Contacts of the strand formed by residues 245 - 249 (chain E) in PDB entry 1KYZ
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 245 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E ILE* 3.7 26.0 - - + -
216E ASN* 4.0 23.1 - - - +
219E VAL* 4.3 9.4 - - + -
227E GLY 3.4 3.4 - - - +
229E ASN* 4.3 2.5 - - + -
242E TYR* 3.4 41.7 + - + +
243E PRO 3.1 9.9 - - - +
244E GLY* 1.3 85.6 - - - +
246E GLU* 1.3 68.8 + - - +
247E HIS* 4.0 17.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 246 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227E GLY 2.8 15.5 + - - +
228E ILE* 3.2 23.5 - - + +
229E ASN 2.7 32.2 + - - +
244E GLY 4.3 0.2 - - - -
245E VAL* 1.3 72.3 - - - +
247E HIS* 1.3 60.3 + - - +
248E VAL* 3.4 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 247 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211E THR 3.6 18.4 - - - -
229E ASN* 3.0 38.4 + - + +
236E ILE* 3.7 25.8 - - + +
239E ALA* 3.8 12.0 - - + +
240E PRO 2.9 25.6 + - - -
241E SER* 4.6 9.4 - - - -
242E TYR* 3.5 13.6 - + - -
245E VAL* 4.1 11.2 - - + +
246E GLU* 1.3 76.4 - - - +
248E VAL* 1.3 62.7 + - - +
249E GLY 4.2 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 248 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228E ILE* 3.9 16.2 - - + -
229E ASN 2.9 11.9 + - - +
230E PHE* 3.3 36.8 - - + -
231E ASP 3.3 12.3 + - - -
236E ILE* 3.8 4.0 - - - +
246E GLU* 3.4 25.8 - - - +
247E HIS* 1.3 77.2 - - - +
249E GLY* 1.3 68.2 + - - +
250E GLY* 5.4 0.2 - - - -
257E PRO* 3.9 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 249 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E ASP 3.3 9.0 - - - -
233E PRO* 4.3 17.9 - - - +
236E ILE* 3.9 16.5 - - - +
247E HIS 4.2 1.0 + - - -
248E VAL* 1.3 81.5 - - - +
250E GLY* 1.3 56.2 + - - -
----------------------------------------------------------
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