +
471D CYS* 1.3 69.5 + - - +
473D SER* 2.8 26.9 + - - -
474D GLU* 2.9 21.6 + - - +
496D LYS* 6.1 1.3 - - + -
500D GLU* 3.8 33.7 - - - +
503D GLU* 2.7 36.9 + - - -
543D ARG* 4.5 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 471 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467D VAL* 3.3 15.7 + - - +
468D ILE 4.1 1.3 - - - +
470D LYS* 1.3 76.4 - - - +
472D TYR* 1.3 58.7 + - - +
474D GLU* 2.8 39.4 + - - +
477D MET* 3.8 21.0 - - - +
496D LYS* 4.3 5.5 - - - +
547D LEU* 4.1 15.7 - - + -
550D ALA* 4.1 22.2 - - + -
551D ALA* 4.5 10.8 - - - -
658D TYR* 4.2 18.4 - - - -
667D GLN* 4.9 3.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 472 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468D ILE* 2.8 25.4 + - + +
469D SER 4.1 1.8 - - - +
471D CYS* 1.3 70.7 - - - +
473D SER* 1.3 55.0 + - - +
474D GLU 2.9 16.7 + - - +
475D ARG* 4.4 1.2 + - - +
550D ALA* 2.9 45.8 - - + -
553D LEU* 3.0 11.1 + - - +
554D PRO* 2.8 18.0 - - - +
555D THR* 2.5 33.4 + - - -
556D PHE* 2.9 44.2 - - + -
559D ALA* 3.9 6.1 - - + -
667D GLN* 3.4 16.6 + - - +
668D LYS 4.5 13.5 - - - +
669D PRO* 5.3 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 473 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469D SER 2.9 16.0 + - - -
470D LYS* 2.8 21.6 + - - -
472D TYR* 1.3 69.8 - - - +
474D GLU* 1.3 62.7 + - - +
475D ARG* 3.8 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