Contacts of the helix formed by residues 323 - 328 (chain M) in PDB entry 1KYO
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 323 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47L THR* 3.8 16.2 - - + +
89L GLY 4.1 14.1 - - - +
90L LEU* 5.0 1.1 - - - -
91L ALA* 4.0 26.5 - - + +
106L SER* 4.7 8.5 - - - -
107L SER* 3.4 35.9 - - - -
108L LEU* 3.5 18.2 - - + +
319M ASN 4.3 1.3 - - - +
320M TYR* 3.1 20.2 - - + +
322M LYS* 1.3 76.2 - - - +
324M LYS* 1.3 72.5 + - + +
325M ASN 3.1 0.9 - - - -
326M ALA* 3.1 22.1 + - - +
327M VAL* 3.4 13.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 324 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91L ALA* 4.7 10.7 - - + +
258M ASN* 3.3 30.3 - - - +
261M THR 5.7 1.6 - - - -
320M TYR* 3.1 40.7 + - + +
321M THR 4.8 0.2 - - - +
323M LEU* 1.3 90.3 - - + +
325M ASN* 1.3 56.9 + - - +
326M ALA 3.2 1.7 + - - -
327M VAL* 3.5 14.3 - - + +
328M GLN* 3.3 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 325 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254M GLU* 2.9 25.9 + - - +
278M LYS* 4.2 6.9 - - - +
321M THR 3.2 20.2 + - - +
322M LYS* 4.3 15.0 - - + -
323M LEU 3.1 1.5 - - - +
324M LYS* 1.3 80.9 - - + +
326M ALA* 1.3 56.4 + - - -
327M VAL 3.7 0.2 - - - -
328M GLN* 2.9 32.3 - - - +
329M ASN* 3.3 30.4 + - - +
336M ILE* 3.4 23.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 326 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46L HIS* 3.3 21.3 - - + +
47L THR* 4.0 13.9 - - + -
108L LEU* 4.0 13.5 - - + -
322M LYS 4.3 3.6 - - - +
323M LEU* 3.1 21.2 + - - +
325M ASN* 1.3 80.4 - - - +
327M VAL* 1.3 61.0 + - - +
329M ASN* 3.3 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 327 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46L HIS* 4.2 16.6 - - - +
47L THR* 3.2 36.3 - - + +
106L SER* 6.2 2.5 - - - -
380L GLY 5.0 5.3 - - - +
381L ASN* 5.4 7.0 - - - +
382L PRO* 5.3 6.5 - - + -
323M LEU* 3.8 11.0 - - + +
324M LYS* 3.5 20.4 - - + +
326M ALA* 1.3 74.0 - - - +
328M GLN* 1.3 77.2 + - + +
329M ASN 3.1 6.8 + - - -
330M GLU* 4.0 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 328 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254M GLU* 4.6 2.0 + - - -
278M LYS* 4.5 14.4 + - - +
324M LYS 3.3 15.1 + - - +
325M ASN* 2.9 34.1 - - - +
327M VAL* 1.3 82.4 - - + +
329M ASN* 1.3 64.4 + - - +
330M GLU* 3.1 14.2 + - - +
331M SER* 4.5 4.2 + - - -
----------------------------------------------------------
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