Contacts of the helix formed by residues 497 - 503 (chain H) 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 ASN 497 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314H ASN 5.2 8.6 + - - +
315H TRP* 3.6 25.0 + - + -
495H ILE* 3.7 5.2 - - + +
496H ALA* 1.3 77.7 - - + +
498H PRO* 1.3 69.9 - - - +
499H GLU* 2.9 51.6 + - - +
500H ALA* 2.8 25.2 + - + +
501H VAL* 3.3 8.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 498 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496H ALA 3.4 9.2 - - - +
497H ASN* 1.3 87.9 - - - +
499H GLU* 1.3 68.9 + - - +
501H VAL* 3.2 20.5 + - + +
502H GLN* 3.3 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 499 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315H TRP* 3.8 16.3 - - + -
497H ASN* 2.9 27.3 + - - +
498H PRO* 1.3 86.1 - - - +
500H ALA* 1.3 60.1 + - - +
502H GLN* 3.5 17.9 + - + +
503H GLN* 3.6 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 500 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G PRO* 3.5 24.6 - - + +
315H TRP* 3.5 44.9 - - + +
495H ILE* 3.5 24.7 - - + -
497H ASN* 2.8 11.8 + - + +
499H GLU* 1.3 71.6 - - - +
501H VAL* 1.4 65.8 + - - +
503H GLN* 3.1 12.5 + - - +
504H LEU* 3.9 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 501 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479H TYR* 6.1 1.3 - - + -
486H ILE* 4.4 14.4 - - + -
492H VAL* 3.7 32.5 - - + +
493H LYS* 5.9 1.1 - - + -
495H ILE* 4.1 29.4 - - + +
497H ASN 3.9 11.4 - - - +
498H PRO* 3.2 14.7 + - + +
499H GLU 3.2 0.4 - - - -
500H ALA* 1.4 75.9 - - - +
502H GLN* 1.3 60.6 + - + +
504H LEU* 3.0 27.5 + - + +
505H ILE* 3.7 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 502 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498H PRO* 3.4 15.4 + - + +
499H GLU* 3.7 11.7 - - + +
500H ALA 3.2 0.6 - - - -
501H VAL* 1.3 77.9 - - - +
503H GLN* 1.3 65.0 + - - +
504H LEU 3.0 0.4 - - - -
505H ILE* 3.2 34.1 + - - +
507H LYS* 3.2 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 503 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G PRO* 3.3 31.1 - - + +
7G GLU 3.6 3.7 + - - -
8G THR* 3.8 20.8 + - - -
9G PRO* 4.1 7.5 - - + +
315H TRP* 3.0 42.8 - - - +
499H GLU 3.6 4.3 + - - +
500H ALA 3.1 10.6 + - - +
502H GLN* 1.3 80.9 - - - +
504H LEU* 1.4 58.8 + - - +
505H ILE 3.3 3.4 + - - +
523H PHE* 3.8 13.0 - - - -
524H ASP 4.8 5.7 - - - +
526H VAL* 4.1 9.5 - - - +
----------------------------------------------------------
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