Contacts of the helix formed by residues 468 - 478 (chain D) in PDB entry 5UH8
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 ASN 468 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461D VAL* 3.7 15.1 - - - +
466D ALA* 3.9 1.9 - - - +
467D GLN* 1.3 78.1 - - - +
469D ILE* 1.3 62.0 + - - +
470D LYS* 3.3 25.1 - - - +
471D SER* 2.9 28.1 + - - -
472D ALA* 3.2 22.2 + - - +
525F ASP* 3.7 26.7 + - + +
526F TYR* 3.8 47.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 469 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1103C TYR* 6.0 0.7 - - + -
1107C VAL* 4.0 31.6 - - + +
457D MET* 4.1 41.2 - - + +
458D LYS 5.0 0.2 - - - +
461D VAL* 4.4 9.3 - - + +
468D ASN* 1.3 77.6 - - + +
470D LYS* 1.3 66.9 + - + +
472D ALA* 3.4 3.3 - - - +
473D LYS* 3.2 19.9 + - - +
448F VAL* 5.4 8.0 - - + +
451F VAL* 5.1 4.5 - - + -
452F SER* 3.9 29.2 - - - +
455F LEU* 3.7 32.0 - - + +
526F TYR* 5.2 2.2 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
468D ASN* 3.3 18.0 - - - +
469D ILE* 1.3 80.6 - - + +
471D SER* 1.3 65.4 + - - +
473D LYS* 3.1 25.0 + - + +
474D ARG* 3.3 6.8 + - - +
448F VAL* 5.2 7.2 - - + -
449F ASP* 4.2 21.8 - - - +
452F SER* 4.1 25.0 + - - +
528F ASP 4.7 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 471 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466D ALA* 3.8 17.1 - - - +
467D GLN* 4.5 5.3 + - - +
468D ASN* 2.9 21.6 + - - -
470D LYS* 1.3 73.7 - - - +
472D ALA* 1.3 66.6 + - - +
474D ARG* 3.0 32.2 + - - +
475D MET* 3.0 27.4 + - - +
525F ASP 5.9 0.4 - - - -
528F ASP 5.7 1.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 472 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457D MET* 3.9 32.8 - - + +
460D LEU* 3.8 8.0 - - + +
461D VAL* 4.7 1.8 - - + +
466D ALA* 3.7 15.7 - - + +
468D ASN 3.2 18.2 + - - +
469D ILE* 3.4 10.8 - - - +
470D LYS 3.2 0.2 - - - -
471D SER* 1.3 78.5 - - - +
473D LYS* 1.3 60.1 + - - +
475D MET* 3.4 11.1 + - - +
476D VAL* 3.4 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 473 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1103C TYR* 4.4 2.6 + - - -
453D LYS* 3.0 32.3 - - - +
457D MET* 3.6 20.8 - - - -
469D ILE 3.2 6.5 + - - +
470D LYS* 3.1 19.4 + - + +
471D SER 3.1 0.2 - - - -
472D ALA* 1.3 79.8 - - - +
474D ARG* 1.3 63.9 + - - +
476D VAL* 3.1 14.7 + - - +
477D GLU* 3.1 37.6 + - - +
448F VAL* 3.5 43.9 - - + +
449F ASP* 5.3 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 474 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470D LYS 3.3 7.6 + - - +
471D SER* 3.0 31.8 + - - +
473D LYS* 1.3 78.7 - - - +
475D MET* 1.3 62.8 + - + +
477D GLU* 4.0 11.1 - - - +
478D ARG* 3.1 43.2 + - - +
480D ARG* 5.0 19.9 - - - +
528F ASP* 4.2 27.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 475 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460D LEU* 4.1 16.4 - - + -
465D HIS* 3.3 39.9 - - + +
466D ALA* 3.9 9.0 - - + -
471D SER* 3.0 20.4 + - - +
472D ALA 3.6 9.0 - - - +
473D LYS 3.1 0.4 - - - -
474D ARG* 1.3 78.7 - - + +
476D VAL* 1.3 61.8 + - - +
479D GLN 3.1 15.1 + - - -
480D ARG* 3.1 40.2 + - + +
482D GLN* 3.6 44.9 - - + +
483D VAL* 4.3 5.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 476 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449D LEU* 3.9 36.6 - - + +
450D GLU* 5.7 1.8 - - - +
453D LYS* 4.6 19.7 - - + +
456D VAL* 4.7 8.1 - - + -
457D MET* 4.0 17.0 - - + -
460D LEU* 3.8 17.7 - - + -
472D ALA 3.4 15.5 - - - +
473D LYS* 3.1 6.6 + - - +
475D MET* 1.3 75.0 - - - +
477D GLU* 1.3 62.1 + - + +
479D GLN* 2.8 27.4 + - - +
483D VAL* 4.3 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 477 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797C ARG* 4.8 0.2 + - - -
798C ASP* 4.1 16.5 - - - +
799C GLY* 5.2 5.5 - - - -
841C HIS* 5.3 14.8 + - - +
453D LYS* 4.1 14.4 + - - +
473D LYS* 3.1 47.7 + - + +
474D ARG* 4.1 10.8 - - - +
476D VAL* 1.3 77.0 - - + +
478D ARG* 1.3 73.4 + - - +
479D GLN* 3.4 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 478 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780C VAL* 5.3 14.4 - - - +
797C ARG* 4.0 12.8 + - - +
798C ASP 3.9 5.3 + - - -
799C GLY* 3.2 33.3 + - - -
800C ASP* 3.1 27.1 + - - +
474D ARG* 3.1 35.5 + - + +
475D MET 4.0 2.5 - - - +
477D GLU* 1.3 83.8 + - - +
479D GLN* 1.3 71.3 + - - +
480D ARG* 3.6 37.3 - - - +
----------------------------------------------------------
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