Contacts of the helix formed by residues 469 - 479 (chain A) in PDB entry 1YOM
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 469 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A LYS* 5.2 1.1 - - - +
467A GLY 5.8 0.7 - - - +
468A MET* 1.3 78.2 - - - +
470A ASN* 1.3 67.3 + - - +
471A ARG* 3.8 15.9 - - + +
472A GLU* 3.3 33.2 + - - +
473A VAL* 3.4 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A PHE* 4.3 12.3 + - - +
428A ILE* 4.0 27.6 + - + +
429A LYS* 3.2 33.8 - - - +
469A VAL* 1.3 72.4 - - - +
471A ARG* 1.3 69.9 + - - +
473A VAL* 3.2 7.1 + - - +
474A LEU* 3.0 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A LEU* 5.5 4.6 - - - +
469A VAL* 3.3 10.0 - - + +
470A ASN* 1.3 80.0 - - - +
472A GLU* 1.3 51.9 + - - +
474A LEU* 3.5 32.8 + - - +
475A ASP* 2.7 56.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A GLY 4.8 3.8 - - - +
468A MET* 4.0 25.3 - - + +
469A VAL* 3.3 40.3 + - - +
470A ASN 3.2 0.8 - - - -
471A ARG* 1.3 76.4 - - - +
473A VAL* 1.3 57.0 + - - +
475A ASP* 3.9 9.0 - - + +
476A GLN* 2.7 47.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ILE* 4.6 8.5 - - + +
429A LYS* 4.0 27.4 - - + +
465A TYR* 3.7 57.2 - - + +
468A MET* 4.0 12.1 - - + -
469A VAL 3.6 12.8 - - - +
470A ASN* 3.2 9.4 + - - +
472A GLU* 1.3 76.5 - - - +
474A LEU* 1.3 61.2 + - + +
476A GLN* 4.9 0.9 - - - -
477A VAL* 3.1 36.1 + - + +
481A TYR* 6.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ILE* 4.2 22.9 - - + -
433A PRO* 5.6 3.1 - - + -
436A ALA* 3.9 28.9 - - + +
437A LEU* 4.1 28.7 - - + -
470A ASN* 3.0 18.1 + - + +
471A ARG* 3.5 38.4 - - - +
473A VAL* 1.3 73.2 - - + +
475A ASP* 1.3 68.9 + - - +
477A VAL* 4.5 1.7 - - - +
478A GLU* 2.9 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A ARG* 2.7 48.4 + - - +
472A GLU* 3.4 12.8 - - + +
474A LEU* 1.3 80.3 - - - +
476A GLN* 1.3 58.5 + - + +
478A GLU* 3.3 6.0 - - - +
479A ARG* 3.3 59.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A MET* 4.6 13.0 - - - +
472A GLU* 2.7 32.6 + - + +
473A VAL* 4.4 2.0 - - - +
475A ASP* 1.3 73.1 - - + +
477A VAL* 1.3 56.1 + - + +
478A GLU 3.1 1.6 - - - -
479A ARG* 3.3 35.0 + - - +
480A GLY 2.9 9.5 + - - -
481A TYR* 2.7 64.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A PRO* 4.0 16.2 - - + -
448A TRP* 3.6 25.8 - - + -
465A TYR* 4.0 33.9 - - + +
473A VAL* 3.1 22.8 + - + +
474A LEU* 4.5 2.0 - - - +
476A GLN* 1.3 75.2 - - + +
478A GLU* 1.3 62.8 + - + +
480A GLY* 3.2 8.8 + - - -
481A TYR* 3.8 15.9 - - + +
482A ARG* 3.4 23.9 + - - +
503A LYS* 5.4 3.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A PRO* 4.2 9.2 - - + +
437A LEU* 3.9 29.1 - - + +
438A TYR* 5.3 2.8 + - - -
474A LEU* 2.9 26.8 + - + +
475A ASP* 3.3 7.2 - - - +
476A GLN 3.1 0.2 - - - -
477A VAL* 1.3 80.6 - - + +
479A ARG* 1.3 58.6 + - + +
480A GLY* 3.3 1.4 + - - -
503A LYS* 3.6 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 479 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A ASP* 3.3 47.4 + - - +
476A GLN* 3.3 37.2 + - - +
478A GLU* 1.3 77.5 - - + +
480A GLY* 1.3 57.1 + - - +
481A TYR 3.7 0.8 + - - -
----------------------------------------------------------
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