Contacts of the helix formed by residues 485 - 489 (chain D) in PDB entry 1YKN
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 LEU 485 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446D PRO* 3.7 34.8 - - + -
456D TRP* 4.2 29.3 - - + +
457D ARG 4.2 2.9 - - - +
458D PRO* 3.7 25.2 - - + +
483D ASP* 3.0 16.0 + - - +
484D PRO* 1.3 78.7 - - + +
486D ILE* 1.3 64.1 + - - +
487D PRO 3.4 0.4 - - - -
488D MET* 3.2 31.8 + - + +
489D CYS* 3.4 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 486 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458D PRO* 3.9 15.0 - - + -
479D TYR* 3.8 26.5 - - + -
480D PHE 3.5 25.1 - - - +
482D GLY 4.9 1.3 - - - +
483D ASP* 3.1 23.3 + - + +
485D LEU* 1.3 76.9 - - - +
487D PRO* 1.3 71.6 - - + +
488D MET 3.1 1.2 + - - -
489D CYS 3.5 6.6 + - - +
492D VAL* 3.7 32.6 - - + +
493D LYS* 5.2 0.2 - - - +
501D VAL* 4.3 8.3 - - + -
505D ILE* 4.0 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 487 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483D ASP 4.0 2.5 - - - +
484D PRO* 3.3 20.4 - - + +
486D ILE* 1.3 96.7 - - + +
488D MET* 1.3 57.9 + - + +
489D CYS 3.6 0.4 - - - -
492D VAL* 5.5 0.7 - - + -
493D LYS* 3.6 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 488 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455D ASP* 5.0 3.6 - - - +
456D TRP 5.9 0.2 - - - -
484D PRO* 3.5 23.8 - - + +
485D LEU* 3.2 20.8 + - + +
486D ILE 3.1 1.6 + - - -
487D PRO* 1.3 80.9 - - + +
489D CYS* 1.3 62.3 + - - +
490D PRO* 3.3 9.0 - - - +
493D LYS* 3.5 16.0 + - - +
1E PRO* 3.5 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 489 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449D TRP* 5.0 0.9 - - - -
456D TRP 4.6 7.0 - - - +
457D ARG* 3.4 37.5 - - - -
458D PRO* 3.8 22.7 - - + -
485D LEU 3.4 4.5 + - - +
486D ILE 3.5 2.0 + - - -
488D MET* 1.3 75.8 - - - +
490D PRO* 1.3 72.7 - - - +
491D ILE* 3.2 18.8 - - - -
492D VAL* 3.6 20.3 - - + +
493D LYS* 3.0 24.9 + - - +
----------------------------------------------------------
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