Contacts of the helix formed by residues 469 - 481 (chain N) in PDB entry 5X22
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 469 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467N GLU 3.5 5.1 + - - +
468N LEU* 1.3 76.4 - - - +
470N LEU* 1.3 63.9 + - - +
471N GLU* 3.4 15.8 + - - +
472N ALA* 2.9 41.2 + - + +
473N LEU* 3.4 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 470 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115N LEU* 4.7 11.2 - - + -
468N LEU* 3.8 21.5 + - + +
469N ASP* 1.3 75.6 - - - +
471N GLU* 1.3 64.4 + - - +
473N LEU* 3.4 2.6 + - + -
474N GLU* 2.9 29.0 + - - +
499N VAL* 3.6 21.4 - - + +
502N PHE* 3.9 26.2 - - + +
503N LEU* 3.6 33.7 - - + +
507N ASN 5.0 0.7 - - - +
508N ARG* 3.9 25.1 - - - +
509N PRO* 4.2 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 471 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469N ASP* 3.4 18.3 + - - +
470N LEU* 1.3 78.2 + - - +
472N ALA* 1.3 58.4 + - - +
474N GLU* 3.2 17.2 + - - +
475N LYS* 2.9 47.3 + - - +
503N LEU* 4.2 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 472 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469N ASP* 2.9 27.8 + - + +
471N GLU* 1.3 77.1 - - - +
473N LEU* 1.3 58.5 + - - +
475N LYS* 3.0 13.8 + - - +
476N GLU* 2.9 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 473 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115N LEU* 4.0 15.0 - - + +
468N LEU* 4.0 19.5 - - + -
469N ASP 3.4 10.9 + - - +
470N LEU* 3.8 9.4 - - + +
472N ALA* 1.3 79.9 - - - +
474N GLU* 1.3 56.9 + - - +
476N GLU* 4.3 11.2 - - + -
477N LEU* 2.9 53.6 + - + +
495N ARG* 3.5 33.7 - - - +
499N VAL* 3.8 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 474 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470N LEU 2.9 15.2 + - - +
471N GLU* 3.2 17.9 - - - +
472N ALA 3.1 0.2 - - - -
473N LEU* 1.3 78.4 - - - +
475N LYS* 1.3 58.4 + - + +
477N LEU* 3.8 1.2 - - - +
478N LEU* 2.9 44.4 + - + +
496N LEU* 3.7 25.4 - - + +
499N VAL* 4.3 4.9 - - + +
500N ARG* 2.7 33.5 + - - +
503N LEU* 3.5 20.8 - - + +
1388N ARG* 3.8 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 475 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471N GLU* 2.9 35.6 + - - +
472N ALA* 3.0 11.2 + - - +
474N GLU* 1.3 77.5 - - + +
476N GLU* 1.3 64.0 + - - +
478N LEU* 3.2 12.8 + - + +
479N GLU* 2.9 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 476 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426D LYS* 5.3 10.0 + - - -
472N ALA* 2.9 28.5 + - + +
473N LEU* 3.8 14.1 - - + +
475N LYS* 1.3 82.0 - - - +
477N LEU* 1.3 59.2 + - + +
479N GLU* 3.1 13.8 + - - +
480N GLU* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 477 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473N LEU* 2.9 42.1 + - + +
474N GLU 3.9 2.9 - - - +
476N GLU* 1.3 75.7 - - + +
478N LEU* 1.3 59.6 - - - +
480N GLU* 3.1 10.7 + - + +
481N MET* 2.9 32.4 + - - +
492N ALA* 3.8 30.8 - - + +
495N ARG* 3.7 44.2 - - + +
496N LEU* 3.7 22.7 - - + +
499N VAL* 3.8 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 478 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474N GLU* 2.9 33.6 + - + +
475N LYS* 3.2 11.0 + - + +
477N LEU* 1.3 73.8 - - - +
479N GLU* 1.3 70.2 + - - +
481N MET* 3.1 21.9 + - + +
482N LYS* 3.8 11.3 + - - +
496N LEU* 3.7 21.1 - - + -
500N ARG* 3.9 23.6 - - - +
1390N LEU* 4.4 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 479 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475N LYS* 2.9 21.6 + - + +
476N GLU* 3.3 15.0 - - - +
478N LEU* 1.3 80.0 - - - +
480N GLU* 1.3 62.5 + - - +
482N LYS* 3.1 48.5 + - - +
483N HIS* 4.2 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 480 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476N GLU 2.9 14.1 + - - +
477N LEU* 3.1 18.3 + - + +
479N GLU* 1.3 75.2 - - - +
481N MET* 1.3 60.3 + - - +
482N LYS 3.1 4.2 + - - -
483N HIS* 3.4 18.8 + - - +
488N ARG* 2.6 53.6 + - - +
489N ARG* 4.0 7.6 + - - +
492N ALA* 3.7 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 481 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477N LEU 2.9 17.9 + - - +
478N LEU* 3.1 22.6 + - + +
480N GLU* 1.3 77.2 - - - +
482N LYS* 1.3 58.2 + - + +
483N HIS 3.4 0.7 - - - -
489N ARG* 3.2 53.8 - - + +
492N ALA* 3.8 2.2 - - + -
493N ARG* 3.5 20.4 - - + -
496N LEU* 4.5 11.4 - - + -
1390N LEU* 4.3 11.0 - - + -
1391N GLU* 3.7 44.5 - - + +
----------------------------------------------------------
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