Contacts of the helix formed by residues 465 - 472 (chain D) in PDB entry 6RKU
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 GLN 465 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462D LEU* 3.3 45.7 - - + +
463D SER 4.8 0.6 - - - +
464D SER* 1.3 83.3 + - - +
466D GLU* 1.3 62.7 + - - -
467D VAL* 3.2 4.0 + - - +
468D ALA* 3.3 15.0 + - + +
469D THR* 2.9 39.0 + - - +
474D LEU* 5.2 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 466 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402D GLY* 4.1 28.5 + - - +
406D LYS* 4.8 13.6 - - - +
444D LEU* 4.7 14.5 - - + +
445D PRO 5.2 3.1 - - - +
464D SER* 2.8 25.7 + - - +
465D GLN* 1.3 78.1 - - - +
467D VAL* 1.3 65.2 + - + +
469D THR* 4.2 7.2 - - - -
470D LEU* 2.9 41.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
422D LEU* 5.2 11.4 - - + -
444D LEU* 4.3 21.5 - - + +
446D LEU* 4.4 18.4 - - + -
450D ILE* 5.7 7.2 - - + -
464D SER* 5.4 5.8 - - - +
465D GLN* 3.2 0.9 - - - -
466D GLU* 1.3 78.4 - - + +
468D ALA* 1.3 57.6 + - - +
470D LEU* 3.8 1.4 - - - +
471D ILE* 2.9 40.1 + - + +
510D LEU* 6.1 3.8 - - + -
513D PHE* 4.8 19.5 - - + -
514D PHE* 4.9 17.5 - - + -
518D MET* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 468 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465D GLN* 3.3 16.5 + - + +
467D VAL* 1.3 79.4 - - - +
469D THR* 1.3 55.3 + - - +
470D LEU 3.1 0.2 + - - -
471D ILE* 3.4 9.8 - - - +
472D THR 2.7 38.3 + - - +
473D ALA 5.9 0.2 - - - -
474D LEU* 4.1 35.4 - - + -
513D PHE* 5.8 8.0 - - + -
518D MET* 6.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 469 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402D GLY* 5.4 8.7 - - - -
403D LEU* 5.5 2.0 - - + +
465D GLN* 2.9 34.2 + - - +
466D GLU* 3.8 8.2 - - - -
468D ALA* 1.3 76.2 - - - +
470D LEU* 1.3 68.9 + - + +
472D THR 3.5 9.8 - - - +
489D ARG* 4.3 7.8 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
402D GLY 3.7 17.3 - - - +
403D LEU* 3.6 47.3 - - + +
407D LEU* 3.7 23.4 - - + +
420D LEU* 6.3 3.4 - - + -
444D LEU* 3.7 34.1 - - + -
466D GLU* 2.9 24.0 + - + +
467D VAL 4.0 1.6 - - - +
469D THR* 1.3 83.3 - - + +
471D ILE* 1.3 65.4 + - - +
489D ARG* 3.6 17.4 + - - +
490D TYR* 4.6 12.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 471 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420D LEU* 5.6 9.9 - - + -
467D VAL* 2.9 28.5 + - + +
468D ALA* 3.4 13.7 - - - +
470D LEU* 1.3 80.0 - - - +
472D THR* 1.3 90.6 + - + +
487D LYS* 5.4 0.5 - - - +
489D ARG* 4.0 34.6 + - - +
490D TYR* 5.4 7.0 - - + +
493D ILE* 4.6 23.3 - - + -
514D PHE* 4.8 8.5 - - + -
518D MET* 4.5 16.8 - - + -
521D ILE* 4.0 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 472 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468D ALA* 2.7 14.8 + - - +
469D THR* 3.5 12.6 - - - +
471D ILE* 1.3 102.4 - - + +
473D ALA* 1.3 60.9 + - - +
474D LEU* 3.3 15.6 + - - +
483D TYR 6.0 0.2 - - - -
484D ASN* 4.8 14.9 - - + +
487D LYS* 3.3 36.3 - - - +
488D LEU* 4.8 5.6 - - + -
489D ARG* 5.0 6.4 + - - +
518D MET* 4.2 14.1 - - - -
521D ILE* 5.9 3.8 - - + -
----------------------------------------------------------
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