Contacts of the helix formed by residues 476 - 488 (chain D) in PDB entry 2DB3
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 ALA 476 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472D VAL* 3.6 12.6 - - + -
473D ASN* 2.8 15.7 + - + +
475D TYR* 1.3 96.1 - - + +
477D LYS* 1.3 65.6 + - - +
478D ARG 3.4 2.2 - - - -
479D SER* 3.3 11.4 + - - +
480D LYS* 3.1 21.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 477 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472D VAL* 3.6 25.4 - - + -
473D ASN 3.2 12.6 + - - +
474D LYS* 3.4 20.0 + - + +
476D ALA* 1.3 77.3 - - - +
478D ARG* 1.3 52.8 + - - +
480D LYS* 3.1 4.6 + - - +
481D LEU* 2.7 31.9 + - - +
564D TYR* 2.9 50.0 + - + +
565D ASP* 3.0 26.3 + - - +
566D MET 4.7 0.8 - - - +
592D PHE* 3.4 30.7 + - + -
594D ASP* 4.3 13.9 + - - +
597D LYS* 4.2 13.9 - - - +
598D ASP* 4.8 0.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
474D LYS 4.8 1.2 + - - -
475D TYR 5.0 3.8 + - - +
476D ALA 3.4 1.0 - - - +
477D LYS* 1.3 78.6 - - - +
479D SER* 1.3 62.7 + - - +
481D LEU* 3.4 2.5 + - + +
482D ILE* 3.0 27.6 + - + +
504D PHE* 3.8 27.5 - - - -
505D LEU* 4.4 14.1 - - + -
508D PHE* 3.1 53.1 - - + -
564D TYR* 3.6 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 479 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475D TYR 5.2 3.9 + - - -
476D ALA* 3.3 12.3 + - - -
477D LYS 3.3 0.4 - - - -
478D ARG* 1.3 74.3 - - - +
480D LYS* 1.3 68.4 + - - +
482D ILE* 3.0 9.0 + - - +
483D GLU* 2.8 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 480 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470D TYR* 3.8 38.9 + - - -
472D VAL* 4.1 19.3 - - + -
476D ALA* 3.1 10.0 + - + +
477D LYS* 3.1 11.0 + - - +
479D SER* 1.3 79.0 - - - +
481D LEU* 1.3 63.3 + - - +
483D GLU* 2.8 36.1 + - - +
484D ILE* 2.9 43.3 + - + +
592D PHE* 3.6 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 481 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477D LYS 2.7 20.1 + - - +
478D ARG* 3.5 7.4 - - + +
480D LYS* 1.3 73.1 - - - +
482D ILE* 1.3 57.4 + - - +
484D ILE* 3.1 4.4 + - - +
485D LEU* 2.8 47.3 + - + +
494D VAL* 4.5 11.4 - - + -
505D LEU* 4.0 25.6 - - + -
509D LEU* 3.9 34.3 - - + -
562D ILE* 4.0 22.7 - - + -
564D TYR* 3.9 17.3 - - + -
592D PHE* 3.8 8.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 482 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478D ARG* 3.0 19.1 + - + +
479D SER* 3.6 9.2 - - - +
481D LEU* 1.3 75.7 - - + +
483D GLU* 1.3 54.8 + - - +
485D LEU* 4.4 5.6 - - - +
486D SER* 2.7 51.8 + - - +
508D PHE* 3.8 16.6 - - + -
509D LEU* 4.2 18.8 - - + -
512D LYS* 3.7 36.1 - - + +
514D PHE* 4.7 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 483 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479D SER 2.8 12.3 + - - +
480D LYS* 2.8 46.3 + - - +
482D ILE* 1.3 80.8 - - - +
484D ILE* 1.3 64.6 + - - +
486D SER* 3.7 4.4 - - - -
487D GLU* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 484 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470D TYR* 4.5 2.9 - - + -
480D LYS* 2.9 31.6 + - + +
481D LEU 3.7 5.2 - - - +
483D GLU* 1.3 76.2 - - - +
485D LEU* 1.3 61.6 + - + +
487D GLU* 3.4 13.5 + - - +
488D GLN* 3.1 24.8 + - - +
560D HIS* 3.7 29.6 - - + +
562D ILE* 3.9 14.4 - - + -
588D ARG* 4.3 7.6 - - - +
590D THR* 4.0 18.2 - - + +
592D PHE* 3.8 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 485 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481D LEU* 2.8 46.0 + - + +
482D ILE* 4.0 2.2 - - - +
484D ILE* 1.3 71.7 - - - +
486D SER* 1.3 65.1 + - - +
488D GLN 3.2 9.3 - - - +
489D ALA* 3.1 28.5 + - + +
492D THR* 3.8 36.1 - - + +
494D VAL* 5.0 0.4 - - + -
509D LEU* 3.7 34.5 - - + -
514D PHE* 3.7 21.7 - - + -
542D VAL* 4.2 17.0 - - + -
562D ILE* 4.6 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 486 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482D ILE* 2.7 40.9 + - - +
483D GLU* 3.7 5.6 - - - -
485D LEU* 1.3 73.4 - - - +
487D GLU* 1.3 62.4 + - - +
488D GLN* 4.6 0.3 - - - -
514D PHE* 3.7 15.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 487 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483D GLU 3.1 16.1 + - - +
484D ILE* 3.6 12.3 - - - +
485D LEU 3.2 0.2 - - - -
486D SER* 1.3 80.2 - - - +
488D GLN* 1.3 64.3 + - + +
588D ARG* 4.4 14.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 488 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484D ILE* 3.1 20.3 + - - +
485D LEU* 3.2 6.8 + - - +
486D SER 4.5 0.2 - - - -
487D GLU* 1.3 86.6 - - + +
489D ALA* 1.3 61.8 + - - +
490D ASP* 4.7 10.5 - - + +
492D THR* 4.4 6.6 - - - +
559D LYS* 4.8 16.5 + - - +
560D HIS* 5.2 4.3 + - - -
588D ARG* 3.8 26.7 + - - +
----------------------------------------------------------
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