Contacts of the helix formed by residues 477 - 485 (chain H) in PDB entry 2R6C
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 VAL 477 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467H LEU* 5.1 1.8 - - + +
470H HIS* 4.3 8.5 - - + +
471H MSE 4.3 14.6 - - - +
474H SER* 3.2 27.8 + - - +
476H ASP* 1.3 77.4 - - + +
478H ALA* 1.3 65.4 + - - +
479H LEU 3.1 1.8 - - - -
480H VAL* 2.9 19.2 + - - +
481H VAL* 3.0 28.0 + - + +
540H VAL* 3.8 21.8 - - + -
545H LEU* 4.1 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 478 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471H MSE 3.5 31.1 - - + +
474H SER 3.4 2.8 + - - -
475H ARG* 3.4 43.5 - - - +
476H ASP 3.5 0.4 - - - -
477H VAL* 1.3 79.1 - - - +
479H LEU* 1.3 56.8 + - + +
481H VAL* 3.3 6.9 + - - +
482H GLN* 3.0 29.4 + - - +
502H TYR* 3.7 7.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 479 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475H ARG 3.6 18.6 + - - +
476H ASP* 3.9 18.6 + - - +
477H VAL 3.1 0.8 - - - -
478H ALA* 1.3 76.9 - - + +
480H VAL* 1.3 64.5 + - + +
482H GLN* 3.7 25.1 + - - +
483H GLU* 3.8 12.8 + - - +
505H TYR* 3.7 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 480 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476H ASP* 4.0 13.2 - - - +
477H VAL* 2.9 9.4 + - - +
479H LEU* 1.3 75.5 - - + +
481H VAL* 1.3 67.0 + - - +
482H GLN 3.2 0.6 + - - -
483H GLU* 3.7 4.0 + - - +
484H ARG* 3.3 35.6 + - + +
545H LEU* 3.8 29.6 - - + -
549H ILE* 4.7 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 481 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467H LEU* 4.4 13.7 - - + -
471H MSE 4.0 25.8 - - + -
477H VAL* 3.0 35.4 + - + +
478H ALA* 3.6 8.1 - - - +
480H VAL* 1.3 80.5 - - + +
482H GLN* 1.3 55.3 + - - +
484H ARG* 4.7 3.1 - - - -
485H ILE* 2.7 62.0 + - + +
489H PHE* 4.3 4.7 - - + -
502H TYR* 3.8 11.7 - - - +
545H LEU* 5.4 1.3 - - + -
549H ILE* 5.0 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 482 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478H ALA 3.0 11.1 + - - +
479H LEU* 3.8 25.0 - - - +
480H VAL 3.2 0.4 - - - -
481H VAL* 1.3 76.8 - - - +
483H GLU* 1.3 60.3 + - - +
485H ILE 2.9 16.2 - - - +
486H GLY* 4.2 6.0 - - - +
502H TYR* 3.3 59.7 + - + +
506H GLU* 4.8 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 483 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479H LEU 3.8 8.3 + - - +
480H VAL* 3.7 6.8 + - - +
481H VAL 3.5 0.2 - - - -
482H GLN* 1.3 80.7 - - - +
484H ARG* 1.3 67.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 484 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480H VAL* 3.3 26.8 + - + +
481H VAL 3.3 1.5 + - - +
482H GLN 3.2 0.6 - - - -
483H GLU* 1.3 90.1 - - + +
485H ILE* 1.3 61.9 + - - +
486H GLY 4.2 0.2 + - - -
488H ARG* 4.1 9.5 + - - -
545H LEU* 5.3 2.2 - - - +
546H GLU* 3.0 53.3 + - - +
549H ILE* 3.9 40.4 - - + +
553H LEU* 3.8 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 485 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467H LEU* 3.7 22.4 - - + -
481H VAL* 2.7 47.9 + - + +
482H GLN 2.9 12.4 - - - +
483H GLU 5.0 0.2 - - - -
484H ARG* 1.3 75.5 - - - +
486H GLY* 1.3 69.1 + - - +
487H GLY* 3.6 10.1 - - - -
488H ARG* 3.6 26.9 - - + +
489H PHE* 4.0 15.3 - - + +
502H TYR* 3.2 3.1 + - - -
549H ILE* 3.9 22.0 - - + -
552H VAL* 4.0 21.8 - - + -
553H LEU* 4.6 7.2 - - + -
----------------------------------------------------------
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